QSMxT#
Author: Ashley Stewart
Date: 25 Aug 2025
License:
Note: If this notebook uses neuroimaging tools from Neurocontainers, those tools retain their original licenses. Please see Neurodesk citation guidelines for details.
Citation and Resources:#
Tools included in this workflow#
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
Dataset#
Bollmann, S., & Stewart, A. (2023, August 7). QSM DICOM testdata for QSMxT pipeline. Retrieved from osf.io/ru43c
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 module
await module.load('qsmxt/8.1.1')
!qsmxt --version
[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
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[INFO]: Loaded DICOM session in 12.08 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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/jovyan/workspace/books/examples/quantitative_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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert/temp_output (378x420x288x1)
Conversion required 0.569626 seconds (0.569482 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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/jovyan/workspace/books/examples/quantitative_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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert/temp_output (224x224x160x1)
Conversion required 0.132017 seconds (0.131958 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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/jovyan/workspace/books/examples/quantitative_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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert/temp_output_ph (224x224x160x1)
Conversion required 0.134536 seconds (0.134486 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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/jovyan/workspace/books/examples/quantitative_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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert/temp_output (378x420x288x1)
Conversion required 0.587742 seconds (0.587388 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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/jovyan/workspace/books/examples/quantitative_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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert/temp_output (224x224x160x1)
Conversion required 0.135592 seconds (0.135537 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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert" -f "temp_output" -z n -m o "/home/jovyan/workspace/books/examples/quantitative_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/jovyan/workspace/books/examples/quantitative_imaging/bids/temp_convert/temp_output_ph (224x224x160x1)
Conversion required 0.157362 seconds (0.157280 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: 0%| | 0/46 [00:00<?, ?it/s]
Loading NIfTIs: 100%|█████████████████████████| 46/46 [00:00<00:00, 1608.93it/s]
[INFO]: Finished
!tree bids
bids
├── derivatives
│ ├── qsmxt-2026-07-08-231723
│ │ ├── command.txt
│ │ ├── pypeline.log
│ │ ├── qsmxt.log
│ │ ├── references.txt
│ │ ├── settings.json
│ │ ├── 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
│ └── workflow
│ └── qsmxt-workflow
│ ├── d3.js
│ ├── graph.json
│ ├── graph1.json
│ ├── index.html
│ ├── sub-1
│ │ └── ses-20170705
│ │ ├── qsm_acq-acqmp2ragehighres0p5isoslab_T1w
│ │ │ ├── ants_register-t1-to-qsm
│ │ │ │ ├── _0x8add63149fb60f65825d4533b500d28b.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── command.txt
│ │ │ │ ├── result_ants_register-t1-to-qsm.pklz
│ │ │ │ └── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_0GenericAffine.mat
│ │ │ ├── ants_transform-segmentation-to-qsm
│ │ │ │ ├── _0x1aba3ff5aad0aa08d4abbf6f6852765f.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── command.txt
│ │ │ │ ├── result_ants_transform-segmentation-to-qsm.pklz
│ │ │ │ └── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_segmentation_trans.nii
│ │ │ ├── copyfile
│ │ │ │ ├── _0xf432ac486c407cb00fe59c277d794666.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_copyfile.pklz
│ │ │ ├── fastsurfer_segment-t1
│ │ │ │ ├── _0x188e9fcd5eff220b7a056270d06a680b.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── command.txt
│ │ │ │ ├── output
│ │ │ │ │ ├── mri
│ │ │ │ │ │ └── orig
│ │ │ │ │ └── scripts
│ │ │ │ ├── result_fastsurfer_segment-t1.pklz
│ │ │ │ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg.mgz
│ │ │ │ └── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii.nii
│ │ │ ├── func_getfirst-canonical-magnitude
│ │ │ │ ├── _0x788b5348be15330ae45b79e460cf7187.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ │ ├── func_read-json-me
│ │ │ │ ├── _0x144e564dc25f8e365ed6f00f2abead74.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_read-json-me.pklz
│ │ │ ├── func_read-json-se
│ │ │ │ ├── _0x72cb7f8be01310b24634ddcf10b1a83f.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_read-json-se.pklz
│ │ │ ├── nibabel_as-canonical
│ │ │ │ ├── _0xa2fadef26dd7130075b619d925012840.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_nibabel_as-canonical.pklz
│ │ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ │ ├── _0x7b14b6326566696de7e007be93751628.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── result_nibabel_numpy_nilearn_t1w-seg-resampled.pklz
│ │ │ │ └── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii_resampled.nii
│ │ │ ├── nibabel_read-nii
│ │ │ │ ├── _0x4097895e9852c0697d5d54864002018f.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_nibabel_read-nii.pklz
│ │ │ └── numpy_numpy_nibabel_mgz2nii
│ │ │ ├── _0x62966909fa42aec915cd382597a22c25.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ │ └── qsm_acq-acqqsmp21mmisote20_T2starw
│ │ ├── ants_register-t1-to-qsm
│ │ │ ├── _0x38609871ffac5eea5f1a31ff5fe629df.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_ants_register-t1-to-qsm.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_0GenericAffine.mat
│ │ ├── ants_transform-segmentation-to-qsm
│ │ │ ├── _0xc61ab0ff6503c3d2761abf12c3e1e8e2.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_ants_transform-segmentation-to-qsm.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_segmentation_trans.nii
│ │ ├── combine_lists1
│ │ │ ├── _0x957e4f72fdbdbb98f5cdd60ec4c954b0.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_combine_lists1.pklz
│ │ ├── combine_lists2
│ │ │ ├── _0xf16b531894dd579a33c9fe21d44a083f.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_combine_lists2.pklz
│ │ ├── copy_qsm_json_sidecar
│ │ │ ├── _0x7d544c09b6f1d39c0716807a28a2265b.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copy_qsm_json_sidecar.pklz
│ │ ├── copyfile
│ │ │ ├── _0x022c90e246b893954b73d1e804838bcb.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copyfile.pklz
│ │ ├── create_permutations
│ │ │ ├── _0x2e8f15878166b0add8fef362fa85b230.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_create_permutations.pklz
│ │ ├── fastsurfer_segment-t1
│ │ │ ├── _0x188e9fcd5eff220b7a056270d06a680b.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── output
│ │ │ │ ├── mri
│ │ │ │ │ └── orig
│ │ │ │ └── scripts
│ │ │ ├── result_fastsurfer_segment-t1.pklz
│ │ │ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg.mgz
│ │ │ └── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii.nii
│ │ ├── func_getfirst-canonical-magnitude
│ │ │ ├── _0x1b63afb3dd5af51487ba397b2dcf6098.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ ├── func_read-json-me
│ │ │ ├── _0x5e106ee0599197e5625ef88f0660b18f.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-me.pklz
│ │ ├── func_read-json-se
│ │ │ ├── _0xfeb4ac7f344d5cc3b1629f65b836541b.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-se.pklz
│ │ ├── mask_workflow
│ │ │ ├── fsl-bet
│ │ │ │ ├── _0xff69f2a5855724ce572f8e5f9140b54e.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── command.txt
│ │ │ │ ├── result_fsl-bet.pklz
│ │ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw_bet-mask.nii.gz
│ │ │ └── scipy_numpy_nibabel_bet_erode
│ │ │ ├── _0x982609323d3198b8dfc976a4f4ee82ed.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result_scipy_numpy_nibabel_bet_erode.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw_bet-mask_ero.nii.gz
│ │ ├── nibabel_as-canonical
│ │ │ ├── _0xf98ff8a7f2a18eaed7101514d479ecc3.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_as-canonical.pklz
│ │ ├── nibabel_numpy_analyse-qsm
│ │ │ ├── _0x58d070128511477b563b770bf2734196.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── mapflow
│ │ │ │ └── _nibabel_numpy_analyse-qsm0
│ │ │ │ ├── _0xa068fc207f0274231599f0b97c1a1f02.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── result__nibabel_numpy_analyse-qsm0.pklz
│ │ │ │ └── sub-1_ses-20170705_desc-qsmxt-2026-07-08-231723_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-07-08-231723_dseg_analysis.csv
│ │ │ └── result_nibabel_numpy_analyse-qsm.pklz
│ │ ├── nibabel_numpy_nilearn_axial-resampling
│ │ │ ├── _0xe12366ceeb1f0a32d5707d8a80726c08.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_nilearn_axial-resampling.pklz
│ │ ├── nibabel_numpy_nilearn_qsm-resampled
│ │ │ ├── _0x68b1d05ab768d88b585c7983623302ac.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_nilearn_qsm-resampled.pklz
│ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ ├── _0x32b89dbabfa31bb6e0816c429f7217b9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result_nibabel_numpy_nilearn_t1w-seg-resampled.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii_resampled.nii
│ │ ├── nibabel_numpy_qsm-average
│ │ │ ├── _0xb9d27ecc0b1bed8c3b619b03b9fc3e14.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_qsm-average.pklz
│ │ ├── nibabel_numpy_qsm-referenced
│ │ │ ├── _0x18f82eec3cb9d7e0fdf6b522491a8bc8.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result_nibabel_numpy_qsm-referenced.pklz
│ │ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp_rts_ref.json
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp_rts_ref.nii
│ │ ├── nibabel_numpy_scale-phase
│ │ │ ├── _0xc35995126cd3a6c0292ca521e44119ce.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result_nibabel_numpy_scale-phase.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled.nii
│ │ ├── nibabel_read-nii
│ │ │ ├── _0x79608220c2b37e7182fc84bea0818646.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_read-nii.pklz
│ │ ├── numpy_numpy_nibabel_mgz2nii
│ │ │ ├── _0x8819736995390d1485bb737a846e1399.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ │ └── qsm_workflow
│ │ ├── mrt_romeo
│ │ │ ├── _0xb868f17a0dbbf033977f6019659cdf8f.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_mrt_romeo.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped.nii
│ │ ├── nibabel-numpy_normalize-phase
│ │ │ ├── _0xa0c0aa7eca70387c1b2afa443eeb6a02.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result_nibabel-numpy_normalize-phase.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized.nii
│ │ ├── qsmjl_rts
│ │ │ ├── _0x273b0853fd2c3be3ce674803bea8c3b9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_qsmjl_rts.pklz
│ │ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp_rts.nii
│ │ └── qsmjl_vsharp
│ │ ├── _0xa995e3845f6b49516c5a6bf60bf459a4.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── command.txt
│ │ ├── result_qsmjl_vsharp.pklz
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw_bet-mask_ero_vsharp-mask.nii
│ │ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp.nii
│ └── sub-2
│ └── ses-20170705
│ ├── qsm_acq-acqmp2ragehighres0p5isoslab_T1w
│ │ ├── ants_register-t1-to-qsm
│ │ │ ├── _0x25392947db1a042dab18a8543f77def5.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_ants_register-t1-to-qsm.pklz
│ │ │ └── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_0GenericAffine.mat
│ │ ├── ants_transform-segmentation-to-qsm
│ │ │ ├── _0x9132bcfbc51736c130e0183e1336792a.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_ants_transform-segmentation-to-qsm.pklz
│ │ │ └── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_T1w_segmentation_trans.nii
│ │ ├── copyfile
│ │ │ ├── _0xd49a7e6d6d1a74f5e08c165a27d392ce.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copyfile.pklz
│ │ ├── fastsurfer_segment-t1
│ │ │ ├── _0xeb7c7bda2f492a0e69b25cb2a2922074.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── output
│ │ │ │ ├── mri
│ │ │ │ │ └── orig
│ │ │ │ └── scripts
│ │ │ ├── result_fastsurfer_segment-t1.pklz
│ │ │ ├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg.mgz
│ │ │ └── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii.nii
│ │ ├── func_getfirst-canonical-magnitude
│ │ │ ├── _0x03c3cdb62bbb7f8bda661ed556e0c721.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ ├── func_read-json-me
│ │ │ ├── _0x3c32850b2bb48d3c75bc2139a661b46a.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-me.pklz
│ │ ├── func_read-json-se
│ │ │ ├── _0x8b636c2f04c38752c303e14dc6742ab6.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-se.pklz
│ │ ├── nibabel_as-canonical
│ │ │ ├── _0xeb2e53ddca789796aeb1ed47bb3edd0f.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_as-canonical.pklz
│ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ ├── _0x87f3375c0f66ec2798dd29c2c86b3c62.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result_nibabel_numpy_nilearn_t1w-seg-resampled.pklz
│ │ │ └── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii_resampled.nii
│ │ ├── nibabel_read-nii
│ │ │ ├── _0x5e5622da1ab5981ba0849d4ab3cd36f9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_read-nii.pklz
│ │ └── numpy_numpy_nibabel_mgz2nii
│ │ ├── _0xc5d33454b83e24bfdd03c202ce6bff8b.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ └── qsm_acq-acqqsmp21mmisote20_T2starw
│ ├── ants_register-t1-to-qsm
│ │ ├── _0x9f1816dbcc9ede688eb7cc3412a22e8d.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── command.txt
│ │ ├── result_ants_register-t1-to-qsm.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_0GenericAffine.mat
│ ├── ants_transform-segmentation-to-qsm
│ │ ├── _0x79c0da0c70c3cccf53c3a1c119dc2cf5.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── command.txt
│ │ ├── result_ants_transform-segmentation-to-qsm.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_segmentation_trans.nii
│ ├── combine_lists1
│ │ ├── _0x8779911627a8e2bec443b7585f452745.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_combine_lists1.pklz
│ ├── combine_lists2
│ │ ├── _0x90e62c716dad041ed5d28236f2dfe8e4.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_combine_lists2.pklz
│ ├── copy_qsm_json_sidecar
│ │ ├── _0x4b62e7369163d93f2679c7a4f3b39b82.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_copy_qsm_json_sidecar.pklz
│ ├── copyfile
│ │ ├── _0xc6a9798a325481e562e1f4d6ffbec589.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_copyfile.pklz
│ ├── create_permutations
│ │ ├── _0xe49e6704a68718b86445426437cf1696.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_create_permutations.pklz
│ ├── fastsurfer_segment-t1
│ │ ├── _0xeb7c7bda2f492a0e69b25cb2a2922074.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── command.txt
│ │ ├── output
│ │ │ ├── mri
│ │ │ │ └── orig
│ │ │ └── scripts
│ │ ├── result_fastsurfer_segment-t1.pklz
│ │ ├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg.mgz
│ │ └── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii.nii
│ ├── func_getfirst-canonical-magnitude
│ │ ├── _0xfd733851b489d3e1c4cabb72cfbd3029.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_getfirst-canonical-magnitude.pklz
│ ├── func_read-json-me
│ │ ├── _0x1ff5d4b396e15ee28bd436b2a008c4c8.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_read-json-me.pklz
│ ├── func_read-json-se
│ │ ├── _0xde76191a825831514e19b11ab197cedc.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_read-json-se.pklz
│ ├── mask_workflow
│ │ ├── fsl-bet
│ │ │ ├── _0x6fe1a5c00a2e5744af8f7ba682837def.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── command.txt
│ │ │ ├── result_fsl-bet.pklz
│ │ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw_bet-mask.nii.gz
│ │ └── scipy_numpy_nibabel_bet_erode
│ │ ├── _0xb561bd6c7d5a69689e898fced4443583.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── result_scipy_numpy_nibabel_bet_erode.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw_bet-mask_ero.nii.gz
│ ├── nibabel_as-canonical
│ │ ├── _0x2921f623c1f4a3c33b2caff319649b3e.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_as-canonical.pklz
│ ├── nibabel_numpy_analyse-qsm
│ │ ├── _0x87224ccda179b8f490c93c71c10dfaa9.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── mapflow
│ │ │ └── _nibabel_numpy_analyse-qsm0
│ │ │ ├── _0x50d1afa1f28f48a85090bc31e0610069.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result__nibabel_numpy_analyse-qsm0.pklz
│ │ │ └── sub-2_ses-20170705_desc-qsmxt-2026-07-08-231723_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-07-08-231723_dseg_analysis.csv
│ │ └── result_nibabel_numpy_analyse-qsm.pklz
│ ├── nibabel_numpy_nilearn_axial-resampling
│ │ ├── _0xadc834728dcf0c3482a551a708bb40c7.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_nilearn_axial-resampling.pklz
│ ├── nibabel_numpy_nilearn_qsm-resampled
│ │ ├── _0x5dc4af4ee68b8a50a2af0c4240a2a3b9.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_nilearn_qsm-resampled.pklz
│ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ ├── _0x923be48f2382cedbee486f442466c41c.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── result_nibabel_numpy_nilearn_t1w-seg-resampled.pklz
│ │ └── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w_dseg_nii_resampled.nii
│ ├── nibabel_numpy_qsm-average
│ │ ├── _0x8ef5503baaf3e6578f186dfe933e9b46.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_qsm-average.pklz
│ ├── nibabel_numpy_qsm-referenced
│ │ ├── _0x021220ba8c59eda3c72b767e0a137b0f.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── result_nibabel_numpy_qsm-referenced.pklz
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp_rts_ref.json
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp_rts_ref.nii
│ ├── nibabel_numpy_scale-phase
│ │ ├── _0xd822f204c8e1cbf1b5b111c7cb2fda4f.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── result_nibabel_numpy_scale-phase.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled.nii
│ ├── nibabel_read-nii
│ │ ├── _0xb66dc33fb57c97c24b3f732c52c5eb3b.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_read-nii.pklz
│ ├── numpy_numpy_nibabel_mgz2nii
│ │ ├── _0xaf382cf972394f32ab37788ef9136fd0.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ └── qsm_workflow
│ ├── mrt_romeo
│ │ ├── _0x74a9e290a7b83852de94dc4a90385bf0.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── command.txt
│ │ ├── result_mrt_romeo.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped.nii
│ ├── nibabel-numpy_normalize-phase
│ │ ├── _0x94168531d79b15a14b23966af407cac9.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── result_nibabel-numpy_normalize-phase.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized.nii
│ ├── qsmjl_rts
│ │ ├── _0xb6c8e699a9dfc35e589161fd8f89ec78.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── command.txt
│ │ ├── result_qsmjl_rts.pklz
│ │ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp_rts.nii
│ └── qsmjl_vsharp
│ ├── _0x15ca2eef605bb01a4a45ff3322686a3f.json
│ ├── _inputs.pklz
│ ├── _node.pklz
│ ├── _report
│ │ └── report.rst
│ ├── command.txt
│ ├── result_qsmjl_vsharp.pklz
│ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw_bet-mask_ero_vsharp-mask.nii
│ └── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw_scaled_romeo-unwrapped_normalized_vsharp.nii
├── log_2026-07-08_23-16-53641047.txt
├── log_2026-07-08_23-40-16427708.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
205 directories, 494 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==0.13.2 numpy==2.3.5 nibabel==5.3.3 pandas==2.3.3 nilearn==0.13.1
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]}])
nv_T1
[HF-patcher] sub-1: path → url
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/jovyan/workspace/books/examples/quantitative_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: 52.048 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=16
260708-23:40:39,56 nipype.workflow INFO:
Workflow qsmxt-workflow settings: ['check', 'execution', 'logging', 'monitoring']
260708-23:40:39,87 nipype.workflow INFO:
Running in parallel.
260708-23:40:39,90 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 24 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260708-23:40:39,134 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260708-23:40:39,218 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260708-23:40:39,219 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-me".
260708-23:40:39,220 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260708-23:40:39,220 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260708-23:40:39,221 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260708-23:40:39,221 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-se".
260708-23:40:39,223 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260708-23:40:39,224 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,224 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_read-nii".
260708-23:40:39,224 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_as-canonical".
260708-23:40:39,226 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,226 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260708-23:40:39,226 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000987s.
260708-23:40:39,228 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.000937s.
260708-23:40:39,230 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,237 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.005654s.
260708-23:40:39,222 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260708-23:40:39,274 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260708-23:40:39,225 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260708-23:40:39,276 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/fastsurfer_segment-t1".
260708-23:40:39,277 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-me".
260708-23:40:39,277 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260708-23:40:39,278 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260708-23:40:39,279 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,281 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,284 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.003156s.
260708-23:40:39,284 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000968s.
260708-23:40:39,292 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260708-23:40:39,276 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260708-23:40:39,327 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260708-23:40:39,329 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260708-23:40:39,329 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-se".
260708-23:40:39,330 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260708-23:40:39,331 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_as-canonical".
260708-23:40:39,332 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260708-23:40:39,334 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,336 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,337 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.001101s.
260708-23:40:39,344 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.006606s.
260708-23:40:39,330 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_read-nii".
260708-23:40:39,381 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260708-23:40:39,385 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:39,390 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.003589s.
260708-23:40:41,93 nipype.workflow INFO:
[Job 0] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
260708-23:40:41,94 nipype.workflow INFO:
[Job 1] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
260708-23:40:41,95 nipype.workflow INFO:
[Job 2] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
260708-23:40:41,95 nipype.workflow INFO:
[Job 3] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
260708-23:40:41,96 nipype.workflow INFO:
[Job 6] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
260708-23:40:41,97 nipype.workflow INFO:
[Job 7] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
260708-23:40:41,98 nipype.workflow INFO:
[Job 8] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
260708-23:40:41,99 nipype.workflow INFO:
[Job 9] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
260708-23:40:41,100 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 18 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:40:41,178 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260708-23:40:41,180 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260708-23:40:41,181 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260708-23:40:41,182 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_register-t1-to-qsm".
260708-23:40:41,184 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260708-23:40:41,184 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-se".
260708-23:40:41,185 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260708-23:40:41,188 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260708-23:40:41,189 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:41,191 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.000939s.
260708-23:40:41,183 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_read-json-me".
260708-23:40:41,236 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260708-23:40:41,241 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:41,244 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.001063s.
260708-23:40:43,94 nipype.workflow INFO:
[Job 12] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
260708-23:40:43,95 nipype.workflow INFO:
[Job 13] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
260708-23:40:43,96 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 15 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:43,142 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260708-23:40:43,143 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260708-23:40:43,144 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_read-nii".
260708-23:40:43,145 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_as-canonical".
260708-23:40:43,147 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260708-23:40:43,151 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:43,158 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.005597s.
260708-23:40:43,146 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260708-23:40:43,202 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:43,208 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.004429s.
260708-23:40:45,96 nipype.workflow INFO:
[Job 14] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
260708-23:40:45,97 nipype.workflow INFO:
[Job 15] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
260708-23:40:45,98 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 14 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:45,146 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260708-23:40:45,147 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260708-23:40:45,149 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-se".
260708-23:40:45,150 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260708-23:40:45,154 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:45,157 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.001092s.
260708-23:40:45,149 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_read-json-me".
260708-23:40:45,200 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260708-23:40:45,205 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:45,207 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.001081s.
260708-23:40:47,98 nipype.workflow INFO:
[Job 18] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
260708-23:40:47,100 nipype.workflow INFO:
[Job 19] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
260708-23:40:47,101 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:47,158 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260708-23:40:47,162 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260708-23:40:47,164 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_read-nii".
260708-23:40:47,166 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_as-canonical".
260708-23:40:47,168 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260708-23:40:47,168 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260708-23:40:47,170 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:47,173 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:47,180 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.005362s.
260708-23:40:47,189 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.012339s.
260708-23:40:49,100 nipype.workflow INFO:
[Job 20] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
260708-23:40:49,102 nipype.workflow INFO:
[Job 21] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
260708-23:40:49,103 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:49,152 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260708-23:40:49,154 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260708-23:40:49,155 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_getfirst-canonical-magnitude".
260708-23:40:49,156 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260708-23:40:49,156 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_scale-phase".
260708-23:40:49,158 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260708-23:40:49,161 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:49,163 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000342s.
260708-23:40:49,166 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
260708-23:40:49,522 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.353832s.
260708-23:40:51,103 nipype.workflow INFO:
[Job 24] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
260708-23:40:51,104 nipype.workflow INFO:
[Job 26] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
260708-23:40:51,106 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 11 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:51,183 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260708-23:40:51,185 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260708-23:40:51,186 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_getfirst-canonical-magnitude".
260708-23:40:51,186 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260708-23:40:51,187 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/func_getfirst-canonical-magnitude".
260708-23:40:51,188 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260708-23:40:51,189 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:51,190 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:51,190 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000324s.
260708-23:40:51,191 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000324s.
260708-23:40:53,105 nipype.workflow INFO:
[Job 27] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
260708-23:40:53,106 nipype.workflow INFO:
[Job 29] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
260708-23:40:53,108 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:53,167 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260708-23:40:53,169 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260708-23:40:53,171 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_scale-phase".
260708-23:40:53,172 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260708-23:40:53,172 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/func_getfirst-canonical-magnitude".
260708-23:40:53,173 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260708-23:40:53,178 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260708-23:40:53,179 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000322s.
260708-23:40:53,185 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
260708-23:40:53,522 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.336521s.
260708-23:40:55,107 nipype.workflow INFO:
[Job 31] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
260708-23:40:55,109 nipype.workflow INFO:
[Job 32] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
260708-23:40:55,110 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:55,168 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260708-23:40:55,170 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260708-23:40:55,173 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_axial-resampling".
260708-23:40:55,173 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260708-23:40:55,179 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
260708-23:40:55,187 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.006883s.
260708-23:40:55,172 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_axial-resampling".
260708-23:40:55,224 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260708-23:40:55,226 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
260708-23:40:55,231 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.003676s.
260708-23:40:57,109 nipype.workflow INFO:
[Job 36] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
260708-23:40:57,111 nipype.workflow INFO:
[Job 41] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
260708-23:40:57,112 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 10 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:40:57,166 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260708-23:40:57,168 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260708-23:40:57,169 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/mrt_romeo".
260708-23:40:57,169 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260708-23:40:57,171 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/mrt_romeo".
260708-23:40:57,172 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260708-23:40:57,189 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
260708-23:40:57,190 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
260708-23:40:59,112 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 31.84/56.51, Free processors: 0/16.
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_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:41:27,453 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 30.25992s.
260708-23:41:27,655 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 30.461691s.
260708-23:41:29,152 nipype.workflow INFO:
[Job 46] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
260708-23:41:29,153 nipype.workflow INFO:
[Job 50] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
260708-23:41:29,155 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 10 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:41:29,212 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260708-23:41:29,214 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/nibabel-numpy_normalize-phase".
260708-23:41:29,215 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260708-23:41:29,225 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
260708-23:41:29,321 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.094159s.
260708-23:41:31,154 nipype.workflow INFO:
[Job 53] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
260708-23:41:31,160 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:41:31,211 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260708-23:41:31,213 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/nibabel-numpy_normalize-phase".
260708-23:41:31,214 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260708-23:41:31,226 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
260708-23:41:31,324 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.097429s.
260708-23:41:33,157 nipype.workflow INFO:
[Job 55] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
260708-23:41:33,159 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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
260708-23:44:06,733 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 205.543589s.
260708-23:44:09,309 nipype.workflow INFO:
[Job 5] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
260708-23:44:09,312 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:44:09,356 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260708-23:44:09,360 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/fastsurfer_segment-t1".
260708-23:44:09,361 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260708-23:44:09,378 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260708-23:44:11,310 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 32.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:45:51,588 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 312.294888s.
260708-23:45:53,456 nipype.workflow INFO:
[Job 4] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
260708-23:45:53,457 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:45:53,506 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260708-23:45:53,508 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260708-23:45:53,511 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/numpy_numpy_nibabel_mgz2nii".
260708-23:45:53,512 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260708-23:45:53,515 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260708-23:45:53,511 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_register-t1-to-qsm".
260708-23:45:53,566 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260708-23:45:53,574 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260708-23:45:53,739 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.223331s.
260708-23:45:55,458 nipype.workflow INFO:
[Job 25] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
260708-23:45:55,460 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:45:55,517 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:45:55,520 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:45:55,521 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:45:55,544 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260708-23:45:55,520 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260708-23:45:55,578 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_transform-segmentation-to-qsm".
260708-23:45:55,579 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260708-23:45:55,737 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260708-23:45:57,464 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 6 jobs ready. Free memory (GB): 32.51/56.51, Free processors: 0/16.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:45:58,150 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 2.411669s.
260708-23:45:58,629 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 3.082841s.
260708-23:45:59,463 nipype.workflow INFO:
[Job 34] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
260708-23:45:59,466 nipype.workflow INFO:
[Job 35] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
260708-23:45:59,467 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:45:59,541 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260708-23:45:59,546 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/copyfile".
260708-23:45:59,548 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260708-23:45:59,552 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260708-23:45:59,992 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.437566s.
260708-23:46:01,463 nipype.workflow INFO:
[Job 44] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
260708-23:46:01,465 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
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-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:47:19,42 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 85.465556s.
260708-23:47:19,543 nipype.workflow INFO:
[Job 11] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
260708-23:47:19,546 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:47:19,611 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260708-23:47:19,615 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/fastsurfer_segment-t1".
260708-23:47:19,616 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260708-23:47:19,632 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260708-23:47:21,545 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 32.51/56.51, Free processors: 0/16.
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.fastsurfer_segment-t1
260708-23:49:24,257 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 314.877138s.
260708-23:49:25,713 nipype.workflow INFO:
[Job 10] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
260708-23:49:25,717 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:49:25,780 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260708-23:49:25,786 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260708-23:49:25,787 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_register-t1-to-qsm".
260708-23:49:25,788 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260708-23:49:25,792 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260708-23:49:25,790 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/numpy_numpy_nibabel_mgz2nii".
260708-23:49:25,794 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260708-23:49:25,797 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260708-23:49:26,29 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.23055s.
260708-23:49:27,713 nipype.workflow INFO:
[Job 28] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
260708-23:49:27,715 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:49:27,776 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:49:27,781 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260708-23:49:27,785 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:49:27,788 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:49:27,790 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_transform-segmentation-to-qsm".
260708-23:49:27,796 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260708-23:49:27,819 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260708-23:49:27,822 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260708-23:49:28,682 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.857147s.
260708-23:49:29,716 nipype.workflow INFO:
[Job 38] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
260708-23:49:29,718 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 34.51/56.51, Free processors: 1/16.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:49:29,776 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260708-23:49:29,779 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists2".
260708-23:49:29,781 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260708-23:49:29,785 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
260708-23:49:29,787 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.001047s.
260708-23:49:30,820 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 2.999494s.
260708-23:49:31,716 nipype.workflow INFO:
[Job 37] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
260708-23:49:31,717 nipype.workflow INFO:
[Job 47] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
260708-23:49:31,719 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260708-23:52:24,696 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 305.062683s.
260708-23:52:25,870 nipype.workflow INFO:
[Job 16] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
260708-23:52:25,872 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 48.51/56.51, Free processors: 10/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260708-23:52:25,918 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260708-23:52:25,921 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260708-23:52:25,923 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/fastsurfer_segment-t1".
260708-23:52:25,925 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260708-23:52:25,928 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/numpy_numpy_nibabel_mgz2nii".
260708-23:52:25,930 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260708-23:52:25,933 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260708-23:52:25,939 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260708-23:52:26,196 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.261822s.
260708-23:52:27,872 nipype.workflow INFO:
[Job 30] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
260708-23:52:27,874 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260708-23:52:27,954 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:52:27,959 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:52:27,960 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:52:27,985 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260708-23:52:29,875 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 34.51/56.51, Free processors: 1/16.
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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260708-23:52:30,927 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 2.940348s.
260708-23:52:31,876 nipype.workflow INFO:
[Job 39] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
260708-23:52:31,878 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260708-23:52:47,450 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 201.656872s.
260708-23:52:49,895 nipype.workflow INFO:
[Job 17] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
260708-23:52:49,897 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:52:49,955 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260708-23:52:49,962 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260708-23:52:49,962 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_register-t1-to-qsm".
260708-23:52:49,964 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260708-23:52:49,967 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/ants_transform-segmentation-to-qsm".
260708-23:52:49,969 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260708-23:52:49,968 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260708-23:52:50,94 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260708-23:52:51,898 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 34.51/56.51, Free processors: 1/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:52:52,469 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 2.37352s.
260708-23:52:53,898 nipype.workflow INFO:
[Job 40] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
260708-23:52:53,900 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:52:53,972 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260708-23:52:53,977 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqmp2ragehighres0p5isoslab_T1w/copyfile".
260708-23:52:53,979 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260708-23:52:53,983 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260708-23:52:54,413 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.428196s.
260708-23:52:55,901 nipype.workflow INFO:
[Job 48] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
260708-23:52:55,907 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:13,551 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 83.530781s.
260708-23:54:13,977 nipype.workflow INFO:
[Job 23] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
260708-23:54:13,979 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:14,37 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260708-23:54:14,41 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/fsl-bet".
260708-23:54:14,43 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260708-23:54:14,47 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
260708-23:54:15,979 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:16,873 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 2.824232s.
260708-23:54:17,979 nipype.workflow INFO:
[Job 45] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
260708-23:54:17,981 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:18,32 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260708-23:54:18,38 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/fsl-bet".
260708-23:54:18,40 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260708-23:54:18,45 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
260708-23:54:19,982 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:20,889 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 2.8426679999999998s.
260708-23:54:21,982 nipype.workflow INFO:
[Job 49] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
260708-23:54:21,984 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:22,39 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode".
260708-23:54:22,42 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode".
260708-23:54:22,43 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/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/scipy_numpy_nibabel_bet_erode".
260708-23:54:22,44 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/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/mask_workflow/scipy_numpy_nibabel_bet_erode".
260708-23:54:22,45 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode".
260708-23:54:22,48 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
260708-23:54:22,45 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode".
260708-23:54:22,99 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
260708-23:54:22,471 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.421316s.
260708-23:54:22,536 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.435492s.
260708-23:54:23,984 nipype.workflow INFO:
[Job 52] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
260708-23:54:23,986 nipype.workflow INFO:
[Job 54] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
260708-23:54:23,987 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:24,46 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260708-23:54:24,49 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260708-23:54:24,53 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_vsharp".
260708-23:54:24,51 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_vsharp".
260708-23:54:24,54 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260708-23:54:24,55 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260708-23:54:24,76 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
260708-23:54:24,78 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
260708-23:54:25,987 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 40.51/56.51, Free processors: 4/16.
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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:41,945 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 17.867279s.
260708-23:54:42,1 nipype.workflow INFO:
[Job 57] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
260708-23:54:42,3 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.51/56.51, Free processors: 6/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:42,57 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260708-23:54:42,61 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_rts".
260708-23:54:42,62 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260708-23:54:42,75 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
260708-23:54:42,139 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 18.059751s.
260708-23:54:44,4 nipype.workflow INFO:
[Job 56] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
260708-23:54:44,5 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.11/56.51, Free processors: 6/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:54:44,66 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260708-23:54:44,70 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/qsm_workflow/qsmjl_rts".
260708-23:54:44,71 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260708-23:54:44,82 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
260708-23:54:46,7 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 39.70/56.51, Free processors: 4/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:04,449 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 22.372184s.
260708-23:55:06,26 nipype.workflow INFO:
[Job 59] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
260708-23:55:06,28 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.11/56.51, Free processors: 6/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:06,104 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260708-23:55:06,106 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-average".
260708-23:55:06,107 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260708-23:55:06,109 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
260708-23:55:06,110 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000234s.
260708-23:55:06,448 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 22.364327s.
260708-23:55:08,28 nipype.workflow INFO:
[Job 58] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
260708-23:55:08,29 nipype.workflow INFO:
[Job 61] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
260708-23:55:08,31 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:08,82 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260708-23:55:08,84 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260708-23:55:08,86 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-average".
260708-23:55:08,86 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260708-23:55:08,88 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
260708-23:55:08,89 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000235s.
260708-23:55:08,86 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_qsm-resampled".
260708-23:55:08,137 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260708-23:55:08,140 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260708-23:55:08,142 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.001703s.
260708-23:55:10,30 nipype.workflow INFO:
[Job 60] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
260708-23:55:10,31 nipype.workflow INFO:
[Job 63] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
260708-23:55:10,33 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:10,86 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260708-23:55:10,88 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260708-23:55:10,90 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_qsm-resampled".
260708-23:55:10,90 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260708-23:55:10,93 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-referenced".
260708-23:55:10,93 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260708-23:55:10,98 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.003109s.
260708-23:55:10,93 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260708-23:55:10,93 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260708-23:55:10,147 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists1".
260708-23:55:10,148 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260708-23:55:10,150 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
260708-23:55:10,152 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.000959s.
260708-23:55:10,155 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
260708-23:55:10,533 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.376863s.
260708-23:55:12,32 nipype.workflow INFO:
[Job 62] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
260708-23:55:12,34 nipype.workflow INFO:
[Job 66] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
260708-23:55:12,34 nipype.workflow INFO:
[Job 67] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
260708-23:55:12,36 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:12,91 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260708-23:55:12,93 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260708-23:55:12,94 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_qsm-referenced".
260708-23:55:12,95 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260708-23:55:12,96 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists1".
260708-23:55:12,97 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260708-23:55:12,99 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
260708-23:55:12,100 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.000439s.
260708-23:55:12,106 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
260708-23:55:12,95 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260708-23:55:12,148 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copy_qsm_json_sidecar".
260708-23:55:12,149 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260708-23:55:12,151 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
260708-23:55:12,152 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.000601s.
260708-23:55:12,509 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.401938s.
260708-23:55:14,34 nipype.workflow INFO:
[Job 64] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
260708-23:55:14,35 nipype.workflow INFO:
[Job 65] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
260708-23:55:14,36 nipype.workflow INFO:
[Job 70] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
260708-23:55:14,37 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:14,101 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260708-23:55:14,104 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260708-23:55:14,105 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copy_qsm_json_sidecar".
260708-23:55:14,105 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260708-23:55:14,106 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/create_permutations".
260708-23:55:14,109 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260708-23:55:14,110 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
260708-23:55:14,111 nipype.workflow INFO:
[Node] Executing "create_permutations" <nipype.interfaces.utility.wrappers.Function>
260708-23:55:14,112 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.000776s.
260708-23:55:14,113 nipype.workflow INFO:
[Node] Finished "create_permutations", elapsed time 0.000996s.
260708-23:55:16,36 nipype.workflow INFO:
[Job 68] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
260708-23:55:16,37 nipype.workflow INFO:
[Job 69] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations).
260708-23:55:16,38 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:18,39 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:55:18,85 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260708-23:55:18,88 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm1".
260708-23:55:18,88 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm2" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm2".
260708-23:55:18,89 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm3" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm3".
260708-23:55:18,90 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm1" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:55:18,90 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm2" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:55:18,91 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm3" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:55:18,88 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm0" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm0".
260708-23:55:18,139 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260708-23:55:18,142 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:55:20,41 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 4/16.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:56:11,901 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm3", elapsed time 53.809345s.
260708-23:56:12,89 nipype.workflow INFO:
[Job 79] Completed (_nibabel_numpy_analyse-qsm3).
260708-23:56:12,91 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 38.51/56.51, Free processors: 5/16.
Currently running:
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:56:12,314 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm0", elapsed time 54.171044s.
260708-23:56:12,474 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm1", elapsed time 54.383293s.
260708-23:56:13,880 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm2", elapsed time 55.789437s.
260708-23:56:14,91 nipype.workflow INFO:
[Job 76] Completed (_nibabel_numpy_analyse-qsm0).
260708-23:56:14,92 nipype.workflow INFO:
[Job 77] Completed (_nibabel_numpy_analyse-qsm1).
260708-23:56:14,93 nipype.workflow INFO:
[Job 78] Completed (_nibabel_numpy_analyse-qsm2).
260708-23:56:14,94 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:56:14,147 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260708-23:56:14,151 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260708-23:56:14,155 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm0" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm0".
260708-23:56:14,157 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm0" - collecting precomputed outputs
260708-23:56:14,157 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm0" found cached.
260708-23:56:14,158 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm1".
260708-23:56:14,159 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm1" - collecting precomputed outputs
260708-23:56:14,159 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm1" found cached.
260708-23:56:14,160 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm2" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm2".
260708-23:56:14,161 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm2" - collecting precomputed outputs
260708-23:56:14,161 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm2" found cached.
260708-23:56:14,162 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm3" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm3".
260708-23:56:14,163 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm3" - collecting precomputed outputs
260708-23:56:14,163 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm3" found cached.
260708-23:56:16,93 nipype.workflow INFO:
[Job 72] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm).
260708-23:56:16,95 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:56:16,154 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260708-23:56:16,157 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copyfile".
260708-23:56:16,158 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260708-23:56:16,161 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260708-23:56:16,394 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.231478s.
260708-23:56:18,94 nipype.workflow INFO:
[Job 74] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile).
260708-23:56:18,96 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260708-23:57:35,230 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 309.289606s.
260708-23:57:36,166 nipype.workflow INFO:
[Job 22] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
260708-23:57:36,167 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260708-23:57:36,217 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260708-23:57:36,220 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/numpy_numpy_nibabel_mgz2nii".
260708-23:57:36,221 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260708-23:57:36,224 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260708-23:57:36,516 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.291224s.
260708-23:57:38,165 nipype.workflow INFO:
[Job 33] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
260708-23:57:38,167 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260708-23:57:38,213 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:57:38,216 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:57:38,217 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260708-23:57:38,217 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260708-23:57:38,220 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/ants_transform-segmentation-to-qsm".
260708-23:57:38,221 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260708-23:57:38,243 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260708-23:57:38,245 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260708-23:57:39,104 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.857537s.
260708-23:57:40,167 nipype.workflow INFO:
[Job 43] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
260708-23:57:40,170 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 54.51/56.51, Free processors: 15/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
260708-23:57:40,218 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260708-23:57:40,221 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/combine_lists2".
260708-23:57:40,222 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260708-23:57:40,224 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
260708-23:57:40,226 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.000573s.
260708-23:57:41,162 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 2.91776s.
260708-23:57:42,170 nipype.workflow INFO:
[Job 42] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
260708-23:57:42,171 nipype.workflow INFO:
[Job 51] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
260708-23:57:42,172 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260708-23:57:42,214 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260708-23:57:42,216 nipype.workflow INFO:
[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/create_permutations".
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260708-23:57:42,221 nipype.workflow INFO:
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260708-23:57:44,173 nipype.workflow INFO:
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260708-23:57:46,221 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm0" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm0".
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260708-23:57:46,222 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm1" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm1".
260708-23:57:46,223 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm2" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm2".
260708-23:57:46,223 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm3" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm3".
260708-23:57:46,224 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:57:46,225 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm1" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
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[Node] Executing "_nibabel_numpy_analyse-qsm3" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:57:46,226 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm2" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260708-23:57:48,177 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 48.51/56.51, Free processors: 12/16.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
260708-23:58:26,277 nipype.workflow INFO:
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260708-23:58:28,215 nipype.workflow INFO:
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* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
260708-23:58:34,989 nipype.workflow INFO:
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260708-23:58:36,287 nipype.workflow INFO:
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260708-23:58:36,289 nipype.workflow INFO:
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260708-23:58:36,290 nipype.workflow INFO:
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260708-23:58:36,291 nipype.workflow INFO:
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260708-23:58:36,293 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm2" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm2".
260708-23:58:36,294 nipype.workflow INFO:
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260708-23:58:36,295 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm3" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm3".
260708-23:58:36,296 nipype.workflow INFO:
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260708-23:58:38,224 nipype.workflow INFO:
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260708-23:58:38,226 nipype.workflow INFO:
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260708-23:58:38,276 nipype.workflow INFO:
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[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copyfile".
260708-23:58:38,280 nipype.workflow INFO:
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260708-23:58:38,283 nipype.workflow INFO:
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260708-23:58:38,523 nipype.workflow INFO:
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260708-23:58:40,226 nipype.workflow INFO:
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260708-23:58:40,230 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
[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-2026-07-08-231723
├── 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
bids/derivatives/qsmxt-2026-07-08-234037
├── 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-acqqsmp21mmisote20_T2starw_qsm-analysis
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-07-08-231723_Chimap_sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-07-08-231723_dseg_analysis.csv
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-07-08-231723_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-07-08-234037_dseg_analysis.csv
│ │ ├── sub-1_ses-20170705_desc-qsmxt-2026-07-08-234037_Chimap_sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-07-08-231723_dseg_analysis.csv
│ │ └── sub-1_ses-20170705_desc-qsmxt-2026-07-08-234037_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-07-08-234037_dseg_analysis.csv
│ ├── 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-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-acqqsmp21mmisote20_T2starw_qsm-analysis
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-07-08-231723_Chimap_sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-07-08-231723_dseg_analysis.csv
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-07-08-231723_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-07-08-234037_dseg_analysis.csv
│ │ ├── sub-2_ses-20170705_desc-qsmxt-2026-07-08-234037_Chimap_sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-07-08-231723_dseg_analysis.csv
│ │ └── sub-2_ses-20170705_desc-qsmxt-2026-07-08-234037_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-07-08-234037_dseg_analysis.csv
│ ├── 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
├── command.txt
├── pypeline.log
├── qsmxt.log
├── references.txt
└── settings.json
20 directories, 52 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
== 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
QSM results#
Let’s view one of the 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 | 589 | -0.234321 | 0.124799 | -0.018637 | -0.022385 | 0.034550 |
| 1 | 4th-Ventricle | 1566 | -0.127341 | 0.032586 | -0.047447 | -0.048508 | 0.029171 |
| 2 | Brain-Stem | 18799 | -0.279382 | 0.102235 | -0.045265 | -0.041376 | 0.028795 |
| 3 | CSF | 826 | -1.393693 | 0.945752 | 0.025916 | 0.027566 | 0.142895 |
| 4 | Left-Accumbens-area | 513 | -0.141920 | 0.128334 | 0.021755 | 0.020113 | 0.030727 |
| ... | ... | ... | ... | ... | ... | ... | ... |
| 91 | ctx-rh-superiorfrontal | 29531 | -0.133054 | 0.251870 | -0.004172 | -0.009383 | 0.024582 |
| 92 | ctx-rh-superiorparietal | 12211 | -0.084225 | 0.306628 | -0.015874 | -0.014755 | 0.022164 |
| 93 | ctx-rh-superiortemporal | 16265 | -0.111082 | 0.248737 | 0.006409 | 0.013009 | 0.024436 |
| 94 | ctx-rh-supramarginal | 12050 | -0.056940 | 0.239688 | 0.019274 | 0.020006 | 0.022669 |
| 95 | ctx-rh-transversetemporal | 1261 | -0.004825 | 0.129559 | 0.034757 | 0.035869 | 0.013964 |
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_img = nib.load(glob("bids/derivatives/qsmxt-*-*/sub*/ses*/anat*/*Chimap.nii*")[0])
seg_img = nib.load(glob("bids/derivatives/qsmxt-*-*/sub*/ses*/anat*/*space-qsm*dseg.nii*")[0])
from nilearn.image import resample_to_img
# Resample the segmentation image to match the QSM image space
# Use 'nearest' interpolation to preserve the integer labels of the segmentation.
print("Resampling segmentation to match QSM dimensions...")
seg_resampled_img = resample_to_img(seg_img, qsm_img, interpolation='nearest')
print("Resampling complete.")
Resampling segmentation to match QSM dimensions...
Resampling complete.
# Get data arrays
qsm = qsm_img.get_fdata()
seg = seg_resampled_img.get_fdata()
# Check shapes to confirm they match
print(f"Shape of QSM data: {qsm.shape}")
print(f"Shape of resampled segmentation data: {seg.shape}")
if qsm.shape != seg.shape:
raise ValueError("FATAL: Shapes not match after resampling. Check your input files.")
Shape of QSM data: (224, 224, 160)
Shape of resampled segmentation data: (224, 224, 160)
# --- Flatten the arrays now that they have the same dimensions ---
qsm = qsm.flatten()
seg = seg.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 | -0.041 | 0.029 |
| White matter | -0.002 | 0.028 |
| CSF | 0.028 | 0.143 |
| Thalamus | 0.030 | 0.034 |
| 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()
Dependencies in Jupyter/Python#
Using the package watermark to document system environment and software versions used in this notebook, alongside the Neurodesktop version extracted from the
JUPYTER_IMAGEorNEURODESKTOP_VERSIONenvironment variables.
import os
%load_ext watermark
%watermark
%watermark --iversions
neurodesktop_version = (
os.environ.get('JUPYTER_IMAGE', '').split(':')[-1] or
os.environ.get('NEURODESKTOP_VERSION', 'unknown')
)
print(f"Neurodesktop version: {neurodesktop_version}")
Last updated: 2026-07-08T23:58:45.836090+00:00
Python implementation: CPython
Python version : 3.13.13
IPython version : 9.12.0
Compiler : GCC 14.3.0
OS : Linux
Release : 6.8.0-111-generic
Machine : x86_64
Processor : x86_64
CPU cores : 16
Architecture: 64bit
ipyniivue : 2.4.4
json : 2.0.9
matplotlib: 3.10.9
nibabel : 5.3.3
nilearn : 0.13.1
numpy : 2.3.5
pandas : 2.3.3
seaborn : 0.13.2
Neurodesktop version: 2026-06-04