7T coil comparison: processing of phantom data

7T coil comparison: processing of phantom data#

Setup environment#

# Imports
from datetime import datetime, timedelta
import os
import json
import glob
import matplotlib.pyplot as plt
import numpy as np
import nibabel as nib
import pandas as pd
from scipy.stats import iqr
import shutil
import zipfile
from scipy.interpolate import interp1d
from scipy.ndimage import uniform_filter1d
from pathlib import Path

# Define constants
GAMMA = 2.675e8;  # [rad / (s T)]

%matplotlib inline

start_time = datetime.now()

# Download data from OpenNeuro ⏳

!openneuro-py download --dataset ds005090 --target-dir data-phantom/

👋 Hello! This is openneuro-py 2024.2.0. Great to see you! 🤗

   👉 Please report problems 🤯 and bugs 🪲 at
      https://github.com/hoechenberger/openneuro-py/issues

🌍 Preparing to download ds005090 …

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📁 Traversing directories for ds005090 : 397 entities [00:04, 108.82 entities/s]
📁 Traversing directories for ds005090 : 418 entities [00:04, 97.23 entities/s] 
📥 Retrieving up to 418 files (5 concurrent downloads). 

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sub-MNI_acq-famp_TB1TFL.nii.gz:  74%|█████▉  | 696k/938k [00:00<00:00, 6.13MB/s]

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sub-MNI_acq-coilQaTra_GFactor.nii.gz:  70%|▋| 11.1M/15.9M [00:01<00:00, 13.0MB/s

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sub-MSSM_acq-coilQaSagLarge_SNR.nii.gz:  84%|▊| 3.30M/3.94M [00:00<00:00, 5.73MB

                                                                                

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sub-NTNU_acq-coilQaTra_GFactor.nii.gz:  44%|▍| 6.76M/15.5M [00:00<00:00, 10.5MB/

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sub-UCL_acq-anat_TB1TFL.nii.gz:  84%|██████▋ | 709k/847k [00:00<00:00, 7.22MB/s]

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✅ Finished downloading ds005090.
 
🧠 Please enjoy your brains.

# Define path (needs to be run in the root directory of the project)
path_data = os.path.join(os.getcwd(), "data-phantom/")
print(f"path_data: {path_data}")
path_labels = os.path.join(path_data, "derivatives", "labels")
path_qc = os.path.join(path_data, "qc")
subjects = [os.path.basename(subject_path) for subject_path in sorted(glob.glob(os.path.join(path_data, "sub-*")))]
print(f"subjects: {subjects}")
path_results = os.path.join(path_data, "derivatives", "results")

# Create results directory
os.makedirs(path_results, exist_ok=True)

path_data: /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/
subjects: ['sub-CRMBM', 'sub-MGH', 'sub-MNI', 'sub-MPI', 'sub-MSSM', 'sub-NTNU', 'sub-UCL']

Convert TFL and DREAM flip angle maps to B1+ in units of nT/V#

# Convert the TFL flip angle maps to B1+ efficiency maps [nT/V] (inspired by code from Kyle Gilbert)
# The approach consists in calculating the B1+ efficiency using a 1ms, pi-pulse at the acquisition voltage,
# then scale the efficiency by the ratio of the measured flip angle to the requested flip angle in the pulse sequence.

for subject in subjects:
    os.chdir(os.path.join(path_data, subject, "fmap"))

    # Fetch the reference voltage from the JSON sidecar 
    with open(f"{subject}_acq-famp_TB1TFL.json", "r") as f:
        metadata = json.load(f)
        ref_voltage = metadata.get("TxRefAmp", "N/A")
        if (ref_voltage == "N/A"):
            ref_token = "N/A"
            for token in metadata.get("SeriesDescription", "N/A").split("_"):
                if token.startswith("RefV"): ref_token = token
            ref_voltage = float(ref_token[4:-1])
        
    print(f"ref_voltage [V]: {ref_voltage} ({subject}_acq-famp_TB1TFL)")
                
    # Fetch the flip angle from the JSON sidecar 
    with open(f"{subject}_acq-famp_TB1TFL.json", "r") as f:
        metadata = json.load(f)
        requested_fa = metadata.get("FlipAngle", "N/A")
        print(f"flip angle [degrees]: {requested_fa} ({subject}_acq-famp_TB1TFL)")

    # Open flip angle map with nibabel
    nii = nib.load(f"{subject}_acq-famp_TB1TFL.nii.gz")
    meas_fa = nii.get_fdata()

    # Account for the power loss between the coil and the socket. That number was given by Siemens.
    voltage_at_socket = ref_voltage * 10 ** -0.095

    # Compute B1 map in [T/V]
    # Siemens maps are in units of flip angle * 10 (in degrees)
    b1_map = ((meas_fa / 10) / requested_fa) * (np.pi / (GAMMA * 1e-3 * voltage_at_socket))

    # Convert to [nT/V]
    b1_map = b1_map * 1e9

    # Save B1 map in [T/V] as NIfTI file
    nii_b1 = nib.Nifti1Image(b1_map, nii.affine, nii.header)
    nib.save(nii_b1, f"{subject}_TFLTB1map.nii.gz")

ref_voltage [V]: 224.5 (sub-CRMBM_acq-famp_TB1TFL)

flip angle [degrees]: 90 (sub-CRMBM_acq-famp_TB1TFL)

ref_voltage [V]: 419.5 (sub-MGH_acq-famp_TB1TFL)
flip angle [degrees]: 89.99 (sub-MGH_acq-famp_TB1TFL)

ref_voltage [V]: 464 (sub-MNI_acq-famp_TB1TFL)
flip angle [degrees]: 89.99 (sub-MNI_acq-famp_TB1TFL)
ref_voltage [V]: 408 (sub-MPI_acq-famp_TB1TFL)
flip angle [degrees]: 90 (sub-MPI_acq-famp_TB1TFL)

ref_voltage [V]: 422 (sub-MSSM_acq-famp_TB1TFL)
flip angle [degrees]: 68 (sub-MSSM_acq-famp_TB1TFL)

ref_voltage [V]: 408 (sub-NTNU_acq-famp_TB1TFL)
flip angle [degrees]: 90 (sub-NTNU_acq-famp_TB1TFL)

ref_voltage [V]: 270 (sub-UCL_acq-famp_TB1TFL)
flip angle [degrees]: 90 (sub-UCL_acq-famp_TB1TFL)

# load DREAM FA maps acquired with different reference voltages
# threshold FA maps to 20deg < FA < 50deg
# combine FA maps by averaging non-zero estimates of FA in each pixel

voltages = ["1.5", "0.66"]

for subject in subjects:
    
    b1_maps = []
    os.chdir(os.path.join(path_data, subject, "fmap"))

    # Fetch the reference voltage from the JSON sidecar 
    with open(f"{subject}_acq-famp_TB1DREAM.json", "r") as f:
        metadata = json.load(f)
        ref_voltage = metadata.get("TxRefAmp", "N/A")
        if (ref_voltage == "N/A"):
            ref_token = "N/A"
            for token in metadata.get("SeriesDescription", "N/A").split("_"):
                if token.startswith("RefV"): ref_token = token
            ref_voltage = float(ref_token[4:-1])
    
    # Open refV flip angle map with nibabel
    nii = nib.load(f"{subject}_acq-famp_TB1DREAM.nii.gz")
    meas_fa = nii.get_fdata()
    #thresholding
    meas_fa[meas_fa < 200] = np.nan
    meas_fa[meas_fa > 500] = np.nan

    # Fetch the flip angle from the JSON sidecar 
    with open(f"{subject}_acq-famp_TB1DREAM.json", "r") as f:
        metadata = json.load(f)
        requested_fa = metadata.get("FlipAngle", "N/A")
        #convert measured FA to percent of requested FA (note that measured FA map is in degrees * 10)
        meas_fa = (meas_fa/10) / requested_fa

    # Account for the power loss between the coil and the socket. That number was given by Siemens.
    voltage_at_socket = ref_voltage * 10 ** -0.095
    # Compute B1 map in [T/V]
    b1_map = meas_fa * (np.pi / (GAMMA * 1e-3 * voltage_at_socket))
    # Convert to [nT/V]
    b1_map = b1_map * 1e9
    
    b1_maps.append(b1_map)

    for voltage in voltages:
        
        #check if map exists
        my_file = Path(f"{subject}_acq-famp-{voltage}_TB1DREAM.nii.gz")
        
        if my_file.is_file():
            
            # Fetch the reference voltage from the JSON sidecar 
            with open(f"{subject}_acq-famp-{voltage}_TB1DREAM.json", "r") as f:
                metadata = json.load(f)
                ref_voltage = metadata.get("TxRefAmp", "N/A")
                if (ref_voltage == "N/A"):
                    ref_token = "N/A"
                    for token in metadata.get("SeriesDescription", "N/A").split("_"):
                        if token.startswith("RefV"): ref_token = token
                    ref_voltage = float(ref_token[4:-1])
                
            # Open flip angle map with nibabel
            nii = nib.load(f"{subject}_acq-famp-{voltage}_TB1DREAM.nii.gz")
            meas_fa = nii.get_fdata()
            #thresholding
            meas_fa[meas_fa < 200] = np.nan
            meas_fa[meas_fa > 500] = np.nan
        
            # Fetch the flip angle from the JSON sidecar 
            with open(f"{subject}_acq-famp-{voltage}_TB1DREAM.json", "r") as f:
                metadata = json.load(f)
                requested_fa = metadata.get("FlipAngle", "N/A")
                #convert measured FA to percent of requested FA (note that measured FA map is in degrees * 10)
                meas_fa = (meas_fa/10) / requested_fa
        else:
            meas_fa = np.full((nii.header).get_data_shape(),np.nan)

        # Account for the power loss between the coil and the socket. That number was given by Siemens.
        voltage_at_socket = ref_voltage * 10 ** -0.095
        # Compute B1 map in [T/V]
        # Siemens maps are in units of flip angle * 10 (in degrees)
        b1_map = meas_fa * (np.pi / (GAMMA * 1e-3 * voltage_at_socket))
        # Convert to [nT/V]
        b1_map = b1_map * 1e9
        
        b1_maps.append(b1_map)
 
    # compute mean of non-zero values
    avgB1=np.nanmean(b1_maps,axis=0)
    
    # Save as NIfTI file
    nii_avgB1 = nib.Nifti1Image(avgB1, nii.affine, nii.header)
    nib.save(nii_avgB1, f"{subject}_DREAMTB1avgB1map.nii.gz")

/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16162/3268472193.py:89: RuntimeWarning: Mean of empty slice
  avgB1=np.nanmean(b1_maps,axis=0)

# Split SNR data across multiple volumes. The first volume corresponds to the SoS SNR reconstruction, which is
#  what we will use for SNR comparison.
for subject in subjects:
    os.chdir(os.path.join(path_data, subject, "fmap"))
    !sct_image -i {subject}_acq-coilQaSagLarge_SNR.nii.gz -split t -o {subject}_acq-coilQaSagLarge_SNR.nii.gz

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-CRMBM_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-CRMBM_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-MGH_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-MGH_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-MNI_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-MNI_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-MPI_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-MPI_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-MSSM_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-MSSM_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-NTNU_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-NTNU_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_image -i sub-UCL_acq-coilQaSagLarge_SNR.nii.gz -split t -o sub-UCL_acq-coilQaSagLarge_SNR.nii.gz
--

Generate output files...

Generate approximate mask of spinal cord#

The purpose of this section is to generate an approximate mask of the spinal cord that will be used to quantify B1+ values inside the phantom. To do this, we identified a representative human subject, overlaid it on the anthropomorphic phantom, created a few pointwise labels along the spinal cord, interpolated those points using bsplines, and then created a cylindrical mask of 10mm diameter along the generated centerline.

os.chdir(os.path.join(path_data, "sub-CRMBM", "fmap"))

# Create labels on TFL B1+ map along an approximate spinal cord
! sct_label_utils -i "sub-CRMBM_acq-anat_TB1TFL.nii.gz" -create 49,108,23,1:49,99,23,1:49,88,23,1:50,76,23,1:55,63,23,1:62,51,23,1:68,35,23,1:72,26,23,1 -o "label_cord.nii.gz"
# Create spinal cord centerline
! sct_get_centerline -i "label_cord.nii.gz" -method fitseg -o "centerline_spinalcord.nii.gz"
# Create mask of 10mm diameter around centerline
! sct_create_mask -i "sub-CRMBM_acq-anat_TB1TFL.nii.gz" -p centerline,"centerline_spinalcord.nii.gz" -size 10mm -f cylinder -o "sub-CRMBM_TFLTB1map_mask.nii.gz"

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-CRMBM_acq-anat_TB1TFL.nii.gz -create 49,108,23,1:49,99,23,1:49,88,23,1:50,76,23,1:55,63,23,1:62,51,23,1:68,35,23,1:72,26,23,1 -o label_cord.nii.gz
--

Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_get_centerline -i label_cord.nii.gz -method fitseg -o centerline_spinalcord.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_create_mask -i sub-CRMBM_acq-anat_TB1TFL.nii.gz -p centerline,centerline_spinalcord.nii.gz -size 10mm -f cylinder -o sub-CRMBM_TFLTB1map_mask.nii.gz
--

  OK: centerline_spinalcord.nii.gz
Creating temporary folder (/tmp/sct_2024-11-04_16-29-20_create-mask_krhkpavt)

Orientation:
  AIR

Dimensions:
(56, 88, 144, 1, 2.467333, 2.361111, 2.361111, 1)

Create mask...
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.

Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'uint8', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-20_create-mask_krhkpavt

Co-register fmap data#

The purpose of this section if to co-register phantom data across sites, to produce figures showing consistent placement of the phantom across sites, and to be able to use a single mask of the approximate spinal cord for quantitative analysis.

The co-registration uses programatically-created labels that correspond to the posterior tip of the phantom, at the inflexion point:

# Create dictionary of labels across sites
labels_phantom_TFL = {
    'sub-CRMBM': '68,88,23',
    'sub-MGH': '61,98,26',
    'sub-MNI': '69,87,26',
    'sub-MPI': '67,95,27',
    'sub-MSSM': '73,65,28',
    'sub-NTNU': '64,96,29',
    'sub-UCL': '68,97,28',
}

# Define reference subject and suffix
subject_ref = 'sub-CRMBM'
suffix_ref = 'TFLTB1map'
suffixes = ["TFLTB1map", "DREAMTB1avgB1map", "acq-coilQaSagLarge_SNR_T0000"]

# Create labels for all suffixes, for all subjects
for subject in subjects:
    print(f"👉 CREATE LABELS FOR: {subject}")
    os.chdir(os.path.join(path_data, subject, "fmap"))
    !sct_label_utils -i {subject}_{suffix_ref}.nii.gz -create {labels_phantom_TFL[subject]},1 -o {subject}_{suffix_ref}_label.nii.gz
    # Register label from TFLTB1map to other metric using the qform matrix (ie: no optimization)
    for suffix in [other_suffixes for other_suffixes in suffixes if other_suffixes != suffix_ref]:
        !sct_register_multimodal -i {subject}_{suffix_ref}_label.nii.gz -d {subject}_{suffix}.nii.gz -identity 1
        !sct_apply_transfo -i {subject}_{suffix_ref}_label.nii.gz -d {subject}_{suffix}.nii.gz -w warp_{subject}_{suffix_ref}_label2{subject}_{suffix}.nii.gz -x label -o {subject}_{suffix}_label.nii.gz

# Register other scans to the reference scan
for subject in subjects:
    print(f"👉 REGISTER: {subject}")
    for suffix in suffixes:
        os.chdir(os.path.join(path_data, subject, "fmap"))
        # Perform registration
        !sct_register_multimodal -i {subject}_{suffix}.nii.gz -ilabel {subject}_{suffix}_label.nii.gz -d {path_data}{subject_ref}/fmap/{subject_ref}_{suffix}.nii.gz -dlabel {path_data}{subject_ref}/fmap/{subject_ref}_{suffix}_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0

# Register TFL B1+ spinal cord mask to DREAM and SNR reference scan
os.chdir(os.path.join(path_data, subject_ref, "fmap"))
for suffix in [other_suffixes for other_suffixes in suffixes if other_suffixes != suffix_ref]:
    !sct_register_multimodal -i {subject_ref}_{suffix_ref}_mask.nii.gz -d {subject_ref}_{suffix}.nii.gz -identity 1 -o {subject_ref}_{suffix}_mask.nii.gz

👉 CREATE LABELS FOR: sub-CRMBM

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-CRMBM_TFLTB1map.nii.gz -create 68,88,23,1 -o sub-CRMBM_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_TFLTB1map_label.nii.gz -d sub-CRMBM_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-CRMBM_TFLTB1map_label.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File created: sub-CRMBM_TFLTB1map_label_reg.nii.gz

mv /tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp/warp_src2dest.nii.gz warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_TFLTB1map_label.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-23_register-wrapper_1y1rq3mp

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-CRMBM_TFLTB1map_label.nii.gz -d sub-CRMBM_DREAMTB1avgB1map.nii.gz -w warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_DREAMTB1avgB1map.nii.gz -x label -o sub-CRMBM_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-24_apply-transfo-3d-label_tovd5tf6)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-24_apply-transfo-3d-label_tovd5tf6/dilated_data.nii -o sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -t warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_DREAMTB1avgB1map.nii.gz -r sub-CRMBM_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-CRMBM_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-24_apply-transfo-3d-label_tovd5tf6

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_TFLTB1map_label.nii.gz -d sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-CRMBM_TFLTB1map_label.nii.gz (88, 144, 56)

  Destination ......... sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-CRMBM_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-CRMBM_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8/warp_src2dest.nii.gz warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_TFLTB1map_label.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-25_register-wrapper_vjd1qua8

Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-CRMBM_TFLTB1map_label.nii.gz -d sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...


Get dimensions of data...

  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-31_apply-transfo-3d-label_1x5ovik_)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-31_apply-transfo-3d-label_1x5ovik_/dilated_data.nii -o sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-CRMBM_TFLTB1map_label2sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...
File sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-31_apply-transfo-3d-label_1x5ovik_

👉 CREATE LABELS FOR: sub-MGH

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-MGH_TFLTB1map.nii.gz -create 61,98,26,1 -o sub-MGH_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MGH_TFLTB1map_label.nii.gz -d sub-MGH_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MGH_TFLTB1map_label.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-MGH_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MGH_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un/warp_src2dest.nii.gz warp_sub-MGH_TFLTB1map_label2sub-MGH_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MGH_TFLTB1map_label2sub-MGH_DREAMTB1avgB1map.nii.gz
File created: sub-MGH_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un/warp_dest2src.nii.gz warp_sub-MGH_DREAMTB1avgB1map2sub-MGH_TFLTB1map_label.nii.gz
File created: warp_sub-MGH_DREAMTB1avgB1map2sub-MGH_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-34_register-wrapper_86dht5un

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MGH_TFLTB1map_label.nii.gz -d sub-MGH_DREAMTB1avgB1map.nii.gz -w warp_sub-MGH_TFLTB1map_label2sub-MGH_DREAMTB1avgB1map.nii.gz -x label -o sub-MGH_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-36_apply-transfo-3d-label_lub9ux23)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-36_apply-transfo-3d-label_lub9ux23/dilated_data.nii -o sub-MGH_DREAMTB1avgB1map_label.nii.gz -t warp_sub-MGH_TFLTB1map_label2sub-MGH_DREAMTB1avgB1map.nii.gz -r sub-MGH_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MGH/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-MGH_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-36_apply-transfo-3d-label_lub9ux23

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MGH_TFLTB1map_label.nii.gz -d sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:

  Source .............. sub-MGH_TFLTB1map_label.nii.gz (88, 144, 56)
  Destination ......... sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MGH_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-MGH_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l/warp_src2dest.nii.gz warp_sub-MGH_TFLTB1map_label2sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MGH_TFLTB1map_label2sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-MGH_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l/warp_dest2src.nii.gz warp_sub-MGH_acq-coilQaSagLarge_SNR_T00002sub-MGH_TFLTB1map_label.nii.gz
File created: warp_sub-MGH_acq-coilQaSagLarge_SNR_T00002sub-MGH_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-37_register-wrapper_g5w0gw0l


Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MGH_TFLTB1map_label.nii.gz -d sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-MGH_TFLTB1map_label2sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-MGH_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-42_apply-transfo-3d-label_osfwfjaj)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-42_apply-transfo-3d-label_osfwfjaj/dilated_data.nii -o sub-MGH_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-MGH_TFLTB1map_label2sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MGH/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.


Take the center of mass of each registered dilated labels...

File sub-MGH_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-42_apply-transfo-3d-label_osfwfjaj

👉 CREATE LABELS FOR: sub-MNI

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-MNI_TFLTB1map.nii.gz -create 69,87,26,1 -o sub-MNI_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MNI_TFLTB1map_label.nii.gz -d sub-MNI_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MNI_TFLTB1map_label.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-MNI_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MNI_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso/warp_src2dest.nii.gz warp_sub-MNI_TFLTB1map_label2sub-MNI_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MNI_TFLTB1map_label2sub-MNI_DREAMTB1avgB1map.nii.gz
File created: sub-MNI_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso/warp_dest2src.nii.gz warp_sub-MNI_DREAMTB1avgB1map2sub-MNI_TFLTB1map_label.nii.gz
File created: warp_sub-MNI_DREAMTB1avgB1map2sub-MNI_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-45_register-wrapper_a1a9uoso

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MNI_TFLTB1map_label.nii.gz -d sub-MNI_DREAMTB1avgB1map.nii.gz -w warp_sub-MNI_TFLTB1map_label2sub-MNI_DREAMTB1avgB1map.nii.gz -x label -o sub-MNI_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...

  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-47_apply-transfo-3d-label_lto41bn5)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-47_apply-transfo-3d-label_lto41bn5/dilated_data.nii -o sub-MNI_DREAMTB1avgB1map_label.nii.gz -t warp_sub-MNI_TFLTB1map_label2sub-MNI_DREAMTB1avgB1map.nii.gz -r sub-MNI_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MNI/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-MNI_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-47_apply-transfo-3d-label_lto41bn5

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MNI_TFLTB1map_label.nii.gz -d sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MNI_TFLTB1map_label.nii.gz (88, 144, 56)

  Destination ......... sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MNI_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-MNI_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r/warp_src2dest.nii.gz warp_sub-MNI_TFLTB1map_label2sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MNI_TFLTB1map_label2sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-MNI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r/warp_dest2src.nii.gz warp_sub-MNI_acq-coilQaSagLarge_SNR_T00002sub-MNI_TFLTB1map_label.nii.gz
File created: warp_sub-MNI_acq-coilQaSagLarge_SNR_T00002sub-MNI_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-48_register-wrapper_s_ktji0r


Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MNI_TFLTB1map_label.nii.gz -d sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-MNI_TFLTB1map_label2sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-MNI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-54_apply-transfo-3d-label_pu7xu6ue)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-54_apply-transfo-3d-label_pu7xu6ue/dilated_data.nii -o sub-MNI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-MNI_TFLTB1map_label2sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MNI/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...
File sub-MNI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-54_apply-transfo-3d-label_pu7xu6ue

👉 CREATE LABELS FOR: sub-MPI

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-MPI_TFLTB1map.nii.gz -create 67,95,27,1 -o sub-MPI_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MPI_TFLTB1map_label.nii.gz -d sub-MPI_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MPI_TFLTB1map_label.nii.gz (90, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-MPI_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja


Concatenate transformations...

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MPI_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja/warp_src2dest.nii.gz warp_sub-MPI_TFLTB1map_label2sub-MPI_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MPI_TFLTB1map_label2sub-MPI_DREAMTB1avgB1map.nii.gz
File created: sub-MPI_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja/warp_dest2src.nii.gz warp_sub-MPI_DREAMTB1avgB1map2sub-MPI_TFLTB1map_label.nii.gz
File created: warp_sub-MPI_DREAMTB1avgB1map2sub-MPI_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-57_register-wrapper__6nhysja

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MPI_TFLTB1map_label.nii.gz -d sub-MPI_DREAMTB1avgB1map.nii.gz -w warp_sub-MPI_TFLTB1map_label2sub-MPI_DREAMTB1avgB1map.nii.gz -x label -o sub-MPI_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  90 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-29-59_apply-transfo-3d-label_2ydt_mmz)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-29-59_apply-transfo-3d-label_2ydt_mmz/dilated_data.nii -o sub-MPI_DREAMTB1avgB1map_label.nii.gz -t warp_sub-MPI_TFLTB1map_label2sub-MPI_DREAMTB1avgB1map.nii.gz -r sub-MPI_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MPI/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-MPI_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-29-59_apply-transfo-3d-label_2ydt_mmz

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MPI_TFLTB1map_label.nii.gz -d sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MPI_TFLTB1map_label.nii.gz (90, 144, 56)

  Destination ......... sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MPI_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-MPI_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3/warp_src2dest.nii.gz warp_sub-MPI_TFLTB1map_label2sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MPI_TFLTB1map_label2sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-MPI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3/warp_dest2src.nii.gz warp_sub-MPI_acq-coilQaSagLarge_SNR_T00002sub-MPI_TFLTB1map_label.nii.gz
File created: warp_sub-MPI_acq-coilQaSagLarge_SNR_T00002sub-MPI_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-00_register-wrapper_md4vdjg3

Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MPI_TFLTB1map_label.nii.gz -d sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-MPI_TFLTB1map_label2sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-MPI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  90 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-05_apply-transfo-3d-label_9gnejb4y)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-05_apply-transfo-3d-label_9gnejb4y/dilated_data.nii -o sub-MPI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-MPI_TFLTB1map_label2sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MPI/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...
File sub-MPI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-05_apply-transfo-3d-label_9gnejb4y

👉 CREATE LABELS FOR: sub-MSSM

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-MSSM_TFLTB1map.nii.gz -create 73,65,28,1 -o sub-MSSM_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MSSM_TFLTB1map_label.nii.gz -d sub-MSSM_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MSSM_TFLTB1map_label.nii.gz (88, 128, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-MSSM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File created: sub-MSSM_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg/warp_src2dest.nii.gz warp_sub-MSSM_TFLTB1map_label2sub-MSSM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MSSM_TFLTB1map_label2sub-MSSM_DREAMTB1avgB1map.nii.gz

File created: sub-MSSM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg/warp_dest2src.nii.gz warp_sub-MSSM_DREAMTB1avgB1map2sub-MSSM_TFLTB1map_label.nii.gz
File created: warp_sub-MSSM_DREAMTB1avgB1map2sub-MSSM_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-08_register-wrapper_arvdqdkg

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MSSM_TFLTB1map_label.nii.gz -d sub-MSSM_DREAMTB1avgB1map.nii.gz -w warp_sub-MSSM_TFLTB1map_label2sub-MSSM_DREAMTB1avgB1map.nii.gz -x label -o sub-MSSM_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 128 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-10_apply-transfo-3d-label_iecpyh7z)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-10_apply-transfo-3d-label_iecpyh7z/dilated_data.nii -o sub-MSSM_DREAMTB1avgB1map_label.nii.gz -t warp_sub-MSSM_TFLTB1map_label2sub-MSSM_DREAMTB1avgB1map.nii.gz -r sub-MSSM_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MSSM/fmap
Copy affine matrix from destination space to make sure qform/sform are the same.

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-MSSM_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-10_apply-transfo-3d-label_iecpyh7z

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MSSM_TFLTB1map_label.nii.gz -d sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-MSSM_TFLTB1map_label.nii.gz (88, 128, 56)

  Destination ......... sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MSSM_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-MSSM_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se/warp_src2dest.nii.gz warp_sub-MSSM_TFLTB1map_label2sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MSSM_TFLTB1map_label2sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-MSSM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se/warp_dest2src.nii.gz warp_sub-MSSM_acq-coilQaSagLarge_SNR_T00002sub-MSSM_TFLTB1map_label.nii.gz
File created: warp_sub-MSSM_acq-coilQaSagLarge_SNR_T00002sub-MSSM_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-11_register-wrapper_myleh6se

Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-MSSM_TFLTB1map_label.nii.gz -d sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-MSSM_TFLTB1map_label2sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-MSSM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...


Get dimensions of data...

  88 x 128 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-17_apply-transfo-3d-label_ed15lfvy)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-17_apply-transfo-3d-label_ed15lfvy/dilated_data.nii -o sub-MSSM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-MSSM_TFLTB1map_label2sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MSSM/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.


Take the center of mass of each registered dilated labels...

File sub-MSSM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-17_apply-transfo-3d-label_ed15lfvy

👉 CREATE LABELS FOR: sub-NTNU

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-NTNU_TFLTB1map.nii.gz -create 64,96,29,1 -o sub-NTNU_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-NTNU_TFLTB1map_label.nii.gz -d sub-NTNU_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-NTNU_TFLTB1map_label.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-NTNU_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File created: sub-NTNU_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f/warp_src2dest.nii.gz warp_sub-NTNU_TFLTB1map_label2sub-NTNU_DREAMTB1avgB1map.nii.gz
File created: warp_sub-NTNU_TFLTB1map_label2sub-NTNU_DREAMTB1avgB1map.nii.gz

File created: sub-NTNU_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f/warp_dest2src.nii.gz warp_sub-NTNU_DREAMTB1avgB1map2sub-NTNU_TFLTB1map_label.nii.gz
File created: warp_sub-NTNU_DREAMTB1avgB1map2sub-NTNU_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-20_register-wrapper_xwt6p49f

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-NTNU_TFLTB1map_label.nii.gz -d sub-NTNU_DREAMTB1avgB1map.nii.gz -w warp_sub-NTNU_TFLTB1map_label2sub-NTNU_DREAMTB1avgB1map.nii.gz -x label -o sub-NTNU_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-22_apply-transfo-3d-label_x2qrmu5m)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-22_apply-transfo-3d-label_x2qrmu5m/dilated_data.nii -o sub-NTNU_DREAMTB1avgB1map_label.nii.gz -t warp_sub-NTNU_TFLTB1map_label2sub-NTNU_DREAMTB1avgB1map.nii.gz -r sub-NTNU_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-NTNU/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-NTNU_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-22_apply-transfo-3d-label_x2qrmu5m

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-NTNU_TFLTB1map_label.nii.gz -d sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:

  Source .............. sub-NTNU_TFLTB1map_label.nii.gz (88, 144, 56)
  Destination ......... sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-NTNU_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-NTNU_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu/warp_src2dest.nii.gz warp_sub-NTNU_TFLTB1map_label2sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-NTNU_TFLTB1map_label2sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-NTNU_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu/warp_dest2src.nii.gz warp_sub-NTNU_acq-coilQaSagLarge_SNR_T00002sub-NTNU_TFLTB1map_label.nii.gz
File created: warp_sub-NTNU_acq-coilQaSagLarge_SNR_T00002sub-NTNU_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-23_register-wrapper_p911zmtu

Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-NTNU_TFLTB1map_label.nii.gz -d sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-NTNU_TFLTB1map_label2sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-NTNU_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-28_apply-transfo-3d-label_a8larmvc)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-28_apply-transfo-3d-label_a8larmvc/dilated_data.nii -o sub-NTNU_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-NTNU_TFLTB1map_label2sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-NTNU/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...
File sub-NTNU_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-28_apply-transfo-3d-label_a8larmvc

👉 CREATE LABELS FOR: sub-UCL

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_label_utils -i sub-UCL_TFLTB1map.nii.gz -create 68,97,28,1 -o sub-UCL_TFLTB1map_label.nii.gz
--

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Generating output files...

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-UCL_TFLTB1map_label.nii.gz -d sub-UCL_DREAMTB1avgB1map.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-UCL_TFLTB1map_label.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-UCL_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-UCL_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28/warp_src2dest.nii.gz warp_sub-UCL_TFLTB1map_label2sub-UCL_DREAMTB1avgB1map.nii.gz
File created: warp_sub-UCL_TFLTB1map_label2sub-UCL_DREAMTB1avgB1map.nii.gz
File created: sub-UCL_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28/warp_dest2src.nii.gz warp_sub-UCL_DREAMTB1avgB1map2sub-UCL_TFLTB1map_label.nii.gz
File created: warp_sub-UCL_DREAMTB1avgB1map2sub-UCL_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-31_register-wrapper_hjubby28

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-UCL_TFLTB1map_label.nii.gz -d sub-UCL_DREAMTB1avgB1map.nii.gz -w warp_sub-UCL_TFLTB1map_label2sub-UCL_DREAMTB1avgB1map.nii.gz -x label -o sub-UCL_DREAMTB1avgB1map_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-33_apply-transfo-3d-label_8wuozxlu)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-33_apply-transfo-3d-label_8wuozxlu/dilated_data.nii -o sub-UCL_DREAMTB1avgB1map_label.nii.gz -t warp_sub-UCL_TFLTB1map_label2sub-UCL_DREAMTB1avgB1map.nii.gz -r sub-UCL_DREAMTB1avgB1map.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-UCL/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Take the center of mass of each registered dilated labels...
File sub-UCL_DREAMTB1avgB1map_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-33_apply-transfo-3d-label_8wuozxlu

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-UCL_TFLTB1map_label.nii.gz -d sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1
--


Input parameters:
  Source .............. sub-UCL_TFLTB1map_label.nii.gz (88, 144, 56)

  Destination ......... sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-UCL_TFLTB1map_label_reg.nii.gz already exists. Deleting it..

File created: sub-UCL_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08/warp_src2dest.nii.gz warp_sub-UCL_TFLTB1map_label2sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: warp_sub-UCL_TFLTB1map_label2sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-UCL_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08/warp_dest2src.nii.gz warp_sub-UCL_acq-coilQaSagLarge_SNR_T00002sub-UCL_TFLTB1map_label.nii.gz
File created: warp_sub-UCL_acq-coilQaSagLarge_SNR_T00002sub-UCL_TFLTB1map_label.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-34_register-wrapper_wbebgl08

Finished! Elapsed time: 4s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_apply_transfo -i sub-UCL_TFLTB1map_label.nii.gz -d sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz -w warp_sub-UCL_TFLTB1map_label2sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz -x label -o sub-UCL_acq-coilQaSagLarge_SNR_T0000_label.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  88 x 144 x 56 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-40_apply-transfo-3d-label_d0g6aj52)

Apply transformation and resample to destination space...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct_2024-11-04_16-30-40_apply-transfo-3d-label_d0g6aj52/dilated_data.nii -o sub-UCL_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -t warp_sub-UCL_TFLTB1map_label2sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz -r sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz -n NearestNeighbor # in /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-UCL/fmap

Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...
File sub-UCL_acq-coilQaSagLarge_SNR_T0000_label.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-40_apply-transfo-3d-label_d0g6aj52

👉 REGISTER: sub-CRMBM

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_TFLTB1map.nii.gz -ilabel sub-CRMBM_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n)

Copying input data to tmp folder and convert to nii...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-11.087461948394775, 50.14370059967041, -3.270395278930664]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 45
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[0.00000000e+00 1.66893006e-06 0.00000000e+00]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-CRMBM_TFLTB1map_src_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n/warp_src2dest.nii.gz warp_sub-CRMBM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_dest_reg.nii.gz
File warp_sub-CRMBM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz already exists. Deleting it..
mv /tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-42_register-wrapper_b32gvf5n


Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_DREAMTB1avgB1map.nii.gz -ilabel sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 1
         Function evaluations: 22
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[0. 0. 0.]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-CRMBM_DREAMTB1avgB1map_src_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4/warp_src2dest.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_dest_reg.nii.gz
File warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz already exists. Deleting it..
mv /tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-45_register-wrapper_t534lgc4

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
  Source .............. sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)

  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-11.117252349853516, 50.47705077917857, -2.909301755652923]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 62
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[0.00000000e+00 0.00000000e+00 3.75352307e-09]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_src_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn/warp_src2dest.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_dest_reg.nii.gz
File warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz already exists. Deleting it..
mv /tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-46_register-wrapper_xw_flbzn


Finished! Elapsed time: 8s

👉 REGISTER: sub-MGH

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MGH_TFLTB1map.nii.gz -ilabel sub-MGH_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

  Source .............. sub-MGH_TFLTB1map.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z)

Copying input data to tmp folder and convert to nii...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-1.9035463333129883, 10.127162218093872, 35.712753772735596]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[  9.18391562 -40.01653671  38.98314905]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MGH_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z/warp_src2dest.nii.gz warp_sub-MGH_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-MGH_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-MGH_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-MGH_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-55_register-wrapper_96t_9u1z

Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MGH_DREAMTB1avgB1map.nii.gz -ilabel sub-MGH_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MGH_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-2.8459887504577637, 9.98828125, 34.462745666503906]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[  8.27126169 -40.98875427  37.87203217]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk

Apply transfo source --> dest...

Apply transfo dest --> source...

Generate output files...
File sub-MGH_DREAMTB1avgB1map_reg.nii.gz already exists. Deleting it..

File created: sub-MGH_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk/warp_src2dest.nii.gz warp_sub-MGH_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MGH_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-MGH_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-MGH_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-30-58_register-wrapper_ujzx_6lk

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-MGH_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:

  Source .............. sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-2.645986557006836, 10.48828125, 36.462738037109375]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[  8.47126579 -39.98876953  39.3720398 ]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v


Concatenate transformations...

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MGH_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz already exists. Deleting it..

File created: sub-MGH_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v/warp_src2dest.nii.gz warp_sub-MGH_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MGH_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MGH_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-00_register-wrapper_llnu4r8v

Finished! Elapsed time: 7s

👉 REGISTER: sub-MNI

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MNI_TFLTB1map.nii.gz -ilabel sub-MNI_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MNI_TFLTB1map.nii.gz (88, 144, 56)

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq)

Copying input data to tmp folder and convert to nii...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-5.0127153396606445, 12.580960512161255, 37.777780294418335]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[  6.07474661 -37.56273842  41.04817557]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MNI_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq/warp_src2dest.nii.gz warp_sub-MNI_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-MNI_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-MNI_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-MNI_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-08_register-wrapper_r8n40xjq

Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MNI_DREAMTB1avgB1map.nii.gz -ilabel sub-MNI_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MNI_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-4.612692832946777, 12.250770568847656, 38.44549560546875]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[  6.50455761 -38.72626495  41.8547821 ]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MNI_DREAMTB1avgB1map_reg.nii.gz already exists. Deleting it..
File created: sub-MNI_DREAMTB1avgB1map_reg.nii.gz

mv /tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg/warp_src2dest.nii.gz warp_sub-MNI_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MNI_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-MNI_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-MNI_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-11_register-wrapper_58ykfsfg

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-MNI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:

  Source .............. sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.

Labels src: [[-4.612680435180664, 12.75076293739636, 38.44549560754753]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[  6.50457191 -37.72628784  41.35479737]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MNI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz already exists. Deleting it..

File created: sub-MNI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9/warp_src2dest.nii.gz warp_sub-MNI_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MNI_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MNI_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-12_register-wrapper_yzkhufi9

Finished! Elapsed time: 7s

👉 REGISTER: sub-MPI

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MPI_TFLTB1map.nii.gz -ilabel sub-MPI_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MPI_TFLTB1map.nii.gz (90, 144, 56)

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5)

Copying input data to tmp folder and convert to nii...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-8.676316738128662, 5.191625118255615, 34.30185270309448]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 49
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[  2.41114521 -44.95207381  37.57224798]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MPI_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5/warp_src2dest.nii.gz warp_sub-MPI_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-MPI_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-MPI_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-MPI_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-21_register-wrapper_dotfbyk5

Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MPI_DREAMTB1avgB1map.nii.gz -ilabel sub-MPI_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MPI_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[-9.586259841918945, 5.7471771240234375, 35.135169982910156]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 49
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[  1.5309906  -45.2298584   38.54445648]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h


Concatenate transformations...

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MPI_DREAMTB1avgB1map_reg.nii.gz already exists. Deleting it..
File created: sub-MPI_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h/warp_src2dest.nii.gz warp_sub-MPI_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MPI_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz

File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-MPI_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-MPI_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-24_register-wrapper_q8_x7b4h

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-MPI_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
  Source .............. sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)

  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.

Labels src: [[-9.486261367797852, 5.7471923828125, 34.635162353515625]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 49
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[  1.63099098 -44.7298584   37.54446411]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MPI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz already exists. Deleting it..

File created: sub-MPI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp/warp_src2dest.nii.gz warp_sub-MPI_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MPI_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MPI_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-25_register-wrapper_uwwre7wp

Finished! Elapsed time: 7s

👉 REGISTER: sub-MSSM

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MSSM_TFLTB1map.nii.gz -ilabel sub-MSSM_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MSSM_TFLTB1map.nii.gz (88, 128, 56)

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[2.5, 40.5, 5.0]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[13.58746195 -9.64369893  8.27039528]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-MSSM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n/warp_src2dest.nii.gz warp_sub-MSSM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-MSSM_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-MSSM_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-MSSM_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-34_register-wrapper_inygvt3n


Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MSSM_DREAMTB1avgB1map.nii.gz -ilabel sub-MSSM_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-MSSM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[3.5, 41.0, 5.0]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[14.61725044 -9.97703552  8.4092865 ]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8

Apply transfo source --> dest...

Apply transfo dest --> source...

Generate output files...
File sub-MSSM_DREAMTB1avgB1map_reg.nii.gz already exists. Deleting it..

File created: sub-MSSM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8/warp_src2dest.nii.gz warp_sub-MSSM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-MSSM_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-MSSM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-MSSM_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-37_register-wrapper_wuh5upi8

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-MSSM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
  Source .............. sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)

  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.

Labels src: [[3.5999984741210938, 40.50000007937501, 4.499999908011118]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[14.71725082 -9.9770507   7.40930167]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-MSSM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz already exists. Deleting it..

File created: sub-MSSM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr/warp_src2dest.nii.gz warp_sub-MSSM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-MSSM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-MSSM_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-38_register-wrapper_fv7zn1kr


Finished! Elapsed time: 7s

👉 REGISTER: sub-NTNU

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-NTNU_TFLTB1map.nii.gz -ilabel sub-NTNU_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-NTNU_TFLTB1map.nii.gz (88, 144, 56)

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u)

Copying input data to tmp folder and convert to nii...

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[3.7121474742889404, 5.1349334716796875, 27.99675750732422]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[ 14.79960942 -45.00876546  31.26715279]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-NTNU_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u/warp_src2dest.nii.gz warp_sub-NTNU_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-NTNU_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-NTNU_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-NTNU_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-47_register-wrapper_xiolfu4u

Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-NTNU_DREAMTB1avgB1map.nii.gz -ilabel sub-NTNU_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-NTNU_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[2.867208480834961, 5.4127197265625, 28.968994140625]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[ 13.98445892 -45.5643158   32.37828064]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-NTNU_DREAMTB1avgB1map_reg.nii.gz already exists. Deleting it..
File created: sub-NTNU_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals/warp_src2dest.nii.gz warp_sub-NTNU_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-NTNU_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz

File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-NTNU_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-NTNU_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-50_register-wrapper_oog7yals

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-NTNU_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:

  Source .............. sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[2.7672119140625, 4.4127197265625, 27.468994140625]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz

Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 50
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[ 13.88446426 -46.06433105  30.3782959 ]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-NTNU_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz already exists. Deleting it..

File created: sub-NTNU_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j/warp_src2dest.nii.gz warp_sub-NTNU_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-NTNU_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-NTNU_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-31-51_register-wrapper_e1sl434j


Finished! Elapsed time: 7s

👉 REGISTER: sub-UCL

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-UCL_TFLTB1map.nii.gz -ilabel sub-UCL_TFLTB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-UCL_TFLTB1map.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz (88, 144, 56)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[1.2494821548461914, 49.14424228668213, 24.081058740615845]]
Labels dest: [[-11.087461948394775, 50.143698930740356, -3.270395278930664]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 49
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.08746195  50.14369893  -3.27039528]
Translation:
 [[12.3369441  -0.99945664 27.35145402]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-UCL_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv/warp_src2dest.nii.gz warp_sub-UCL_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz
File created: warp_sub-UCL_TFLTB1map2sub-CRMBM_TFLTB1map.nii.gz

File created: sub-CRMBM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv/warp_dest2src.nii.gz warp_sub-CRMBM_TFLTB1map2sub-UCL_TFLTB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map2sub-UCL_TFLTB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-32-00_register-wrapper_pjq6qmuv

Finished! Elapsed time: 2s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-UCL_DREAMTB1avgB1map.nii.gz -ilabel sub-UCL_DREAMTB1avgB1map_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Source .............. sub-UCL_DREAMTB1avgB1map.nii.gz (80, 80, 11)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[0.36720848083496094, 49.977577209472656, 25.192169189453125]]
Labels dest: [[-11.117250442504883, 50.97703552246094, -3.4092864990234375]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 49
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725044  50.97703552  -3.4092865 ]
Translation:
 [[11.48445892 -0.99945831 28.60145569]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df

Apply transfo source --> dest...

Apply transfo dest --> source...

Generate output files...
File sub-UCL_DREAMTB1avgB1map_reg.nii.gz already exists. Deleting it..

File created: sub-UCL_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df/warp_src2dest.nii.gz warp_sub-UCL_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-UCL_DREAMTB1avgB1map2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_reg.nii.gz
mv /tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-UCL_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-UCL_DREAMTB1avgB1map.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-32-03_register-wrapper_q0gwm9df

Finished! Elapsed time: 0s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz -ilabel sub-UCL_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -d /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -dlabel /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_label.nii.gz -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=im,algo=syn,iter=0
--


Input parameters:
  Source .............. sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)

  Destination ......... /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... label
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz
  smoothWarpXY ... 2
  rot_method ..... pca
Parameter 'algo=syn' has no effect for 'type=label' registration.
Labels src: [[0.36721134185791016, 49.477569580078125, 24.192169189453125]]
Labels dest: [[-11.117252349853516, 50.47705077917857, -2.9093017594064463]]
Degrees of freedom (dof): Tx_Ty_Tz
Optimization terminated successfully.
         Current function value: 0.000000
         Iterations: 2
         Function evaluations: 49
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [-11.11725235  50.47705078  -2.90930176]
Translation:
 [[11.48446369 -0.9994812  27.10147095]]

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MeanSquares[dest_RPI.nii,src_reg.nii,1,4]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz # in /tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File sub-UCL_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz already exists. Deleting it..

File created: sub-UCL_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j/warp_src2dest.nii.gz warp_sub-UCL_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-UCL_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz
mv /tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-UCL_acq-coilQaSagLarge_SNR_T0000.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-32-04_register-wrapper_z42naf4j


Finished! Elapsed time: 7s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_TFLTB1map_mask.nii.gz -d sub-CRMBM_DREAMTB1avgB1map.nii.gz -identity 1 -o sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz
--


Input parameters:

  Source .............. sub-CRMBM_TFLTB1map_mask.nii.gz (88, 144, 56)
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
  Destination ......... sub-CRMBM_DREAMTB1avgB1map.nii.gz (80, 80, 11)
  Init transfo ........ 
  Mask ................ 
  Output name ......... sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Creating temporary folder (/tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs)

Copying input data to tmp folder and convert to nii...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs


Apply transfo source --> dest...


Apply transfo dest --> source...

Generate output files...
File created: sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz
mv /tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs/warp_src2dest.nii.gz warp_sub-CRMBM_TFLTB1map_mask2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: warp_sub-CRMBM_TFLTB1map_mask2sub-CRMBM_DREAMTB1avgB1map.nii.gz
File created: sub-CRMBM_DREAMTB1avgB1map_mask_inv.nii.gz
mv /tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs/warp_dest2src.nii.gz warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_TFLTB1map_mask.nii.gz
File created: warp_sub-CRMBM_DREAMTB1avgB1map2sub-CRMBM_TFLTB1map_mask.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-32-13_register-wrapper_cmy465zs

Finished! Elapsed time: 1s

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_register_multimodal -i sub-CRMBM_TFLTB1map_mask.nii.gz -d sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -identity 1 -o sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz
--


Input parameters:
  Source .............. sub-CRMBM_TFLTB1map_mask.nii.gz (88, 144, 56)

  Destination ......... sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz (512, 512, 13)
  Init transfo ........ 
  Mask ................ 
  Output name ......... sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv

Concatenate transformations...
/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv

/home/runner/work/coil-qc-code/coil-qc-code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv


Apply transfo source --> dest...


Apply transfo dest --> source...


Generate output files...

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz
mv /tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv/warp_src2dest.nii.gz warp_sub-CRMBM_TFLTB1map_mask2sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz
File created: warp_sub-CRMBM_TFLTB1map_mask2sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz

File created: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask_inv.nii.gz
mv /tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv/warp_dest2src.nii.gz warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_TFLTB1map_mask.nii.gz
File created: warp_sub-CRMBM_acq-coilQaSagLarge_SNR_T00002sub-CRMBM_TFLTB1map_mask.nii.gz

Remove temporary files...
rm -rf /tmp/sct_2024-11-04_16-32-14_register-wrapper__pq_surv


Finished! Elapsed time: 4s

# Generate syntax to open registered data in FSLeyes. This should be run from within the `data-phantom/` folder.
for suffix in suffixes:
    print(f"\n👉 CHECKING REGISTRATION FOR: {suffix}\n")
    cmd = f"fsleyes sub-CRMBM/fmap/sub-CRMBM_{suffix}.nii.gz"
    for subject in [other_subjects for other_subjects in subjects if other_subjects != subject_ref]:
        file_reg = os.path.join(path_data, subject, "fmap", f"{subject}_{suffix}_reg.nii.gz")
        cmd = f"{cmd} {file_reg}"
    # Add mask with color and opacity
    cmd = f"{cmd} sub-CRMBM/fmap/sub-CRMBM_{suffix}_mask.nii.gz --cmap yellow -a 30"
    print(cmd+" &")

# TODO: undisplay all scans but the first

👉 CHECKING REGISTRATION FOR: TFLTB1map

fsleyes sub-CRMBM/fmap/sub-CRMBM_TFLTB1map.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MGH/fmap/sub-MGH_TFLTB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MNI/fmap/sub-MNI_TFLTB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MPI/fmap/sub-MPI_TFLTB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MSSM/fmap/sub-MSSM_TFLTB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-NTNU/fmap/sub-NTNU_TFLTB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-UCL/fmap/sub-UCL_TFLTB1map_reg.nii.gz sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz --cmap yellow -a 30 &

👉 CHECKING REGISTRATION FOR: DREAMTB1avgB1map

fsleyes sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MGH/fmap/sub-MGH_DREAMTB1avgB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MNI/fmap/sub-MNI_DREAMTB1avgB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MPI/fmap/sub-MPI_DREAMTB1avgB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MSSM/fmap/sub-MSSM_DREAMTB1avgB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-NTNU/fmap/sub-NTNU_DREAMTB1avgB1map_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-UCL/fmap/sub-UCL_DREAMTB1avgB1map_reg.nii.gz sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz --cmap yellow -a 30 &

👉 CHECKING REGISTRATION FOR: acq-coilQaSagLarge_SNR_T0000

fsleyes sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MGH/fmap/sub-MGH_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MNI/fmap/sub-MNI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MPI/fmap/sub-MPI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-MSSM/fmap/sub-MSSM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-NTNU/fmap/sub-NTNU_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/sub-UCL/fmap/sub-UCL_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz --cmap yellow -a 30 &

Extract values in mask and generate figures#

# Extract B1+ and SNR along the spinal cord mask and save data to CSV files

for subject in subjects:
    os.chdir(os.path.join(path_data, subject, "fmap"))
    
    fname_result_TFLb1plus = os.path.join(path_results, f"{subject}_TFLTB1map.csv")
    fname_result_DREAMb1plus = os.path.join(path_results, f"{subject}_DREAMTB1avgB1map.csv")
    fname_result_SNR = os.path.join(path_results, f"{subject}_acq-coilQaSagLarge_SNR_T0000.csv")

    # For sites other than sub-CRMBM, use the registered qMRI map for metrics extraction
    if subject=='sub-CRMBM':
        file_suffix = ''
    else:
        file_suffix = '_reg'
        
    # Extract metrics within mask defined in the sub-CRMBM space
    !sct_extract_metric -i {subject}_TFLTB1map{file_suffix}.nii.gz -f ../../{subject_ref}/fmap/{subject_ref}_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o "{fname_result_TFLb1plus}"
    !sct_extract_metric -i {subject}_DREAMTB1avgB1map{file_suffix}.nii.gz -f ../../{subject_ref}/fmap/{subject_ref}_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o "{fname_result_DREAMb1plus}"
    !sct_extract_metric -i {subject}_acq-coilQaSagLarge_SNR_T0000{file_suffix}.nii.gz -f ../../{subject_ref}/fmap/{subject_ref}_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o "{fname_result_SNR}"

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-CRMBM_TFLTB1map.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-CRMBM_TFLTB1map.csv
--


Load metric image...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-CRMBM_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-CRMBM_DREAMTB1avgB1map.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-CRMBM_DREAMTB1avgB1map.csv
--


Load metric image...
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-CRMBM_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MGH_TFLTB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MGH_TFLTB1map.csv
--


Load metric image...

Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MGH_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MGH_DREAMTB1avgB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MGH_DREAMTB1avgB1map.csv
--


Load metric image...
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MGH_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MGH_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MGH_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MGH_acq-coilQaSagLarge_SNR_T0000.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MNI_TFLTB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MNI_TFLTB1map.csv
--


Load metric image...

Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MNI_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MNI_DREAMTB1avgB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MNI_DREAMTB1avgB1map.csv
--


Load metric image...
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MNI_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MNI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MNI_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MNI_acq-coilQaSagLarge_SNR_T0000.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MPI_TFLTB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MPI_TFLTB1map.csv
--


Load metric image...

Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MPI_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MPI_DREAMTB1avgB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MPI_DREAMTB1avgB1map.csv
--

Load metric image...
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MPI_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MPI_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MPI_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MPI_acq-coilQaSagLarge_SNR_T0000.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MSSM_TFLTB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MSSM_TFLTB1map.csv
--


Load metric image...

Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MSSM_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MSSM_DREAMTB1avgB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MSSM_DREAMTB1avgB1map.csv
--


Load metric image...
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MSSM_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-MSSM_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MSSM_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-MSSM_acq-coilQaSagLarge_SNR_T0000.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-NTNU_TFLTB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-NTNU_TFLTB1map.csv
--


Load metric image...

Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-NTNU_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-NTNU_DREAMTB1avgB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-NTNU_DREAMTB1avgB1map.csv
--


Load metric image...
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-NTNU_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-NTNU_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-NTNU_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-NTNU_acq-coilQaSagLarge_SNR_T0000.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-UCL_TFLTB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz -method wa -z 19:127 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-UCL_TFLTB1map.csv
--


Load metric image...

Estimation for label: sub-CRMBM_TFLTB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-UCL_TFLTB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-UCL_DREAMTB1avgB1map_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz -method wa -z 14:62 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-UCL_DREAMTB1avgB1map.csv
--


Load metric image...
Estimation for label: sub-CRMBM_DREAMTB1avgB1map_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-UCL_DREAMTB1avgB1map.csv

--
Spinal Cord Toolbox (git-master-a458fa37fd22179dd2a6c13d33b7d191552abee7)

sct_extract_metric -i sub-UCL_acq-coilQaSagLarge_SNR_T0000_reg.nii.gz -f ../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz -method wa -z 151:368 -perslice 1 -o /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-UCL_acq-coilQaSagLarge_SNR_T0000.csv
--


Load metric image...

Estimation for label: sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask

Done! To view results, type:
xdg-open /home/runner/work/coil-qc-code/coil-qc-code/data-phantom/derivatives/results/sub-UCL_acq-coilQaSagLarge_SNR_T0000.csv

Correct SNR using B1+ values#

SNR depends on the effective flip angle at each voxel, which is influenced by the B1+ efficiency and the transmit homogeneity. Therefore, if we want to report SNR values independently of the actual flip angle played out, we need to correct the SNR maps. To do so, we divide the reconstructed SNR maps by \(\sin(\text{FA}_{\text{gre, meas}})\), where \(\text{FA}_{\text{gre, meas}}\) is the actual flip angle map for the GRE SNR scan. By normalizing, we extrapolate to the SNR value that we would achieve with \( \text{FA} = 90^\circ \):

\[\text{SNR}_{90} = \frac{\text{SNR}_{\text{meas}}}{\sin(\text{FA}_{\text{gre, meas}})}\]

\(\text{FA}_{\text{gre, meas}}\) is computed from the TFL B1+ scan as follows:

\[\text{FA}_{\text{gre, meas}} = \text{FA}_{\text{gre, requested}} \times \left( \frac{\text{FA}_{\text{TFL, meas}}}{\text{FA}_{\text{TFL, requested}}} \right)\]

The ratio \(\frac{\text{FA}_{\text{TFL, meas}}}{\text{FA}_{\text{TFL, requested}}}\) is obtained from the TFL B1+ efficiency values, which were previously extracted slicewise and saved as a CSV file.

Before doing this correction, given that the B1+ and SNR maps don’t have the same spatial resolution, we need to interpolate the B1+ array to match its length with that of the SNR array.

Reference: https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.27695

for subject in subjects:
    
    fname_result_TFLb1plus = os.path.join(path_results, f"{subject}_TFLTB1map.csv")
    fname_result_SNR = os.path.join(path_results, f"{subject}_acq-coilQaSagLarge_SNR_T0000.csv")
    fname_result_SNR_corrected = os.path.join(path_results, f"{subject}_acq-coilQaSagLarge_SNR_T0000_corrected.csv")

    # INTERPOLATE B1+ MAP TO MATCH THE LENGTH OF THE SNR DATA
    # =======================================================
    # Read B1 values
    df_b1 = pd.read_csv(fname_result_TFLb1plus)
    b1_map = df_b1["WA()"].values
    # Read SNR values
    df_snr = pd.read_csv(fname_result_SNR)
    snr = df_snr["WA()"].values
    # Create interpolation function based on the length of snr
    x = np.linspace(0, len(b1_map) - 1, len(b1_map))  # x values for original data points
    f = interp1d(x, b1_map, kind='linear')
    # Generate new x values to match the length of the `snr` array
    x_new = np.linspace(0, len(b1_map) - 1, len(snr))
    # Interpolate to get the new y values with the length of `snr`
    b1_map_interp = f(x_new)

    # CORRECT SNR VALUES FOR B1+ INHOMOGENEITY
    # ========================================
    # Fetch the reference voltage for the TFL scan
    # TODO: create a function for this
    with open(os.path.join(path_data, subject, "fmap", f"{subject}_acq-famp_TB1TFL.json"), "r") as f:
        metadata = json.load(f)
        ref_voltage = metadata.get("TxRefAmp", "N/A")
        if (ref_voltage == "N/A"):
            ref_token = "N/A"
            for token in metadata.get("SeriesDescription", "N/A").split("_"):
                if token.startswith("RefV"): ref_token = token
            ref_voltage = float(ref_token[4:-1])
    # Fetch the flip angle for the TFL scan
    with open(os.path.join(path_data, subject, "fmap", f"{subject}_acq-famp_TB1TFL.json"), "r") as f:
        metadata = json.load(f)
        requested_fa_tfl = metadata.get("FlipAngle", "N/A")
    # Account for the power loss between the coil and the socket. That number was given by Siemens.
    voltage_at_socket = ref_voltage * 10 ** -0.095
    # measured-to-requested flip angle using B1 values (in nT/V)
    meas_to_requested_fa = 10 * b1_map_interp * GAMMA * 1e-3 * voltage_at_socket / (np.pi * 1e9)
    # Fetch the requested flip angle for the SNR GRE scan
    with open(os.path.join(path_data, subject, "fmap", f"{subject}_acq-coilQaSagLarge_SNR.json"), "r") as f:
        metadata = json.load(f)
        requested_fa_gre = metadata.get("FlipAngle", "N/A")
    # Correct the SNR values for B1+ inhomogeneity
    snr_corrected = snr / np.sin(np.deg2rad(requested_fa_gre * meas_to_requested_fa))
    # Save corrected SNR values to CSV
    df_snr_corrected = pd.DataFrame(snr_corrected)
    # Insert 'WA()' as the first value in the DataFrame
    df_snr_corrected.loc[-1] = ['WA()'] + [None] * (df_snr_corrected.shape[1] - 1)  # Prepend 'WA()' to the first column
    df_snr_corrected.index = df_snr_corrected.index + 1  # Shift index
    df_snr_corrected = df_snr_corrected.sort_index()  # Sort index to move the new row to the top
    # Save corrected SNR values to CSV
    df_snr_corrected.to_csv(fname_result_SNR_corrected, index=False, header=False)

Generate figures#

g-factor maps#

# Compute the average and maximum 1/g factor in a central ROI
# Display 1/g factor maps and T2w (coil-combined) maps for each site (MSSM excluded, see: https://github.com/spinal-cord-7t/coil-qc-code/issues/61)

sites = ["CRMBM", "MNI", "MPI", "UCL", "MGH", "NTNU"] # MSSM excluded, see: https://github.com/spinal-cord-7t/coil-qc-code/issues/61
site_colors = ['cornflowerblue', 'firebrick', 'limegreen', 'royalblue', 'darkred', 'green']

# map types
map_types = ["acq-coilQaSagSmall_GFactor", "T2starw"]
# legend types
legend_types = ["[1/g]", "[a.u.]"]

mean_gfac = {}

for map_type, legend_type in zip(map_types,legend_types):
    
    # Create a figure with multiple subplots
    fig, axes = plt.subplots(2, 3, figsize=(10, 8))
    font_size = 12
    axes=axes.flatten() 
        
    for i,site in enumerate(sites):
        # T2starw
        if map_type=="T2starw":
            os.chdir(os.path.join(path_data, f"sub-{site}", "anat"))
            map=nib.load(f"sub-{site}_{map_type}.nii.gz")
            data=map.get_fdata()[:,:,round(map.get_fdata().shape[2]/2)]
        # g-factor maps
        else:
            os.chdir(os.path.join(path_data, f"sub-{site}", "fmap"))
            map=nib.load(f"sub-{site}_{map_type}.nii.gz")
            data=(map.get_fdata()[64:191,64:191,round(map.get_fdata().shape[2]/2),5])/1000
            
            gfac_data=(map.get_fdata()[round(map.get_fdata().shape[0]/2)-10:round(map.get_fdata().shape[0]/2)+10,round(map.get_fdata().shape[1]/2)-10:round(map.get_fdata().shape[1]/2)+10,round(map.get_fdata().shape[2]/2),5])
            mean_gfac[site]=np.nanmean(gfac_data)/1000
        
        # Plot    
        splot=axes[i]
        dynmin = 0
        if map_type=="acq-coilQaSagSmall_GFactor":
            dynmax = 1
            axes[-1].axis('off')
            splot.text(0, 3, r'mean 1/g = '+str(round(mean_gfac[site],3)), size=14)
            
            x = [data.shape[0]/2-10, data.shape[1]/2-10] 
            y = [data.shape[0]/2-10, data.shape[1]/2+10] 
            splot.plot(x, y, color="black", linewidth=2) 
            
            x = [data.shape[0]/2-10, data.shape[1]/2+10] 
            y = [data.shape[0]/2+10, data.shape[1]/2+10] 
            splot.plot(x, y, color="black", linewidth=2) 

            x = [data.shape[0]/2+10, data.shape[1]/2+10] 
            y = [data.shape[0]/2+10, data.shape[1]/2-10] 
            splot.plot(x, y, color="black", linewidth=2)

            x = [data.shape[0]/2+10, data.shape[1]/2-10] 
            y = [data.shape[0]/2-10, data.shape[1]/2-10] 
            splot.plot(x, y, color="black", linewidth=2) 
            
        elif map_type=="T2starw":
            dynmax = 2100
            axes[-1].axis('off')
        
        im = splot.imshow((data.T), cmap='viridis', origin='lower',vmin=dynmin,vmax=dynmax) 
        splot.set_title(site, size=font_size, color=site_colors[i])
        splot.axis('off')

    plt.tight_layout()

    # Colorbar
    # Assume that the colorbar should start at the bottom of the lower row of subplots and
    # extend to the top of the upper row of subplots
    cbar_bottom = 0.2  # This might need adjustment
    cbar_height = 0.6  # This represents the total height of both rows of subplots
    cbar_dist = 1.01
    cbar_ax = fig.add_axes([cbar_dist, cbar_bottom, 0.03, cbar_height])
    cbar = plt.colorbar(im, cax=cbar_ax)

    cbar_ax.set_title(legend_type, size=12)
    plt.show()

_images/c916ca8df02bd2f64cf8a4f43525e8b9a54c4d3be9a9764dd7887e20c288b96d.png

_images/2c972699dc27fac44c3aa055aba36032031488d8a839705f07221e3747f28b59.png

B1+ and SNR maps#

sites = ["CRMBM", "UCL", "MNI", "MGH", "MPI", "NTNU", "MSSM"]
colors = ['cornflowerblue', 'royalblue', 'firebrick', 'darkred', 'limegreen', 'green', 'mediumpurple']

# map types
map_types = ["TFLTB1map", "DREAMTB1avgB1map", "acq-coilQaSagLarge_SNR_T0000"]

# Define the dictionary with ranges for each map type
# NIfTI voxel location: (xmin, xmax, ymin, ymax, zdata, zmask)
range_dict = {
    "TFLTB1map": (19, 83, 21, 122, 23, 23),
    "DREAMTB1avgB1map": (18, 79, 14, 62, 5, 5),
    "acq-coilQaSagLarge_SNR_T0000": (217, 317, 176, 335, 6, 6),
}

# legend types
legend_types = ["B1+ [nT/V]", "B1+ [nT/V]", "SNR [a.u.]"]

for map_type, legend_type in zip(map_types,legend_types):
    
    # Create a figure with multiple subplots
    fig, axes = plt.subplots(2, 4, figsize=(10, 8))
    font_size = 12
    axes=axes.flatten() 
        
    for i,site in enumerate(sites):
        # Load data
        os.chdir(os.path.join(path_data, f"sub-{site}", "fmap"))
        if site=='CRMBM':
            map=nib.load(f"sub-{site}_{map_type}.nii.gz")
            if map_type=="TFLTB1map":
                mask=nib.load(f"sub-CRMBM_TFLTB1map_mask.nii.gz")
            elif map_type=="DREAMTB1avgB1map":
                mask=nib.load(f"sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz")
            else: 
                mask=nib.load(f"sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz")
        else:
            map=nib.load(f"sub-{site}_{map_type}_reg.nii.gz")
            if map_type=="TFLTB1map":
                mask=nib.load(f"../../sub-CRMBM/fmap/sub-CRMBM_TFLTB1map_mask.nii.gz")
            elif map_type=="DREAMTB1avgB1map":
                mask=nib.load(f"../../sub-CRMBM/fmap/sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz")
            else: 
                mask=nib.load(f"../../sub-CRMBM/fmap/sub-CRMBM_acq-coilQaSagLarge_SNR_T0000_mask.nii.gz")

        # Crop data for display
        data = map.get_fdata()[
            range_dict[map_type][0]:range_dict[map_type][1],
            range_dict[map_type][2]:range_dict[map_type][3],
            range_dict[map_type][4]]
        mask_data = mask.get_fdata()[
            range_dict[map_type][0]:range_dict[map_type][1],
            range_dict[map_type][2]:range_dict[map_type][3],
            range_dict[map_type][5]]

        # Binarize mask for display purpose
        mask_data = (mask_data > 0.5).astype(int)
        
        # Plot
        dynmin = 0 
        if map_type=="acq-coilQaSagLarge_SNR_T0000":
            dynmax = 310
        else:
            dynmax = 75    
            
        splot=axes[i]
        im1 = splot.imshow((data.T), cmap='viridis', origin='lower',vmin=dynmin,vmax=dynmax)
        # im2 = splot.imshow((mask_data.T), 'gray', origin='lower', alpha=0.2)
        splot.contour(mask_data.T, levels=[0.5], colors='white', linewidths=0.5)
        splot.set_title(site, size=font_size,c=colors[i])
        splot.axis('off')    
    
    # Display mean signal within mask for each site in an additional sub-plot
    for site,color in zip(sites,colors):
        # Read CSV file
        if map_type == "acq-coilQaSagLarge_SNR_T0000":
            file_csv = os.path.join(path_results, f"sub-{site}_{map_type}_corrected.csv")
        else:
            file_csv = os.path.join(path_results, f"sub-{site}_{map_type}.csv")
        df = pd.read_csv(file_csv)
        data = df['WA()'].dropna()
        # Smooth data
        data = uniform_filter1d(data, 10, mode='nearest')
        # Display plot
        axes[-1].plot(data, label=site, c=color)
        axes[-1].legend(fontsize=10, loc='center left', bbox_to_anchor=(1.2, 0.5))
        axes[-1].yaxis.set_label_position("right")
        axes[-1].yaxis.tick_right()
        axes[-1].set_xticks([])  # Remove x-axis ticks
        axes[-1].set_xlabel("← superior    inferior →", fontsize=12, loc='center')
        # axes[-1].set_yticks([])  # Remove y-axis ticks
        axes[-1].invert_xaxis()  # Reverse the x-axis
        axes[-1].yaxis.grid(True, color='grey', linestyle='-', linewidth=0.5)

    # Reduce the space between the rows of subplots
    fig.subplots_adjust(hspace=-0.2)  # Adjust this value as needed to reduce spacing

    # Adjust figure subplots
    plt.tight_layout()
    box = axes[-1].get_position()
    new_height = box.height * 0.76  # Reduce the height of the second subplot by 50%
    axes[-1].set_position([box.x0, box.y0 + 0.068, box.width, new_height])

    # Colorbar
    cbar_bottom = 0.545  # This might need adjustment
    cbar_height = 0.37  # This represents the total height of both rows of subplots
    if (map_type == "TFLTB1map" or map_type == "DREAMTB1avgB1map" or map_type == "acq-coilQaSagLarge_SNR_T0000"):
        cbar_dist = -0.1
    else:
        cbar_dist = 1.01
    cbar_ax = fig.add_axes([0.9, cbar_bottom, 0.02, cbar_height])
    cbar = plt.colorbar(im1, cax=cbar_ax)
    cbar_ax.set_title(legend_type, size=10)
    
    plt.show()

_images/297f46de5f64297bdc93b896ad2394094a1639fa12bb740bae08ee5577b9013e.png

_images/efa4c14feef51539488b7d554c7a772a270c0fc5623b92c9e18fc94b17ca4f9c.png

_images/12491639362bb9350080809c805b2e88da63dee335054547fbad5b1eff651f44.png

Individual coil channels#

sites = ["CRMBM", "UCL", "MNI", "MGH", "MPI", "NTNU", "MSSM"]
        
for i,site in enumerate(sites):

    gre_files=sorted(glob.glob(os.path.join(path_data, f"sub-{site}", "anat", '*uncombined*.nii.gz')))
        
    #Tiled figure in a five-row layout
    rows=int(np.ceil(len(gre_files)/4))
    cols=int(np.ceil(len(gre_files)/rows))

    fig=plt.figure(figsize=(15, 20))
    
    ax = fig.subplots(rows,cols,squeeze=True)
    
    for row in range(rows):
        for col in range(cols):

            i = row*cols+col

            if i < len(gre_files):
            
                #read in files
                data_to_plot=(nib.load(gre_files[i])).get_fdata() #load in nifti object, get only image data
                data_to_plot=np.rot90(data_to_plot[:,:,int(np.floor(data_to_plot.shape[2]/2))]) #central slice
           
                ax[row,col].imshow(data_to_plot,cmap=plt.cm.gray,clim=[0, 300])
                ax[row,col].text(0.5, 0.05, 'Rx channel : ' + str(i+1),horizontalalignment='center', transform=ax[row,col].transAxes,color='white',fontsize=17)
                ax[row,col].axis('off')

    plt.axis('off')
    plt.subplots_adjust(hspace=0,wspace=0)
    fig.suptitle(site, fontsize=20, y=0.9)

_images/1d045d751e361e0530b693c48fdb8a108d99067bac140f2da9e54cf9a04c7754.png

_images/9f448ddd1b324a547502b730a2476d8899ed3308452e156ce9c9cb733a04469f.png

_images/60ead7d66a6bba24125993f59f842514b91a7f4ea0abcb5602bacc097b781098.png

_images/8f0ba84a240f5902ef2199bf456fc6df32d244d8297cc3ba100b96ea59fd100d.png

_images/deebb4d294f70aa5c9765c0a304f962926c6354b4df5bc4f90764d028880e569.png

_images/3c6e0be6183a88458aaed90b73342dfc70c30de3411d9a635a352ac6cf475fc7.png

_images/7503e93342f0915e71aa615fba5a2f505fcb3b3dcc70e32c649fb71c2c6f0dae.png

Finished#

# Indicate duration of data processing

end_time = datetime.now()
total_time = (end_time - start_time).total_seconds()

# Convert seconds to a timedelta object
total_time_delta = timedelta(seconds=total_time)

# Format the timedelta object to a string
formatted_time = str(total_time_delta)

# Pad the string representation if less than an hour
formatted_time = formatted_time.rjust(8, '0')

print(f"Total Runtime [hour:min:sec]: {formatted_time}")

Total Runtime [hour:min:sec]: 0:04:20.342687