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
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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_16172/3268472193.py:89: RuntimeWarning: Mean of empty slice
avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16172/3268472193.py:89: RuntimeWarning: Mean of empty slice
avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16172/3268472193.py:89: RuntimeWarning: Mean of empty slice
avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16172/3268472193.py:89: RuntimeWarning: Mean of empty slice
avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16172/3268472193.py:89: RuntimeWarning: Mean of empty slice
avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16172/3268472193.py:89: RuntimeWarning: Mean of empty slice
avgB1=np.nanmean(b1_maps,axis=0)
/tmp/ipykernel_16172/3268472193.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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-39_create-mask_rrc9892g)
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_2024-11-05_21-30-39_create-mask_rrc9892g
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-42_register-wrapper_rwweey_6)
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_2024-11-05_21-30-42_register-wrapper_rwweey_6
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_2024-11-05_21-30-42_register-wrapper_rwweey_6
/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_2024-11-05_21-30-42_register-wrapper_rwweey_6
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-CRMBM_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-30-42_register-wrapper_rwweey_6/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_2024-11-05_21-30-42_register-wrapper_rwweey_6/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_2024-11-05_21-30-42_register-wrapper_rwweey_6
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-44_apply-transfo-3d-label_4nconse8)
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_2024-11-05_21-30-44_apply-transfo-3d-label_4nconse8/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_2024-11-05_21-30-44_apply-transfo-3d-label_4nconse8
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-45_register-wrapper_qxw8znbk)
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_2024-11-05_21-30-45_register-wrapper_qxw8znbk
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_2024-11-05_21-30-45_register-wrapper_qxw8znbk
/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_2024-11-05_21-30-45_register-wrapper_qxw8znbk
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_2024-11-05_21-30-45_register-wrapper_qxw8znbk/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_2024-11-05_21-30-45_register-wrapper_qxw8znbk/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_2024-11-05_21-30-45_register-wrapper_qxw8znbk
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-51_apply-transfo-3d-label_gzc0jr2k)
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_2024-11-05_21-30-51_apply-transfo-3d-label_gzc0jr2k/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_2024-11-05_21-30-51_apply-transfo-3d-label_gzc0jr2k
👉 CREATE LABELS FOR: sub-MGH
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-54_register-wrapper_f9pqvpno)
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_2024-11-05_21-30-54_register-wrapper_f9pqvpno
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_2024-11-05_21-30-54_register-wrapper_f9pqvpno
/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_2024-11-05_21-30-54_register-wrapper_f9pqvpno
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MGH_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-30-54_register-wrapper_f9pqvpno/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_2024-11-05_21-30-54_register-wrapper_f9pqvpno/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_2024-11-05_21-30-54_register-wrapper_f9pqvpno
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-56_apply-transfo-3d-label_3cjhoh19)
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_2024-11-05_21-30-56_apply-transfo-3d-label_3cjhoh19/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_2024-11-05_21-30-56_apply-transfo-3d-label_3cjhoh19
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-30-57_register-wrapper_312feija)
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_2024-11-05_21-30-57_register-wrapper_312feija
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_2024-11-05_21-30-57_register-wrapper_312feija
/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_2024-11-05_21-30-57_register-wrapper_312feija
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_2024-11-05_21-30-57_register-wrapper_312feija/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_2024-11-05_21-30-57_register-wrapper_312feija/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_2024-11-05_21-30-57_register-wrapper_312feija
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-03_apply-transfo-3d-label_9fjr1n0f)
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_2024-11-05_21-31-03_apply-transfo-3d-label_9fjr1n0f/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_2024-11-05_21-31-03_apply-transfo-3d-label_9fjr1n0f
👉 CREATE LABELS FOR: sub-MNI
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-06_register-wrapper_00_n4ee2)
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_2024-11-05_21-31-06_register-wrapper_00_n4ee2
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_2024-11-05_21-31-06_register-wrapper_00_n4ee2
/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_2024-11-05_21-31-06_register-wrapper_00_n4ee2
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MNI_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-31-06_register-wrapper_00_n4ee2/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_2024-11-05_21-31-06_register-wrapper_00_n4ee2/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_2024-11-05_21-31-06_register-wrapper_00_n4ee2
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-08_apply-transfo-3d-label_mnlqrx79)
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_2024-11-05_21-31-08_apply-transfo-3d-label_mnlqrx79/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_2024-11-05_21-31-08_apply-transfo-3d-label_mnlqrx79
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-10_register-wrapper_i087fdco)
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_2024-11-05_21-31-10_register-wrapper_i087fdco
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_2024-11-05_21-31-10_register-wrapper_i087fdco
/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_2024-11-05_21-31-10_register-wrapper_i087fdco
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_2024-11-05_21-31-10_register-wrapper_i087fdco/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_2024-11-05_21-31-10_register-wrapper_i087fdco/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_2024-11-05_21-31-10_register-wrapper_i087fdco
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-15_apply-transfo-3d-label_olkgm7l8)
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_2024-11-05_21-31-15_apply-transfo-3d-label_olkgm7l8/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_2024-11-05_21-31-15_apply-transfo-3d-label_olkgm7l8
👉 CREATE LABELS FOR: sub-MPI
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-19_register-wrapper_u16d9ra2)
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_2024-11-05_21-31-19_register-wrapper_u16d9ra2
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_2024-11-05_21-31-19_register-wrapper_u16d9ra2
/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_2024-11-05_21-31-19_register-wrapper_u16d9ra2
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MPI_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-31-19_register-wrapper_u16d9ra2/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_2024-11-05_21-31-19_register-wrapper_u16d9ra2/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_2024-11-05_21-31-19_register-wrapper_u16d9ra2
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-20_apply-transfo-3d-label_ancf0w1x)
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_2024-11-05_21-31-20_apply-transfo-3d-label_ancf0w1x/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_2024-11-05_21-31-20_apply-transfo-3d-label_ancf0w1x
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-22_register-wrapper_c1bdui3z)
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_2024-11-05_21-31-22_register-wrapper_c1bdui3z
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_2024-11-05_21-31-22_register-wrapper_c1bdui3z
/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_2024-11-05_21-31-22_register-wrapper_c1bdui3z
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_2024-11-05_21-31-22_register-wrapper_c1bdui3z/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_2024-11-05_21-31-22_register-wrapper_c1bdui3z/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_2024-11-05_21-31-22_register-wrapper_c1bdui3z
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-27_apply-transfo-3d-label_ar7pjae0)
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_2024-11-05_21-31-27_apply-transfo-3d-label_ar7pjae0/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_2024-11-05_21-31-27_apply-transfo-3d-label_ar7pjae0
👉 CREATE LABELS FOR: sub-MSSM
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-31_register-wrapper_x09gnstu)
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_2024-11-05_21-31-31_register-wrapper_x09gnstu
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_2024-11-05_21-31-31_register-wrapper_x09gnstu
/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_2024-11-05_21-31-31_register-wrapper_x09gnstu
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MSSM_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-31-31_register-wrapper_x09gnstu/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_2024-11-05_21-31-31_register-wrapper_x09gnstu/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_2024-11-05_21-31-31_register-wrapper_x09gnstu
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-33_apply-transfo-3d-label_xvgwbq7a)
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_2024-11-05_21-31-33_apply-transfo-3d-label_xvgwbq7a/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_2024-11-05_21-31-33_apply-transfo-3d-label_xvgwbq7a
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl)
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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl
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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl
/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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl
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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl/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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl/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_2024-11-05_21-31-34_register-wrapper_b1uq0gpl
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-40_apply-transfo-3d-label_7456h5tr)
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_2024-11-05_21-31-40_apply-transfo-3d-label_7456h5tr/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_2024-11-05_21-31-40_apply-transfo-3d-label_7456h5tr
👉 CREATE LABELS FOR: sub-NTNU
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-43_register-wrapper_7q61fv92)
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_2024-11-05_21-31-43_register-wrapper_7q61fv92
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_2024-11-05_21-31-43_register-wrapper_7q61fv92
/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_2024-11-05_21-31-43_register-wrapper_7q61fv92
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-NTNU_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-31-43_register-wrapper_7q61fv92/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_2024-11-05_21-31-43_register-wrapper_7q61fv92/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_2024-11-05_21-31-43_register-wrapper_7q61fv92
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-45_apply-transfo-3d-label_2_f1ghaz)
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_2024-11-05_21-31-45_apply-transfo-3d-label_2_f1ghaz/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_2024-11-05_21-31-45_apply-transfo-3d-label_2_f1ghaz
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-46_register-wrapper_mhl42dxz)
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_2024-11-05_21-31-46_register-wrapper_mhl42dxz
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_2024-11-05_21-31-46_register-wrapper_mhl42dxz
/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_2024-11-05_21-31-46_register-wrapper_mhl42dxz
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_2024-11-05_21-31-46_register-wrapper_mhl42dxz/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_2024-11-05_21-31-46_register-wrapper_mhl42dxz/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_2024-11-05_21-31-46_register-wrapper_mhl42dxz
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-52_apply-transfo-3d-label_wfm7znty)
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_2024-11-05_21-31-52_apply-transfo-3d-label_wfm7znty/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_2024-11-05_21-31-52_apply-transfo-3d-label_wfm7znty
👉 CREATE LABELS FOR: sub-UCL
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-55_register-wrapper_9q7mmr9r)
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_2024-11-05_21-31-55_register-wrapper_9q7mmr9r
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_2024-11-05_21-31-55_register-wrapper_9q7mmr9r
/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_2024-11-05_21-31-55_register-wrapper_9q7mmr9r
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-UCL_TFLTB1map_label_reg.nii.gz
mv /tmp/sct_2024-11-05_21-31-55_register-wrapper_9q7mmr9r/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_2024-11-05_21-31-55_register-wrapper_9q7mmr9r/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_2024-11-05_21-31-55_register-wrapper_9q7mmr9r
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-57_apply-transfo-3d-label_o_58cqja)
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_2024-11-05_21-31-57_apply-transfo-3d-label_o_58cqja/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_2024-11-05_21-31-57_apply-transfo-3d-label_o_58cqja
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-31-58_register-wrapper_g6d3tobe)
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_2024-11-05_21-31-58_register-wrapper_g6d3tobe
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_2024-11-05_21-31-58_register-wrapper_g6d3tobe
/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_2024-11-05_21-31-58_register-wrapper_g6d3tobe
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_2024-11-05_21-31-58_register-wrapper_g6d3tobe/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_2024-11-05_21-31-58_register-wrapper_g6d3tobe/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_2024-11-05_21-31-58_register-wrapper_g6d3tobe
Finished! Elapsed time: 4s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-04_apply-transfo-3d-label_mvfh7d2n)
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_2024-11-05_21-32-04_apply-transfo-3d-label_mvfh7d2n/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_2024-11-05_21-32-04_apply-transfo-3d-label_mvfh7d2n
👉 REGISTER: sub-CRMBM
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-06_register-wrapper_m5fg6dff)
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_2024-11-05_21-32-06_register-wrapper_m5fg6dff
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_2024-11-05_21-32-06_register-wrapper_m5fg6dff
/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_2024-11-05_21-32-06_register-wrapper_m5fg6dff
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-CRMBM_TFLTB1map_src_reg.nii.gz
mv /tmp/sct_2024-11-05_21-32-06_register-wrapper_m5fg6dff/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_2024-11-05_21-32-06_register-wrapper_m5fg6dff/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_2024-11-05_21-32-06_register-wrapper_m5fg6dff
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-09_register-wrapper_ytdui1xi)
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_2024-11-05_21-32-09_register-wrapper_ytdui1xi
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_2024-11-05_21-32-09_register-wrapper_ytdui1xi
/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_2024-11-05_21-32-09_register-wrapper_ytdui1xi
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-CRMBM_DREAMTB1avgB1map_src_reg.nii.gz
mv /tmp/sct_2024-11-05_21-32-09_register-wrapper_ytdui1xi/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_2024-11-05_21-32-09_register-wrapper_ytdui1xi/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_2024-11-05_21-32-09_register-wrapper_ytdui1xi
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-11_register-wrapper_qmf3mu89)
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_2024-11-05_21-32-11_register-wrapper_qmf3mu89
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_2024-11-05_21-32-11_register-wrapper_qmf3mu89
/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_2024-11-05_21-32-11_register-wrapper_qmf3mu89
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_2024-11-05_21-32-11_register-wrapper_qmf3mu89/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_2024-11-05_21-32-11_register-wrapper_qmf3mu89/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_2024-11-05_21-32-11_register-wrapper_qmf3mu89
Finished! Elapsed time: 8s
👉 REGISTER: sub-MGH
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-20_register-wrapper_vdxyby3p)
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_2024-11-05_21-32-20_register-wrapper_vdxyby3p
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_2024-11-05_21-32-20_register-wrapper_vdxyby3p
/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_2024-11-05_21-32-20_register-wrapper_vdxyby3p
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MGH_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-05_21-32-20_register-wrapper_vdxyby3p/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_2024-11-05_21-32-20_register-wrapper_vdxyby3p/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_2024-11-05_21-32-20_register-wrapper_vdxyby3p
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-23_register-wrapper_qb26g_jz)
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_2024-11-05_21-32-23_register-wrapper_qb26g_jz
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_2024-11-05_21-32-23_register-wrapper_qb26g_jz
/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_2024-11-05_21-32-23_register-wrapper_qb26g_jz
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_2024-11-05_21-32-23_register-wrapper_qb26g_jz/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_2024-11-05_21-32-23_register-wrapper_qb26g_jz/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_2024-11-05_21-32-23_register-wrapper_qb26g_jz
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-25_register-wrapper_o7qde_t_)
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_2024-11-05_21-32-25_register-wrapper_o7qde_t_
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_2024-11-05_21-32-25_register-wrapper_o7qde_t_
/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_2024-11-05_21-32-25_register-wrapper_o7qde_t_
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_2024-11-05_21-32-25_register-wrapper_o7qde_t_/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_2024-11-05_21-32-25_register-wrapper_o7qde_t_/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_2024-11-05_21-32-25_register-wrapper_o7qde_t_
Finished! Elapsed time: 7s
👉 REGISTER: sub-MNI
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-34_register-wrapper_i82cg36j)
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_2024-11-05_21-32-34_register-wrapper_i82cg36j
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_2024-11-05_21-32-34_register-wrapper_i82cg36j
/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_2024-11-05_21-32-34_register-wrapper_i82cg36j
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MNI_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-05_21-32-34_register-wrapper_i82cg36j/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_2024-11-05_21-32-34_register-wrapper_i82cg36j/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_2024-11-05_21-32-34_register-wrapper_i82cg36j
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q)
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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q
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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q
/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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q
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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q/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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q/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_2024-11-05_21-32-37_register-wrapper_z9mr5n2q
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-39_register-wrapper_finx25uq)
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_2024-11-05_21-32-39_register-wrapper_finx25uq
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_2024-11-05_21-32-39_register-wrapper_finx25uq
/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_2024-11-05_21-32-39_register-wrapper_finx25uq
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_2024-11-05_21-32-39_register-wrapper_finx25uq/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_2024-11-05_21-32-39_register-wrapper_finx25uq/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_2024-11-05_21-32-39_register-wrapper_finx25uq
Finished! Elapsed time: 8s
👉 REGISTER: sub-MPI
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-47_register-wrapper_ybbqv2an)
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_2024-11-05_21-32-47_register-wrapper_ybbqv2an
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_2024-11-05_21-32-47_register-wrapper_ybbqv2an
/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_2024-11-05_21-32-47_register-wrapper_ybbqv2an
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MPI_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-05_21-32-47_register-wrapper_ybbqv2an/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_2024-11-05_21-32-47_register-wrapper_ybbqv2an/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_2024-11-05_21-32-47_register-wrapper_ybbqv2an
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-51_register-wrapper_t841pzf1)
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_2024-11-05_21-32-51_register-wrapper_t841pzf1
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_2024-11-05_21-32-51_register-wrapper_t841pzf1
/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_2024-11-05_21-32-51_register-wrapper_t841pzf1
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_2024-11-05_21-32-51_register-wrapper_t841pzf1/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_2024-11-05_21-32-51_register-wrapper_t841pzf1/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_2024-11-05_21-32-51_register-wrapper_t841pzf1
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-32-52_register-wrapper_526jzgnw)
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_2024-11-05_21-32-52_register-wrapper_526jzgnw
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_2024-11-05_21-32-52_register-wrapper_526jzgnw
/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_2024-11-05_21-32-52_register-wrapper_526jzgnw
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_2024-11-05_21-32-52_register-wrapper_526jzgnw/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_2024-11-05_21-32-52_register-wrapper_526jzgnw/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_2024-11-05_21-32-52_register-wrapper_526jzgnw
Finished! Elapsed time: 7s
👉 REGISTER: sub-MSSM
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-01_register-wrapper_r5voav4r)
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_2024-11-05_21-33-01_register-wrapper_r5voav4r
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_2024-11-05_21-33-01_register-wrapper_r5voav4r
/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_2024-11-05_21-33-01_register-wrapper_r5voav4r
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-MSSM_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-05_21-33-01_register-wrapper_r5voav4r/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_2024-11-05_21-33-01_register-wrapper_r5voav4r/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_2024-11-05_21-33-01_register-wrapper_r5voav4r
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-04_register-wrapper_4kpycvbk)
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_2024-11-05_21-33-04_register-wrapper_4kpycvbk
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_2024-11-05_21-33-04_register-wrapper_4kpycvbk
/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_2024-11-05_21-33-04_register-wrapper_4kpycvbk
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_2024-11-05_21-33-04_register-wrapper_4kpycvbk/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_2024-11-05_21-33-04_register-wrapper_4kpycvbk/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_2024-11-05_21-33-04_register-wrapper_4kpycvbk
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-06_register-wrapper_c3ou709q)
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_2024-11-05_21-33-06_register-wrapper_c3ou709q
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_2024-11-05_21-33-06_register-wrapper_c3ou709q
/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_2024-11-05_21-33-06_register-wrapper_c3ou709q
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_2024-11-05_21-33-06_register-wrapper_c3ou709q/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_2024-11-05_21-33-06_register-wrapper_c3ou709q/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_2024-11-05_21-33-06_register-wrapper_c3ou709q
Finished! Elapsed time: 7s
👉 REGISTER: sub-NTNU
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-14_register-wrapper_j431x_kr)
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_2024-11-05_21-33-14_register-wrapper_j431x_kr
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_2024-11-05_21-33-14_register-wrapper_j431x_kr
/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_2024-11-05_21-33-14_register-wrapper_j431x_kr
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-NTNU_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-05_21-33-14_register-wrapper_j431x_kr/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_2024-11-05_21-33-14_register-wrapper_j431x_kr/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_2024-11-05_21-33-14_register-wrapper_j431x_kr
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-18_register-wrapper_x3de_6s2)
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_2024-11-05_21-33-18_register-wrapper_x3de_6s2
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_2024-11-05_21-33-18_register-wrapper_x3de_6s2
/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_2024-11-05_21-33-18_register-wrapper_x3de_6s2
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_2024-11-05_21-33-18_register-wrapper_x3de_6s2/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_2024-11-05_21-33-18_register-wrapper_x3de_6s2/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_2024-11-05_21-33-18_register-wrapper_x3de_6s2
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-19_register-wrapper_zd46j3xq)
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_2024-11-05_21-33-19_register-wrapper_zd46j3xq
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_2024-11-05_21-33-19_register-wrapper_zd46j3xq
/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_2024-11-05_21-33-19_register-wrapper_zd46j3xq
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_2024-11-05_21-33-19_register-wrapper_zd46j3xq/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_2024-11-05_21-33-19_register-wrapper_zd46j3xq/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_2024-11-05_21-33-19_register-wrapper_zd46j3xq
Finished! Elapsed time: 7s
👉 REGISTER: sub-UCL
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-28_register-wrapper_4zt5gghw)
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_2024-11-05_21-33-28_register-wrapper_4zt5gghw
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_2024-11-05_21-33-28_register-wrapper_4zt5gghw
/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_2024-11-05_21-33-28_register-wrapper_4zt5gghw
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-UCL_TFLTB1map_reg.nii.gz
mv /tmp/sct_2024-11-05_21-33-28_register-wrapper_4zt5gghw/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_2024-11-05_21-33-28_register-wrapper_4zt5gghw/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_2024-11-05_21-33-28_register-wrapper_4zt5gghw
Finished! Elapsed time: 2s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-31_register-wrapper_id0t38l8)
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_2024-11-05_21-33-31_register-wrapper_id0t38l8
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_2024-11-05_21-33-31_register-wrapper_id0t38l8
/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_2024-11-05_21-33-31_register-wrapper_id0t38l8
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_2024-11-05_21-33-31_register-wrapper_id0t38l8/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_2024-11-05_21-33-31_register-wrapper_id0t38l8/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_2024-11-05_21-33-31_register-wrapper_id0t38l8
Finished! Elapsed time: 0s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0)
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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0
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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0
/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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0
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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0/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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0/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_2024-11-05_21-33-33_register-wrapper_ryaaxzu0
Finished! Elapsed time: 7s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-42_register-wrapper_e6hqep1v)
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_2024-11-05_21-33-42_register-wrapper_e6hqep1v
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_2024-11-05_21-33-42_register-wrapper_e6hqep1v
/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_2024-11-05_21-33-42_register-wrapper_e6hqep1v
Apply transfo source --> dest...
Apply transfo dest --> source...
Generate output files...
File created: sub-CRMBM_DREAMTB1avgB1map_mask.nii.gz
mv /tmp/sct_2024-11-05_21-33-42_register-wrapper_e6hqep1v/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_2024-11-05_21-33-42_register-wrapper_e6hqep1v/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_2024-11-05_21-33-42_register-wrapper_e6hqep1v
Finished! Elapsed time: 1s
--
Spinal Cord Toolbox (git-master-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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_2024-11-05_21-33-44_register-wrapper_925ev8yz)
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_2024-11-05_21-33-44_register-wrapper_925ev8yz
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_2024-11-05_21-33-44_register-wrapper_925ev8yz
/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_2024-11-05_21-33-44_register-wrapper_925ev8yz
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_2024-11-05_21-33-44_register-wrapper_925ev8yz/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_2024-11-05_21-33-44_register-wrapper_925ev8yz/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_2024-11-05_21-33-44_register-wrapper_925ev8yz
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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-b7e8bdd2ff71653e98b34becd6f71b82640fbf71)
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()
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()
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)
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]: 0:04:40.812180