QSMxT#
Author: Ashley Stewart
Citation:
QSMxT: Stewart AW, Robinson SD, O’Brien K, et al. QSMxT: Robust masking and artifact reduction for quantitative susceptibility mapping. Magnetic Resonance in Medicine. 2022;87(3):1289-1300. doi:10.1002/mrm.29048
QSMxT: Stewart AW, Bollman S, et al. QSMxT/QSMxT. GitHub; 2022. https://github.com/QSMxT/QSM
Output CPU information#
!cat /proc/cpuinfo | grep 'vendor' | uniq
!cat /proc/cpuinfo | grep 'model name' | uniq
vendor_id : GenuineIntel
model name : Intel(R) Core(TM) Ultra 7 155U
QSMxT Interactive Notebook#
This interactive notebook estimates Quantitative Susceptibility Maps (QSMs) for two gradient-echo (GRE) MRI acquisitions using QSMxT provided by the Neurodesk project.
What is QSM?#
QSM is a form of quantitative MRI (qMRI) that estimates the magnetic susceptibility distribution across an imaged object. Magnetic susceptibility is the degree to which a material becomes magnetised by an external magnetic field. Major contributors to susceptibility include iron, calcium, and myelin, with the susceptibility of water typically approximating a zero-reference, though it is slightly diamagnetic. Read more about QSM here.
What is QSMxT?#
QSMxT is a suite of tools for building and running automated pipelines for QSM that:
is available open-source without any licensing required;
is distributed as a software container making it straightforward to access and install (Neurodesk!)
scales its processing to execute across many acquisitions through jobs parallelisation (using multiple processors or HPCs) provided by Nipype;
automates steps that usually require manual intervention and scripting, including:
DICOM to BIDS conversion;
QSM reconstruction using a range of algorithms;
segmentation using FastSurfer;
group space generation using ANTs;
export of susceptibility statistics by subject and region of interest (ROI) to CSV.
How do I access QSMxT?#
There are a few ways you can access QSMxT:
This notebook: You can access QSMxT in this notebook right now!
If you are running this on a Neurodesk Play instance, you can upload your own data into the sidebar via drag-and-drop.
Neurodesktop: QSMxT is in the applications menu of Neurodesktop.
On Neurodesk Play, upload your own data into the desktop via drag-and-drop.
On a local install of Neurodesk, bring any necessary files into the shared
~/neurodesktop-storagedirectory
Local install: QSMxT can also be installed via the Docker container
HPC install: QSMxT can also be installed via the Singularity container for use on HPCs
Download example DICOMs#
Here, we download some example DICOMs from our OSF repository for QSMxT.
These data include GRE and T1-weighted acquisitions for one subject (duplicated to act as two subjects).
!osf -p ru43c clone . > /dev/null 2>&1
!tar xf osfstorage/dicoms-unsorted.tar
!rm -rf osfstorage/
!tree dicoms-unsorted | head
!echo -e "...\nThere are `ls dicoms-unsorted | wc -l` unsorted DICOMs in ./dicoms-unsorted/"
dicoms-unsorted
├── MR.1.1.dcm
├── MR.1.10.dcm
├── MR.1.100.dcm
├── MR.1.101.dcm
├── MR.1.102.dcm
├── MR.1.103.dcm
├── MR.1.104.dcm
├── MR.1.105.dcm
├── MR.1.106.dcm
...
There are 1216 unsorted DICOMs in ./dicoms-unsorted/
Load QSMxT#
To load QSMxT inside a notebook, we can use the available module system:
import os
os.environ['MODULEPATH'] = '/cvmfs/neurodesk.ardc.edu.au/containers/modules:' + os.environ.get('MODULEPATH', '')
import module
await module.load('qsmxt/8.1.1')
!qsmxt --version
The following have been reloaded with a version change:
1) qsmxt/7.2.2 => qsmxt/8.1.1
[INFO]: QSMxT v8.1.1
Data standardisation#
QSMxT requires input data to conform to the Brain Imaging Data Structure (BIDS).
Luckily, QSMxT also provides scripts that can convert unorganised NIfTI or DICOM images to BIDS. If you are using NIfTI images and do not have DICOMs, see nifti-convert.
Convert DICOM to BIDS#
The DICOM to BIDS conversion must identify which series should be used for QSM reconstruction (e.g. MEGRE), and which series should be used for segmentation (T1-weighted). Because this information is not stored in the DICOM header in a standardised way, it can only be estimated based on other fields, or the user must identify series themselves.
If QSMxT is run interactively, the user will be prompted to identify the relevant series. However, because we are running QSMxT in a notebook, we disable the interactivity using --auto_yes and allow QSMxT to guess the intended purpose of each acquisition. In this case, it makes the right guess:
!dicom-convert dicoms-unsorted bids --auto_yes
/opt/miniconda-4.12.0/lib/python3.8/site-packages/dicompare/io.py:30: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment
Please use with caution. We would be grateful for your help in improving them
from nibabel.nicom.csareader import get_csa_header
[INFO]: Running QSMxT 8.1.1
[INFO]: Command: /opt/miniconda-4.12.0/bin/dicom-convert dicoms-unsorted bids --auto_yes
[INFO]: Python interpreter: /opt/miniconda-4.12.0/bin/python3.8
Loading DICOM files: 100%|█████████████████| 1216/1216 [00:04<00:00, 254.03it/s]
[INFO]: Loaded DICOM session in 4.88 seconds
/opt/miniconda-4.12.0/lib/python3.8/site-packages/dicompare/acquisition.py:144: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
session_df["BaseAcquisition"] = "acq-" + session_df[acquisition_fields].apply(
/opt/miniconda-4.12.0/lib/python3.8/site-packages/dicompare/acquisition.py:195: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
session_df.loc[param_group.index, "AcquisitionSignature"] = signature
/opt/miniconda-4.12.0/lib/python3.8/site-packages/dicompare/acquisition.py:218: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
session_df["RunNumber"] = 1
/opt/miniconda-4.12.0/lib/python3.8/site-packages/dicompare/acquisition.py:301: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
session_df["Acquisition"] = session_df["AcquisitionSignature"].fillna("Unknown").astype(str)
[INFO]: Auto-assigning initial labels
[INFO]: Auto-assigned selections:
Acquisition ... Description
0 acq-mp2ragehighres0p5isoslab ...
1 acq-qsmp21mmisote20 ...
2 acq-qsmp21mmisote20 ...
[3 rows x 7 columns]
[INFO]: Merging selections into dataframe...
[INFO]: Processing base group: ('dev_siemens^SB', 1, 20170705, 'acq-mp2ragehighres0p5isoslab', 'mp2rage_highRes_0p5iso_slab_UNI-DEN', 1, '1.2.276.0.7230010.3.1.3.0.4480.1677042698.772469', 'NA')
[INFO]: Found 1 unique Types in this group
[INFO]: Processing Type group: T1w with 288 rows
[INFO]: Found multiple DICOM paths for Type 'T1w', grouping by EchoNumber
[INFO]: Processing Echo group: 1.0 with 288 rows
[INFO]: Converting group with 288 rows
[INFO]: Running command: '"dcm2niix" -o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert"'
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)
Found 288 DICOM file(s)
Convert 288 DICOM as /home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert/temp_output (378x420x288x1)
Conversion required 0.251406 seconds (0.249745 for core code).
[INFO]: Processing base group: ('dev_siemens^SB', 1, 20170705, 'acq-qsmp21mmisote20', 'QSM_p2_1mmIso_TE20', 1, '1.3.12.2.1107.5.2.43.167001.2017070513471948579426649.0.0.0', 'HC1-7')
[INFO]: Found 1 unique Types in this group
[INFO]: Processing Type group: Mag with 160 rows
[INFO]: Found multiple DICOM paths for Type 'Mag', grouping by EchoNumber
[INFO]: Processing Echo group: 1.0 with 160 rows
[INFO]: Converting group with 160 rows
[INFO]: Running command: '"dcm2niix" -o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert"'
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)
Found 160 DICOM file(s)
Convert 160 DICOM as /home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert/temp_output (224x224x160x1)
Conversion required 0.066910 seconds (0.065767 for core code).
[INFO]: Processing base group: ('dev_siemens^SB', 1, 20170705, 'acq-qsmp21mmisote20', 'QSM_p2_1mmIso_TE20', 1, '1.3.12.2.1107.5.2.43.167001.2017070513471948580526650.0.0.0', 'HC1-7')
[INFO]: Found 1 unique Types in this group
[INFO]: Processing Type group: Phase with 160 rows
[INFO]: Found multiple DICOM paths for Type 'Phase', grouping by EchoNumber
[INFO]: Processing Echo group: 1.0 with 160 rows
[INFO]: Converting group with 160 rows
[INFO]: Running command: '"dcm2niix" -o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert"'
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)
Found 160 DICOM file(s)
Convert 160 DICOM as /home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert/temp_output_ph (224x224x160x1)
Conversion required 0.078257 seconds (0.074531 for core code).
[INFO]: Processing base group: ('dev_siemens^SB', 2, 20170705, 'acq-mp2ragehighres0p5isoslab', 'mp2rage_highRes_0p5iso_slab_UNI-DEN', 1, 2, 'NA')
[INFO]: Found 1 unique Types in this group
[INFO]: Processing Type group: T1w with 288 rows
[INFO]: Found multiple DICOM paths for Type 'T1w', grouping by EchoNumber
[INFO]: Processing Echo group: 1.0 with 288 rows
[INFO]: Converting group with 288 rows
[INFO]: Running command: '"dcm2niix" -o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert"'
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)
Found 288 DICOM file(s)
Convert 288 DICOM as /home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert/temp_output (378x420x288x1)
Conversion required 0.260042 seconds (0.258533 for core code).
[INFO]: Processing base group: ('dev_siemens^SB', 2, 20170705, 'acq-qsmp21mmisote20', 'QSM_p2_1mmIso_TE20', 1, 1, 'HC1-7')
[INFO]: Found 1 unique Types in this group
[INFO]: Processing Type group: Mag with 160 rows
[INFO]: Found multiple DICOM paths for Type 'Mag', grouping by EchoNumber
[INFO]: Processing Echo group: 1.0 with 160 rows
[INFO]: Converting group with 160 rows
[INFO]: Running command: '"dcm2niix" -o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert"'
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)
Found 160 DICOM file(s)
Convert 160 DICOM as /home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert/temp_output (224x224x160x1)
Conversion required 0.077077 seconds (0.075843 for core code).
[INFO]: Processing base group: ('dev_siemens^SB', 2, 20170705, 'acq-qsmp21mmisote20', 'QSM_p2_1mmIso_TE20', 1, 3, 'HC1-7')
[INFO]: Found 1 unique Types in this group
[INFO]: Processing Type group: Phase with 160 rows
[INFO]: Found multiple DICOM paths for Type 'Phase', grouping by EchoNumber
[INFO]: Processing Echo group: 1.0 with 160 rows
[INFO]: Converting group with 160 rows
[INFO]: Running command: '"dcm2niix" -o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert"'
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)
Found 160 DICOM file(s)
Convert 160 DICOM as /home/ashley/repos/example-notebooks/books/structural_imaging/bids/temp_convert/temp_output_ph (224x224x160x1)
Conversion required 0.073196 seconds (0.072460 for core code).
[INFO]: Scanning for multi-coil data to merge...
[INFO]: Scanning for multi-coil runs to combine...
[INFO]: Checking for complex or polar data requiring fixing...
Loading NIfTIs: 100%|███████████████████████████| 6/6 [00:00<00:00, 1443.16it/s]
[INFO]: Finished
!tree bids
bids
├── log_2025-08-25_03-39-16601683.txt
├── log_2025-08-25_03-39-25951254.txt
├── references.txt
├── sub-1
│ └── ses-20170705
│ └── anat
│ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.json
│ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.nii
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.json
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.nii
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.json
│ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.nii
└── sub-2
└── ses-20170705
└── anat
├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.json
├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.nii
├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.json
├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.nii
├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.json
└── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.nii
7 directories, 15 files
Inspect input data#
Here we define a function we will use to visualise NIfTI images so we can view some of the input data:
%%capture
!pip install seaborn numpy nibabel pandas ipyniivue
from glob import glob
from matplotlib import pyplot as plt
import numpy as np
import nibabel as nib
def show_nii(nii_path, title=None, figsize=(4,5), cmap='gray', **imshow_args):
# load data\n",
data_1 = nib.load(nii_path).get_fdata()
# get middle slices\n",
slc_data1 = np.rot90(data_1[np.shape(data_1)[0]//2,:,:])
slc_data2 = np.rot90(data_1[:,np.shape(data_1)[1]//2,:])
slc_data3 = np.rot90(data_1[:,:,np.shape(data_1)[2]//2])
# show slices\n",
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=figsize)
if title: plt.suptitle(title)
axes[0].imshow(slc_data1, cmap=cmap, **imshow_args)
axes[1].imshow(slc_data2, cmap=cmap, **imshow_args)
axes[2].imshow(slc_data3, cmap=cmap, **imshow_args)
axes[0].axis('off')
axes[1].axis('off')
axes[2].axis('off')
fig.tight_layout()
fig.subplots_adjust(top=1.55)
plt.show()
show_nii(glob("bids/sub-*/ses-*/anat/*mag*T2starw*nii*")[0], title="Magnitude", vmax=500)
show_nii(glob("bids/sub-*/ses-*/anat/*phase*T2starw*nii*")[0], title="Phase")
show_nii(glob("bids/sub-*/ses-*/anat/*T1w*nii*")[0], title="T1-weighted")
Interactive Display using Niivue
from ipyniivue import NiiVue
nv_T1 = NiiVue()
nv_T1.load_volumes([{"path": glob("bids/sub-*/ses-*/anat/*T1w*nii*")[0]}])
# Uncomment the following line to interact with the image
# nv_T1
Run QSMxT#
We are now ready to run QSMxT! We will generate susceptibility maps and segmentations, and export analysis CSVs to file.
The usual way of running QSMxT is to use qsmxt bids_dir. This will launch an interactive command-line interface (CLI) to setup your desired pipelines. However, since we are running this in a notebook, we need to use command-line arguments to by-pass the interface and execute a pipeline.
But first, let’s consider our pipeline settings. For QSM reconstruction, QSMxT provides a range of sensible defaults fit for different purposes. We can list the premade QSM pipelines using --list_premades. For the full pipeline details used for each premade pipeline, see qsm_pipelines.json.
!qsmxt --list_premades
=== Premade pipelines ===
default: Default QSMxT settings (GRE; assumes human brain)
gre: Applies suggested settings for 3D-GRE images
epi: Applies suggested settings for 3D-EPI images (assumes human brain)
bet: Applies a traditional BET-masking approach (artefact reduction unavailable; assumes human brain)
fast: Applies a set of fast algorithms
body: Applies suggested settings for non-brain applications
nextqsm: Applies suggested settings for running the NeXtQSM algorithm (assumes human brain)
[INFO]: Finished
For this demonstration, we will go with the fast pipeline. To export segmentations and analysis results, we will use --do_segmentation and --do_analysis. The --auto_yes option avoid the interactive CLI interface that cannot be used in a notebook:
!qsmxt bids \
--premade fast \
--do_qsm \
--do_segmentation \
--do_analysis \
--auto_yes
[INFO]: QSMxT v8.1.1
[INFO]: Python interpreter: /opt/miniconda-4.12.0/bin/python3.8
[INFO]: Command: qsmxt /home/ashley/repos/example-notebooks/books/structural_imaging/bids --premade 'fast' --do_qsm --do_segmentation --do_analysis --auto_yes
[WARNING]: Pipeline is NOT guidelines compliant (see https://doi.org/10.1002/mrm.30006):; Phase-quality-based masking recommended
[INFO]: Available memory: 12.85 GB
[INFO]: Creating QSMxT workflow for sub-1.ses-20170705.acq-acqmp2ragehighres0p5isoslab.T1w...
[INFO]: Creating QSMxT workflow for sub-1.ses-20170705.acq-acqqsmp21mmisote20.T2starw...
[INFO]: Creating QSMxT workflow for sub-2.ses-20170705.acq-acqmp2ragehighres0p5isoslab.T1w...
[INFO]: Creating QSMxT workflow for sub-2.ses-20170705.acq-acqqsmp21mmisote20.T2starw...
[INFO]: Running using MultiProc plugin with n_procs=14
250825-03:41:40,962 nipype.workflow INFO:
Workflow qsmxt-workflow settings: ['check', 'execution', 'logging', 'monitoring']
250825-03:41:40,978 nipype.workflow INFO:
Running in parallel.
250825-03:41:40,984 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 24 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-03:41:41,75 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-me".
250825-03:41:41,76 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_as-canonical".
250825-03:41:41,77 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
250825-03:41:41,78 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/fastsurfer_segment-t1".
250825-03:41:41,78 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000476s.
250825-03:41:41,78 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
250825-03:41:41,79 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
250825-03:41:41,87 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.007659s.
250825-03:41:41,76 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_read-nii".
250825-03:41:41,77 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-me".
250825-03:41:41,129 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
250825-03:41:41,130 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
250825-03:41:41,131 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000454s.
250825-03:41:41,133 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.002607s.
250825-03:41:41,75 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-se".
250825-03:41:41,78 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-se".
250825-03:41:41,179 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
250825-03:41:41,181 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.000784s.
250825-03:41:41,181 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
250825-03:41:41,183 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.0007s.
250825-03:41:42,985 nipype.workflow INFO:
[Job 0] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
250825-03:41:42,986 nipype.workflow INFO:
[Job 1] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
250825-03:41:42,986 nipype.workflow INFO:
[Job 2] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
250825-03:41:42,987 nipype.workflow INFO:
[Job 3] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
250825-03:41:42,987 nipype.workflow INFO:
[Job 6] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
250825-03:41:42,987 nipype.workflow INFO:
[Job 7] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
250825-03:41:42,988 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 18 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:41:43,44 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_register-t1-to-qsm".
250825-03:41:43,48 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
250825-03:41:44,986 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 17 jobs ready. Free memory (GB): 7.72/27.72, Free processors: 0/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:46:45,202 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 302.14979s.
250825-03:46:47,386 nipype.workflow INFO:
[Job 5] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
250825-03:46:47,391 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 17 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:46:47,591 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_read-nii".
250825-03:46:47,596 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-se".
250825-03:46:47,597 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_as-canonical".
250825-03:46:47,622 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
250825-03:46:47,590 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_as-canonical".
250825-03:46:47,599 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_read-nii".
250825-03:46:47,658 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
250825-03:46:47,668 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.007757s.
250825-03:46:47,622 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
250825-03:46:47,622 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
250825-03:46:47,685 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.002565s.
250825-03:46:47,591 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-me".
250825-03:46:47,645 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.018221s.
250825-03:46:47,700 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
250825-03:46:47,652 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
250825-03:46:47,704 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.001192s.
250825-03:46:47,706 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.028843s.
250825-03:46:47,720 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.013783s.
250825-03:46:49,387 nipype.workflow INFO:
[Job 8] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
250825-03:46:49,389 nipype.workflow INFO:
[Job 9] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
250825-03:46:49,391 nipype.workflow INFO:
[Job 12] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
250825-03:46:49,392 nipype.workflow INFO:
[Job 13] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
250825-03:46:49,393 nipype.workflow INFO:
[Job 14] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
250825-03:46:49,394 nipype.workflow INFO:
[Job 15] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
250825-03:46:49,396 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 14 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:46:49,475 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_register-t1-to-qsm".
250825-03:46:49,486 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
250825-03:46:51,389 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 13 jobs ready. Free memory (GB): 7.72/27.72, Free processors: 0/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:49:39,869 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 170.380782s.
250825-03:49:41,621 nipype.workflow INFO:
[Job 11] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
250825-03:49:41,623 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 13 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:49:41,679 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_register-t1-to-qsm".
250825-03:49:41,686 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
250825-03:49:43,626 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 7.72/27.72, Free processors: 0/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-03:50:45,932 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 544.851713s.
250825-03:50:47,699 nipype.workflow INFO:
[Job 4] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
250825-03:50:47,701 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 13 jobs ready. Free memory (GB): 19.72/27.72, Free processors: 8/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
250825-03:50:47,782 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/fastsurfer_segment-t1".
250825-03:50:47,787 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
250825-03:50:49,700 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 7.72/27.72, Free processors: 0/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
250825-03:55:21,170 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 339.48211s.
250825-03:55:22,49 nipype.workflow INFO:
[Job 17] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
250825-03:55:22,51 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 12 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:55:22,172 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-me".
250825-03:55:22,177 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-se".
250825-03:55:22,190 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
250825-03:55:22,190 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
250825-03:55:22,188 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_getfirst-canonical-magnitude".
250825-03:55:22,188 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_as-canonical".
250825-03:55:22,198 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.002381s.
250825-03:55:22,200 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.004421s.
250825-03:55:22,198 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/numpy_numpy_nibabel_mgz2nii".
250825-03:55:22,202 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
250825-03:55:22,205 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.0008s.
250825-03:55:22,208 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
250825-03:55:22,225 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
250825-03:55:22,240 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.023386s.
250825-03:55:22,190 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_read-nii".
250825-03:55:22,253 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
250825-03:55:22,274 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.017205s.
250825-03:55:22,452 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.222932s.
250825-03:55:24,51 nipype.workflow INFO:
[Job 18] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
250825-03:55:24,53 nipype.workflow INFO:
[Job 19] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
250825-03:55:24,54 nipype.workflow INFO:
[Job 20] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
250825-03:55:24,55 nipype.workflow INFO:
[Job 21] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
250825-03:55:24,56 nipype.workflow INFO:
[Job 24] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
250825-03:55:24,64 nipype.workflow INFO:
[Job 25] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
250825-03:55:24,68 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 10 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:55:24,195 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_register-t1-to-qsm".
250825-03:55:24,207 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
250825-03:55:26,55 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 7.72/27.72, Free processors: 0/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:58:56,46 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 211.834933s.
250825-03:58:56,404 nipype.workflow INFO:
[Job 23] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
250825-03:58:56,406 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:58:56,492 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_scale-phase".
250825-03:58:56,496 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_getfirst-canonical-magnitude".
250825-03:58:56,501 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_scale-phase".
250825-03:58:56,504 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_getfirst-canonical-magnitude".
250825-03:58:56,515 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
250825-03:58:56,521 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.002173s.
250825-03:58:56,525 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
250825-03:58:56,526 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
250825-03:58:56,528 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
250825-03:58:56,535 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.002478s.
250825-03:58:56,497 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_numpy_nilearn_t1w-seg-resampled".
250825-03:58:56,554 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
250825-03:58:56,502 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_getfirst-canonical-magnitude".
250825-03:58:56,574 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
250825-03:58:56,581 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.002977s.
250825-03:58:57,198 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.666212s.
250825-03:58:57,246 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.713249s.
250825-03:58:58,406 nipype.workflow INFO:
[Job 26] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
250825-03:58:58,408 nipype.workflow INFO:
[Job 27] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
250825-03:58:58,409 nipype.workflow INFO:
[Job 29] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
250825-03:58:58,410 nipype.workflow INFO:
[Job 31] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
250825-03:58:58,411 nipype.workflow INFO:
[Job 32] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
250825-03:58:58,413 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 13.72/27.72, Free processors: 5/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:58:58,556 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_transform-segmentation-to-qsm".
250825-03:58:58,558 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_axial-resampling".
250825-03:58:58,562 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_axial-resampling".
250825-03:58:58,567 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
250825-03:58:58,574 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
250825-03:58:58,586 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.016913s.
250825-03:58:58,605 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.026816s.
250825-03:58:58,615 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
250825-03:59:00,412 nipype.workflow INFO:
[Job 36] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
250825-03:59:00,433 nipype.workflow INFO:
[Job 41] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
250825-03:59:00,455 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 6 jobs ready. Free memory (GB): 11.72/27.72, Free processors: 4/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:59:00,773 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/mrt_romeo".
250825-03:59:00,778 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/mrt_romeo".
250825-03:59:00,820 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
250825-03:59:00,840 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
250825-03:59:02,435 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 4 jobs ready. Free memory (GB): 7.04/27.72, Free processors: 2/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:59:08,172 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 9.55001s.
250825-03:59:08,429 nipype.workflow INFO:
[Job 35] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
250825-03:59:08,444 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 4 jobs ready. Free memory (GB): 9.04/27.72, Free processors: 3/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:59:14,847 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 18.288881s.
250825-03:59:16,449 nipype.workflow INFO:
[Job 34] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
250825-03:59:16,477 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 11.04/27.72, Free processors: 4/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:59:17,17 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/copyfile".
250825-03:59:17,72 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
250825-03:59:18,484 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 4 jobs ready. Free memory (GB): 10.84/27.72, Free processors: 3/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:59:19,38 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 1.958106s.
250825-03:59:20,459 nipype.workflow INFO:
[Job 44] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
250825-03:59:20,514 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 4 jobs ready. Free memory (GB): 11.04/27.72, Free processors: 4/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-03:59:43,804 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 536.014169s.
250825-03:59:44,477 nipype.workflow INFO:
[Job 10] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
250825-03:59:44,480 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 23.04/27.72, Free processors: 12/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
250825-03:59:44,538 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/numpy_numpy_nibabel_mgz2nii".
250825-03:59:44,538 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/fastsurfer_segment-t1".
250825-03:59:44,540 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
250825-03:59:44,540 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
250825-03:59:44,683 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.142189s.
250825-03:59:46,478 nipype.workflow INFO:
[Job 28] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
250825-03:59:46,481 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 11.04/27.72, Free processors: 4/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
250825-03:59:46,538 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_t1w-seg-resampled".
250825-03:59:46,539 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_transform-segmentation-to-qsm".
250825-03:59:46,541 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
250825-03:59:46,548 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
250825-03:59:47,32 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.48324s.
250825-03:59:48,480 nipype.workflow INFO:
[Job 38] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
250825-03:59:48,482 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 4 jobs ready. Free memory (GB): 9.04/27.72, Free processors: 3/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
250825-03:59:48,534 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists2".
250825-03:59:48,536 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
250825-03:59:48,538 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.001084s.
250825-03:59:49,713 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 3.171211s.
250825-03:59:50,482 nipype.workflow INFO:
[Job 37] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
250825-03:59:50,483 nipype.workflow INFO:
[Job 47] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
250825-03:59:50,485 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 11.04/27.72, Free processors: 4/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
250825-04:07:17,604 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 496.77802s.
250825-04:07:19,31 nipype.workflow INFO:
[Job 50] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
250825-04:07:19,34 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 13.38/27.72, Free processors: 5/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
250825-04:07:19,118 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/nibabel-numpy_normalize-phase".
250825-04:07:19,130 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
250825-04:07:19,216 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.084208s.
250825-04:07:21,33 nipype.workflow INFO:
[Job 55] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
250825-04:07:21,34 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 13.38/27.72, Free processors: 5/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
250825-04:08:00,673 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 539.809623s.
250825-04:08:01,78 nipype.workflow INFO:
[Job 46] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
250825-04:08:01,80 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-04:08:01,156 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/nibabel-numpy_normalize-phase".
250825-04:08:01,171 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
250825-04:08:01,350 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.177227s.
250825-04:08:03,80 nipype.workflow INFO:
[Job 53] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
250825-04:08:03,82 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
250825-04:08:12,404 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 507.863076s.
250825-04:08:13,90 nipype.workflow INFO:
[Job 16] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
250825-04:08:13,92 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:08:13,132 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/numpy_numpy_nibabel_mgz2nii".
250825-04:08:13,132 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/fastsurfer_segment-t1".
250825-04:08:13,134 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
250825-04:08:13,135 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
250825-04:08:13,268 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.132617s.
250825-04:08:15,92 nipype.workflow INFO:
[Job 30] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
250825-04:08:15,94 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-04:08:15,135 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_numpy_nilearn_t1w-seg-resampled".
250825-04:08:15,137 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
250825-04:08:15,135 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_transform-segmentation-to-qsm".
250825-04:08:15,191 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
250825-04:08:15,975 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.782673s.
250825-04:08:17,94 nipype.workflow INFO:
[Job 40] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
250825-04:08:17,96 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 13.72/27.72, Free processors: 5/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-04:08:17,621 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 2.483173s.
250825-04:08:19,96 nipype.workflow INFO:
[Job 39] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
250825-04:08:19,98 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-04:08:19,168 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/copyfile".
250825-04:08:19,173 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
250825-04:08:19,359 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.1851s.
250825-04:08:21,99 nipype.workflow INFO:
[Job 48] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
250825-04:08:21,265 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 15.72/27.72, Free processors: 6/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
250825-04:16:20,275 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 487.088796s.
250825-04:16:21,669 nipype.workflow INFO:
[Job 22] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
250825-04:16:21,670 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:16:21,726 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/numpy_numpy_nibabel_mgz2nii".
250825-04:16:21,727 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/fsl-bet".
250825-04:16:21,729 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
250825-04:16:21,731 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
250825-04:16:21,869 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.140142s.
250825-04:16:23,587 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 1.855826s.
250825-04:16:23,671 nipype.workflow INFO:
[Job 33] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
250825-04:16:23,672 nipype.workflow INFO:
[Job 45] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
250825-04:16:23,673 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:16:23,733 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_t1w-seg-resampled".
250825-04:16:23,733 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/fsl-bet".
250825-04:16:23,734 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/scipy_numpy_nibabel_bet_erode".
250825-04:16:23,734 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
250825-04:16:23,735 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
250825-04:16:23,737 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
250825-04:16:23,733 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_transform-segmentation-to-qsm".
250825-04:16:23,796 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
250825-04:16:24,180 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.383082s.
250825-04:16:24,428 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.691406s.
250825-04:16:25,577 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 1.839091s.
250825-04:16:25,673 nipype.workflow INFO:
[Job 43] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
250825-04:16:25,674 nipype.workflow INFO:
[Job 49] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
250825-04:16:25,675 nipype.workflow INFO:
[Job 52] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
250825-04:16:25,677 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 25.72/27.72, Free processors: 13/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
250825-04:16:25,723 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists2".
250825-04:16:25,723 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_vsharp".
250825-04:16:25,725 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
250825-04:16:25,726 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.000421s.
250825-04:16:25,729 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
250825-04:16:25,723 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/scipy_numpy_nibabel_bet_erode".
250825-04:16:25,776 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
250825-04:16:26,319 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 2.583818s.
250825-04:16:26,371 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.594512s.
250825-04:16:27,675 nipype.workflow INFO:
[Job 42] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
250825-04:16:27,676 nipype.workflow INFO:
[Job 51] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
250825-04:16:27,676 nipype.workflow INFO:
[Job 54] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
250825-04:16:27,677 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 25.72/27.72, Free processors: 12/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
250825-04:16:27,717 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_vsharp".
250825-04:16:27,721 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
250825-04:16:29,677 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 23.72/27.72, Free processors: 10/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
250825-04:18:42,179 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 136.449863s.
250825-04:18:43,810 nipype.workflow INFO:
[Job 56] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
250825-04:18:43,815 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 25.72/27.72, Free processors: 12/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
250825-04:18:43,865 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_rts".
250825-04:18:43,868 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
250825-04:18:45,70 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 137.348991s.
250825-04:18:45,812 nipype.workflow INFO:
[Job 57] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
250825-04:18:45,813 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 25.31/27.72, Free processors: 12/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
250825-04:18:45,855 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_rts".
250825-04:18:45,857 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
250825-04:18:47,814 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 22.90/27.72, Free processors: 10/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
250825-04:19:33,687 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 49.818341s.
250825-04:19:33,859 nipype.workflow INFO:
[Job 58] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
250825-04:19:33,861 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 25.31/27.72, Free processors: 12/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
250825-04:19:33,907 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-average".
250825-04:19:33,909 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
250825-04:19:33,910 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000119s.
250825-04:19:34,836 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 48.978322s.
250825-04:19:35,861 nipype.workflow INFO:
[Job 59] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
250825-04:19:35,863 nipype.workflow INFO:
[Job 60] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
250825-04:19:35,865 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:19:35,905 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-average".
250825-04:19:35,905 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_qsm-resampled".
250825-04:19:35,907 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
250825-04:19:35,907 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 9.4e-05s.
250825-04:19:35,909 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
250825-04:19:35,913 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.002452s.
250825-04:19:37,863 nipype.workflow INFO:
[Job 61] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
250825-04:19:37,864 nipype.workflow INFO:
[Job 62] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
250825-04:19:37,865 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:19:37,905 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-referenced".
250825-04:19:37,907 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
250825-04:19:37,905 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists1".
250825-04:19:37,957 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
250825-04:19:37,958 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.000764s.
250825-04:19:37,905 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_qsm-resampled".
250825-04:19:38,9 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
250825-04:19:38,12 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.002644s.
250825-04:19:38,277 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.369526s.
250825-04:19:39,865 nipype.workflow INFO:
[Job 63] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
250825-04:19:39,868 nipype.workflow INFO:
[Job 64] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
250825-04:19:39,869 nipype.workflow INFO:
[Job 65] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
250825-04:19:39,870 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:19:39,912 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-referenced".
250825-04:19:39,912 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copy_qsm_json_sidecar".
250825-04:19:39,913 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
250825-04:19:39,914 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
250825-04:19:39,917 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.002302s.
250825-04:19:39,912 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists1".
250825-04:19:39,912 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/create_permutations".
250825-04:19:39,965 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
250825-04:19:39,966 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.000361s.
250825-04:19:39,967 nipype.workflow INFO:
[Node] Executing "create_permutations" <nipype.interfaces.utility.wrappers.Function>
250825-04:19:39,968 nipype.workflow INFO:
[Node] Finished "create_permutations", elapsed time 0.000416s.
250825-04:19:40,306 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.392569s.
250825-04:19:41,867 nipype.workflow INFO:
[Job 66] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
250825-04:19:41,867 nipype.workflow INFO:
[Job 67] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
250825-04:19:41,868 nipype.workflow INFO:
[Job 68] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
250825-04:19:41,868 nipype.workflow INFO:
[Job 69] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations).
250825-04:19:41,869 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:19:41,906 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/create_permutations".
250825-04:19:41,906 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copy_qsm_json_sidecar".
250825-04:19:41,908 nipype.workflow INFO:
[Node] Executing "create_permutations" <nipype.interfaces.utility.wrappers.Function>
250825-04:19:41,908 nipype.workflow INFO:
[Node] Finished "create_permutations", elapsed time 0.000223s.
250825-04:19:41,908 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
250825-04:19:41,911 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm0" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm0".
250825-04:19:41,911 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.002299s.
250825-04:19:41,912 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
250825-04:19:43,869 nipype.workflow INFO:
[Job 70] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
250825-04:19:43,870 nipype.workflow INFO:
[Job 71] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations).
250825-04:19:43,872 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 25.72/27.72, Free processors: 13/14.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm
250825-04:19:43,937 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm0" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm0".
250825-04:19:43,939 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
250825-04:19:45,872 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 23.72/27.72, Free processors: 12/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm
250825-04:20:46,897 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm0", elapsed time 64.984031s.
250825-04:20:47,931 nipype.workflow INFO:
[Job 72] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm).
250825-04:20:47,932 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 25.72/27.72, Free processors: 13/14.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm
250825-04:20:47,982 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copyfile".
250825-04:20:47,989 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
250825-04:20:48,126 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.13606s.
250825-04:20:48,444 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm0", elapsed time 64.504081s.
250825-04:20:49,933 nipype.workflow INFO:
[Job 73] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm).
250825-04:20:49,934 nipype.workflow INFO:
[Job 74] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile).
250825-04:20:49,934 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
250825-04:20:49,977 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile" in "/home/ashley/repos/example-notebooks/books/structural_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copyfile".
250825-04:20:49,980 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
250825-04:20:50,37 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.056167s.
250825-04:20:51,935 nipype.workflow INFO:
[Job 75] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile).
250825-04:20:51,937 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 27.72/27.72, Free processors: 14/14.
[INFO]: Warnings occurred!
[INFO]: Finished
View results#
Let’s have a look at the generated qsm folder:
!tree bids/derivatives/qsmxt-*-* --dirsfirst
bids/derivatives/qsmxt-2025-08-25-034120
├── sub-1
│ └── ses-20170705
│ ├── anat
│ │ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_space-orig_dseg.nii
│ │ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_space-qsm_dseg.nii
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_Chimap.json
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_Chimap.nii
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-orig_dseg.nii
│ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_dseg.nii
│ └── extra_data
│ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_desc-t1w-to-qsm_transform.mat
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-t1w-to-qsm_transform.mat
│ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_qsm-analysis.csv
├── sub-2
│ └── ses-20170705
│ ├── anat
│ │ ├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_space-orig_dseg.nii
│ │ ├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_space-qsm_dseg.nii
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_Chimap.json
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_Chimap.nii
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-orig_dseg.nii
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_dseg.nii
│ └── extra_data
│ ├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_desc-t1w-to-qsm_transform.mat
│ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-t1w-to-qsm_transform.mat
│ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_qsm-analysis.csv
├── command.txt
├── pypeline.log
├── qsmxt.log
├── references.txt
└── settings.json
9 directories, 23 files
The references.txt file contains a list of all the algorithms used and relevant citations:
!cat bids/derivatives/qsmxt-*-*/references.txt
== References ==
- QSMxT: Stewart AW, Robinson SD, O'Brien K, et al. QSMxT: Robust masking and artifact reduction for quantitative susceptibility mapping. Magnetic Resonance in Medicine. 2022;87(3):1289-1300. doi:10.1002/mrm.29048
- QSMxT: Stewart AW, Bollman S, et al. QSMxT/QSMxT. GitHub; 2022. https://github.com/QSMxT/QSMxT
- Python package - Nipype: Gorgolewski K, Burns C, Madison C, et al. Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python. Frontiers in Neuroinformatics. 2011;5. Accessed April 20, 2022. doi:10.3389/fninf.2011.00013
- Brain extraction: Smith SM. Fast robust automated brain extraction. Human Brain Mapping. 2002;17(3):143-155. doi:10.1002/hbm.10062
- Brain extraction: Liangfu Chen. liangfu/bet2 - Standalone Brain Extraction Tool. GitHub; 2015. https://github.com/liangfu/bet2
- Unwrapping algorithm - ROMEO: Dymerska B, Eckstein K, Bachrata B, et al. Phase unwrapping with a rapid opensource minimum spanning tree algorithm (ROMEO). Magnetic Resonance in Medicine. 2021;85(4):2294-2308. doi:10.1002/mrm.28563
- Background field removal - V-SHARP: Wu B, Li W, Guidon A et al. Whole brain susceptibility mapping using compressed sensing. Magnetic resonance in medicine. 2012 Jan;67(1):137-47. doi:10.1002/mrm.23000
- QSM algorithm - RTS: Kames C, Wiggermann V, Rauscher A. Rapid two-step dipole inversion for susceptibility mapping with sparsity priors. Neuroimage. 2018 Feb 15;167:276-83. doi:10.1016/j.neuroimage.2017.11.018
- Julia package - QSM.jl: kamesy. GitHub; 2022. https://github.com/kamesy/QSM.jl
- Julia package - MriResearchTools: Eckstein K. korbinian90/MriResearchTools.jl. GitHub; 2022. https://github.com/korbinian90/MriResearchTools.jl
- Python package - nibabel: Brett M, Markiewicz CJ, Hanke M, et al. nipy/nibabel. GitHub; 2019. https://github.com/nipy/nibabel
- Python package - scipy: Virtanen P, Gommers R, Oliphant TE, et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods. 2020;17(3):261-272. doi:10.1038/s41592-019-0686-2
- Python package - numpy: Harris CR, Millman KJ, van der Walt SJ, et al. Array programming with NumPy. Nature. 2020;585(7825):357-362. doi:10.1038/s41586-020-2649-2
- FastSurfer: Henschel L, Conjeti S, Estrada S, Diers K, Fischl B, Reuter M. FastSurfer - A fast and accurate deep learning based neuroimaging pipeline. NeuroImage. 2020;219:117012. doi:10.1016/j.neuroimage.2020.117012
- ANTs: Avants BB, Tustison NJ, Johnson HJ. Advanced Normalization Tools. GitHub; 2022. https://github.com/ANTsX/ANTs
Let’s view one of the QSM results:
QSM results#
show_nii(glob("bids/derivatives/qsmxt-*/sub-*/ses-*/anat/*Chimap.nii*")[0], title="Chimap", figsize=(10,8), cmap='gray', vmin=-0.1, vmax=0.1)
Segmentations#
Segmentations are generated in both the QSM space and the T1-weighted space. Transformations are also made available.
show_nii(glob("bids/derivatives/qsmxt-*/sub-*/ses-*/anat/*qsm_dseg.nii*")[0], title="Segmentation", figsize=(10,8), cmap='Set3', vmin=0, vmax=96)
Analysis CSVs#
CSV files have been exported containing susceptibility values in regions of interest for each subject.
Here we will load the CSVs, inspect the data and generate figures:
# import modules
import pandas as pd
import seaborn as sns
The raw CSV files use names from FreeSurfer as exported by FastSurfer. The full list of regions is available here.
pd.read_csv(glob("bids/derivatives/qsmxt-*-*/sub*/ses*/extra*/*.csv")[0])
| roi | num_voxels | min | max | median | mean | std | |
|---|---|---|---|---|---|---|---|
| 0 | 3rd-Ventricle | 606 | -0.236484 | 0.194673 | -0.020096 | -0.022283 | 0.034961 |
| 1 | 4th-Ventricle | 1558 | -0.128288 | 0.032236 | -0.048718 | -0.050211 | 0.028352 |
| 2 | Brain-Stem | 19086 | -0.142628 | 0.214565 | -0.044262 | -0.040350 | 0.028972 |
| 3 | CSF | 787 | -1.398799 | 0.946090 | 0.024578 | 0.026632 | 0.142303 |
| 4 | Left-Accumbens-area | 510 | -0.143215 | 0.129016 | 0.021351 | 0.020700 | 0.029128 |
| ... | ... | ... | ... | ... | ... | ... | ... |
| 91 | ctx-rh-superiorfrontal | 29949 | -0.133219 | 0.252426 | -0.004022 | -0.009384 | 0.024877 |
| 92 | ctx-rh-superiorparietal | 12138 | -0.083912 | 0.307323 | -0.015906 | -0.015151 | 0.021828 |
| 93 | ctx-rh-superiortemporal | 16633 | -0.091664 | 0.249151 | 0.006783 | 0.012637 | 0.024330 |
| 94 | ctx-rh-supramarginal | 12084 | -0.082145 | 0.240087 | 0.018040 | 0.018828 | 0.022929 |
| 95 | ctx-rh-transversetemporal | 1255 | -0.004546 | 0.111561 | 0.034362 | 0.034584 | 0.013029 |
96 rows × 7 columns
We will select a subset of these ROIs and give them more readable names:
# define regions of interest
# see https://github.com/QSMxT/QSMxT/blob/main/qsmxt/aseg_labels.csv for a full list
rois = {
"Thalamus" : [9, 10, 48, 49],
"Pallidum" : [12, 13, 52, 53],
"Caudate" : [11, 50],
"Putamen" : [12, 51],
"Brain stem" : [16],
"CSF" : [24, 122, 257, 701],
"White matter" : [2, 7, 41, 46, 177]
}
roi_names = { value: key for key in rois for value in rois[key] }
roi_ids = [value for roi in rois.values() for value in roi]
# load a reconstruction
qsm = nib.load(glob("bids/derivatives/qsmxt-*-*/sub*/ses*/anat*/*Chimap.nii*")[0]).get_fdata().flatten()
seg = nib.load(glob("bids/derivatives/qsmxt-*-*/sub*/ses*/anat*/*space-qsm*dseg.nii*")[0]).get_fdata().flatten()
# retain only the rois
qsm = qsm[np.isin(seg, roi_ids)]
seg = seg[np.isin(seg, roi_ids)]
# convert to a dataframe for plotting purposes
seg = pd.Series(seg).map(roi_names)
data = pd.DataFrame({ 'qsm' : qsm, 'seg' : seg })
# summarise data by region including the average and standard deviation
data.groupby('seg')['qsm'].agg(['mean', 'std']).sort_values('mean').round(decimals=3)
| mean | std | |
|---|---|---|
| seg | ||
| Brain stem | -0.040 | 0.029 |
| White matter | -0.002 | 0.028 |
| CSF | 0.027 | 0.142 |
| Thalamus | 0.030 | 0.035 |
| Pallidum | 0.033 | 0.059 |
| Caudate | 0.047 | 0.024 |
| Putamen | 0.048 | 0.033 |
medians = data.groupby('seg')['qsm'].median().sort_values()
order = medians.index
# plot
fig, ax = plt.subplots(figsize=(5,4))
sns.boxplot(data=data, y='qsm', x='seg', fliersize=0, color='lightblue', order=order, ax=ax)
ax.set_xticks(range(len(ax.get_xticks()))) # Set tick positions explicitly
ax.set_xticklabels(ax.get_xticklabels(), ha='right', rotation=45)
ax.set_ylim(-0.2, 0.3)
ax.axhline(y=0, color='pink', linestyle='-', linewidth=1, zorder=-1)
ax.set_xlabel("Region of interest")
ax.set_ylabel("Susceptibility (ppm)")
ax.set_title("QSM")
plt.show()
