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 13.80 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 0.877422 seconds (0.868847 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 0.206054 seconds (0.205700 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 0.201890 seconds (0.201317 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 0.860730 seconds (0.859810 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 0.196467 seconds (0.195609 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 0.205377 seconds (0.204605 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, 757.96it/s]
[INFO]: Finished
!tree bids
bids
├── derivatives
│ ├── qsmxt-2026-03-10-033227
│ │ ├── 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
│ │ │ │ ├── _0x5ffe0b624ae5f4e927ce996cc479a448.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
│ │ │ │ ├── _0xf52936e5588d55787ae47757ddddda88.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
│ │ │ │ ├── _0xc43a717caac730709326731df4716b88.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_copyfile.pklz
│ │ │ ├── fastsurfer_segment-t1
│ │ │ │ ├── _0x08d90ab9ceebcbffa71d534221862cc7.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
│ │ │ │ ├── _0x1c5300fc25c39cd4ac77783cfd100196.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ │ ├── func_read-json-me
│ │ │ │ ├── _0xfc3b94404ba41d358ceb3eb8312a497b.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_read-json-me.pklz
│ │ │ ├── func_read-json-se
│ │ │ │ ├── _0xbf9cf559d516ebebb23a828ca50be513.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_read-json-se.pklz
│ │ │ ├── nibabel_as-canonical
│ │ │ │ ├── _0x6b00203e33e13c8a1fa9a56481ad42d3.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_nibabel_as-canonical.pklz
│ │ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ │ ├── _0x98a3ea3db6e4ff0b25bc9dfafcff626c.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
│ │ │ │ ├── _0x4d295aceb566f171068562db62ad2778.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_nibabel_read-nii.pklz
│ │ │ └── numpy_numpy_nibabel_mgz2nii
│ │ │ ├── _0xdbf887e21be0ceaa64a1b2bf44e93915.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ │ └── qsm_acq-acqqsmp21mmisote20_T2starw
│ │ ├── ants_register-t1-to-qsm
│ │ │ ├── _0xacd783811b0b49d9b2f14fc61cccdb64.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
│ │ │ ├── _0xae2131a5001adc3751c680873aa22dc4.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
│ │ │ ├── _0xa994d1901bf6a7e8845cd728696ee481.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_combine_lists1.pklz
│ │ ├── combine_lists2
│ │ │ ├── _0x8722b5a9ec8e402eeeaf344129c9d3c5.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_combine_lists2.pklz
│ │ ├── copy_qsm_json_sidecar
│ │ │ ├── _0x1e93aed1a3ae36c4525c910e9ee15a03.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copy_qsm_json_sidecar.pklz
│ │ ├── copyfile
│ │ │ ├── _0xc54d509c2342536621e0526a6569847c.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copyfile.pklz
│ │ ├── create_permutations
│ │ │ ├── _0x3bbd2c0f3cdf3c5179bd662ec23edc54.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_create_permutations.pklz
│ │ ├── fastsurfer_segment-t1
│ │ │ ├── _0x08d90ab9ceebcbffa71d534221862cc7.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
│ │ │ ├── _0xc441b0c48f173d53e64291d6673bbb7d.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ ├── func_read-json-me
│ │ │ ├── _0x42f1ae1bf87ca475a60367cab7c78bc9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-me.pklz
│ │ ├── func_read-json-se
│ │ │ ├── _0xc29ebcdc06e8b52c61e7fa908462de06.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-se.pklz
│ │ ├── mask_workflow
│ │ │ ├── fsl-bet
│ │ │ │ ├── _0xd1e11ebf680420a025919402206bcd34.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
│ │ │ ├── _0x83b62f77d250d98c09e13e1353e3b469.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
│ │ │ ├── _0x14625d26bac28527cea74e788b209c07.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_as-canonical.pklz
│ │ ├── nibabel_numpy_analyse-qsm
│ │ │ ├── _0x122484df2e181583c6054f805528806d.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── mapflow
│ │ │ │ └── _nibabel_numpy_analyse-qsm0
│ │ │ │ ├── _0xda3801d279eac2a26505a669f1d4568e.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── result__nibabel_numpy_analyse-qsm0.pklz
│ │ │ │ └── sub-1_ses-20170705_desc-qsmxt-2026-03-10-033227_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-03-10-033227_dseg_analysis.csv
│ │ │ └── result_nibabel_numpy_analyse-qsm.pklz
│ │ ├── nibabel_numpy_nilearn_axial-resampling
│ │ │ ├── _0x9bfe64aba00bc5fa89794f9aa5fe65d7.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_nilearn_axial-resampling.pklz
│ │ ├── nibabel_numpy_nilearn_qsm-resampled
│ │ │ ├── _0x49241febb159bab636fcd45cb4baa2a4.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_nilearn_qsm-resampled.pklz
│ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ ├── _0x9eca13e963ccbbde48af63ae040b600b.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
│ │ │ ├── _0x31e254fad98e323b563427b45e0ba04d.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_qsm-average.pklz
│ │ ├── nibabel_numpy_qsm-referenced
│ │ │ ├── _0xa963fdb69edee9f53a80b2d3819fe322.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
│ │ │ ├── _0x82dbc0908beee85f71ca536db6dded5b.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
│ │ │ ├── _0xd835b3ee0d5b16d0b36e319ff588045b.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_read-nii.pklz
│ │ ├── numpy_numpy_nibabel_mgz2nii
│ │ │ ├── _0x2fb927a78a4c4b1624d14232952bf2c4.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ │ └── qsm_workflow
│ │ ├── mrt_romeo
│ │ │ ├── _0xbdd8e4a6323ab96fe644a5740e1c9ca8.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
│ │ │ ├── _0x675b17750145abd8bab03a8a8c2be6eb.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
│ │ │ ├── _0xb2244daa11f220315d33eb10c72de88f.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
│ │ ├── _0xaf321193b28c1db1282018b3495b23c8.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
│ │ │ ├── _0x086a414ddcf76d2e916e11cdc14df8ed.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
│ │ │ ├── _0x9f26aba170a36f98627b87fdab25523e.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
│ │ │ ├── _0x84f229ef6e28be438808e07d2f658ed1.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copyfile.pklz
│ │ ├── fastsurfer_segment-t1
│ │ │ ├── _0x624932900ab5f1113f9ae307243ee025.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
│ │ │ ├── _0x177ae9dd74ea8076fbbae1c5901799a9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ ├── func_read-json-me
│ │ │ ├── _0x62fe3829bf769416d51384eb361be18f.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-me.pklz
│ │ ├── func_read-json-se
│ │ │ ├── _0x636bbd36a81691ec288c8472b56eecd9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-se.pklz
│ │ ├── nibabel_as-canonical
│ │ │ ├── _0x41c0c875e2f40e14d5af311a8e84e7ff.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_as-canonical.pklz
│ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ ├── _0x0f9df563ff9d3d9dd1c54aaa664fc95c.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
│ │ │ ├── _0x8135649808d88db3239e59f0b613d5c3.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_read-nii.pklz
│ │ └── numpy_numpy_nibabel_mgz2nii
│ │ ├── _0x818638527bf43a3a3c9d7177d378ac7f.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ └── qsm_acq-acqqsmp21mmisote20_T2starw
│ ├── ants_register-t1-to-qsm
│ │ ├── _0x5edf64a053c7ac45a13ea1986fc8ddc4.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
│ │ ├── _0xa6b232c8fe87f81ddb47319f46037360.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
│ │ ├── _0x2d6448c353d434bca7ca7639c2f9534c.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_combine_lists1.pklz
│ ├── combine_lists2
│ │ ├── _0xef2885d3cd6060197cc888f20493c454.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_combine_lists2.pklz
│ ├── copy_qsm_json_sidecar
│ │ ├── _0xabfb99e985984b7911ed978a6e5b599e.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_copy_qsm_json_sidecar.pklz
│ ├── copyfile
│ │ ├── _0xb7671199623460289a6944a684235ad8.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_copyfile.pklz
│ ├── create_permutations
│ │ ├── _0xdad8bbd88c739f22a7610f90a4160304.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_create_permutations.pklz
│ ├── fastsurfer_segment-t1
│ │ ├── _0x624932900ab5f1113f9ae307243ee025.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
│ │ ├── _0x000001289ceecc31471acd85c5a17760.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_getfirst-canonical-magnitude.pklz
│ ├── func_read-json-me
│ │ ├── _0xe60410885a0c4fe4a27244b7320aeb53.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_read-json-me.pklz
│ ├── func_read-json-se
│ │ ├── _0x06610052f25d69f49e0a168c450f7f13.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_read-json-se.pklz
│ ├── mask_workflow
│ │ ├── fsl-bet
│ │ │ ├── _0x7118f68994edd5aba82788c80a09f034.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
│ │ ├── _0x45fa4a80c51e508d8d5a10917ec78ec4.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
│ │ ├── _0x7fe759ea594072501588c0a95bedf302.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_as-canonical.pklz
│ ├── nibabel_numpy_analyse-qsm
│ │ ├── _0xfd715429de9e74c38182259652e64b5a.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── mapflow
│ │ │ └── _nibabel_numpy_analyse-qsm0
│ │ │ ├── _0x638a8e39c0ed049953092b4156cf73cc.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result__nibabel_numpy_analyse-qsm0.pklz
│ │ │ └── sub-2_ses-20170705_desc-qsmxt-2026-03-10-033227_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-03-10-033227_dseg_analysis.csv
│ │ └── result_nibabel_numpy_analyse-qsm.pklz
│ ├── nibabel_numpy_nilearn_axial-resampling
│ │ ├── _0x79d21e1cab285871f2ca5899711fd273.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_nilearn_axial-resampling.pklz
│ ├── nibabel_numpy_nilearn_qsm-resampled
│ │ ├── _0xdb7008687121751de61507dc297e9fb5.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_nilearn_qsm-resampled.pklz
│ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ ├── _0x44b8c27ece95b7c9aecccb1799e6dac6.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
│ │ ├── _0xe1f377cfbcab97094286028eb7bdb7bd.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_qsm-average.pklz
│ ├── nibabel_numpy_qsm-referenced
│ │ ├── _0xc27bfa70ed0f921d2e26ed201e0c5b3a.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
│ │ ├── _0xa2e199e75ead16230fe7c90eed27a2b5.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
│ │ ├── _0x0d7ef4002c9108f9676268d966fc89bd.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_read-nii.pklz
│ ├── numpy_numpy_nibabel_mgz2nii
│ │ ├── _0x0bf95e59b055ec05988f95c58ccda2eb.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ └── qsm_workflow
│ ├── mrt_romeo
│ │ ├── _0xcfbbf6ccf7246b3245ae485edd96ba57.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
│ │ ├── _0xb828af11ce99301caf729fedc234f26f.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
│ │ ├── _0x4ef007d5698ee0f905ed04e30329c6c3.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
│ ├── _0xbf460250741a45cdb387ca70ad8ca90d.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_2026-03-10_03-31-50769175.txt
├── log_2026-03-10_04-01-40410991.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 numpy nibabel pandas nilearn
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-2: 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: 100.517 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=32
260310-04:02:09,272 nipype.workflow INFO:
Workflow qsmxt-workflow settings: ['check', 'execution', 'logging', 'monitoring']
260310-04:02:09,335 nipype.workflow INFO:
Running in parallel.
260310-04:02:09,340 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 24 jobs ready. Free memory (GB): 113.21/113.21, Free processors: 32/32.
260310-04:02:09,416 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260310-04:02:09,702 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260310-04:02:09,708 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260310-04:02:09,708 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".
260310-04:02:09,710 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".
260310-04:02:09,712 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".
260310-04:02:09,713 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260310-04:02:09,714 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260310-04:02:09,719 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,719 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,724 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.001854s.
260310-04:02:09,725 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.004221s.
260310-04:02:09,711 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260310-04:02:09,712 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260310-04:02:09,765 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260310-04:02:09,767 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".
260310-04:02:09,770 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260310-04:02:09,771 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260310-04:02:09,771 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".
260310-04:02:09,773 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260310-04:02:09,774 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260310-04:02:09,775 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260310-04:02:09,777 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260310-04:02:09,777 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,777 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".
260310-04:02:09,779 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260310-04:02:09,780 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260310-04:02:09,781 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260310-04:02:09,783 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260310-04:02:09,784 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260310-04:02:09,784 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260310-04:02:09,788 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260310-04:02:09,794 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.012856s.
260310-04:02:09,794 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".
260310-04:02:09,797 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260310-04:02:09,796 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".
260310-04:02:09,799 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260310-04:02:09,798 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".
260310-04:02:09,801 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,802 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260310-04:02:09,805 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.001265s.
260310-04:02:09,806 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,809 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,815 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.002146s.
260310-04:02:09,769 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,820 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.008749s.
260310-04:02:09,826 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.002382s.
260310-04:02:09,796 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".
260310-04:02:09,849 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260310-04:02:09,799 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".
260310-04:02:09,852 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260310-04:02:09,858 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,871 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260310-04:02:09,884 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.020805s.
260310-04:02:09,796 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".
260310-04:02:09,798 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".
260310-04:02:09,902 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260310-04:02:09,902 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260310-04:02:09,909 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,910 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:09,915 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.00194s.
260310-04:02:09,917 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.002609s.
260310-04:02:11,343 nipype.workflow INFO:
[Job 0] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
260310-04:02:11,345 nipype.workflow INFO:
[Job 1] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
260310-04:02:11,347 nipype.workflow INFO:
[Job 2] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
260310-04:02:11,348 nipype.workflow INFO:
[Job 3] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
260310-04:02:11,350 nipype.workflow INFO:
[Job 6] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
260310-04:02:11,351 nipype.workflow INFO:
[Job 7] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
260310-04:02:11,353 nipype.workflow INFO:
[Job 8] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
260310-04:02:11,354 nipype.workflow INFO:
[Job 9] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
260310-04:02:11,356 nipype.workflow INFO:
[Job 12] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
260310-04:02:11,357 nipype.workflow INFO:
[Job 13] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
260310-04:02:11,360 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 14 jobs ready. Free memory (GB): 81.21/113.21, Free processors: 10/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:02:11,484 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260310-04:02:11,487 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260310-04:02:11,490 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260310-04:02:11,492 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260310-04:02:11,491 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".
260310-04:02:11,493 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".
260310-04:02:11,495 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260310-04:02:11,496 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".
260310-04:02:11,501 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:11,501 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260310-04:02:11,511 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:11,512 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.008437s.
260310-04:02:11,518 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.002447s.
260310-04:02:11,492 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".
260310-04:02:11,494 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260310-04:02:11,545 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260310-04:02:11,549 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".
260310-04:02:11,551 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260310-04:02:11,553 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260310-04:02:11,558 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:11,564 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.002117s.
260310-04:02:11,494 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260310-04:02:11,602 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:11,613 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.006543s.
260310-04:02:13,343 nipype.workflow INFO:
[Job 14] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
260310-04:02:13,346 nipype.workflow INFO:
[Job 15] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
260310-04:02:13,347 nipype.workflow INFO:
[Job 18] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
260310-04:02:13,348 nipype.workflow INFO:
[Job 19] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
260310-04:02:13,351 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:02:13,427 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260310-04:02:13,430 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260310-04:02:13,432 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".
260310-04:02:13,433 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".
260310-04:02:13,435 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260310-04:02:13,435 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260310-04:02:13,440 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:13,442 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:13,451 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.006173s.
260310-04:02:13,451 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.00911s.
260310-04:02:13,434 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260310-04:02:13,489 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260310-04:02:13,489 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".
260310-04:02:13,492 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260310-04:02:13,498 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:13,503 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.001127s.
260310-04:02:13,508 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".
260310-04:02:13,510 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260310-04:02:13,520 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
260310-04:02:14,172 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.649148s.
260310-04:02:15,344 nipype.workflow INFO:
[Job 20] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
260310-04:02:15,346 nipype.workflow INFO:
[Job 21] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
260310-04:02:15,346 nipype.workflow INFO:
[Job 24] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
260310-04:02:15,347 nipype.workflow INFO:
[Job 26] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
260310-04:02:15,349 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:02:15,409 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260310-04:02:15,412 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260310-04:02:15,413 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260310-04:02:15,415 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260310-04:02:15,414 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".
260310-04:02:15,417 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260310-04:02:15,417 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".
260310-04:02:15,418 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260310-04:02:15,418 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".
260310-04:02:15,420 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260310-04:02:15,423 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:15,423 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
260310-04:02:15,426 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000705s.
260310-04:02:15,415 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".
260310-04:02:15,468 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260310-04:02:15,473 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:15,423 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260310-04:02:15,477 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.00106s.
260310-04:02:15,479 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.001459s.
260310-04:02:15,786 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.361114s.
260310-04:02:17,347 nipype.workflow INFO:
[Job 27] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
260310-04:02:17,350 nipype.workflow INFO:
[Job 29] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
260310-04:02:17,351 nipype.workflow INFO:
[Job 31] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
260310-04:02:17,353 nipype.workflow INFO:
[Job 32] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
260310-04:02:17,356 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 6 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:02:17,457 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260310-04:02:17,461 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260310-04:02:17,463 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".
260310-04:02:17,465 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260310-04:02:17,466 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".
260310-04:02:17,468 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260310-04:02:17,473 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
260310-04:02:17,474 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
260310-04:02:17,486 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.009185s.
260310-04:02:17,492 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.011686s.
260310-04:02:19,349 nipype.workflow INFO:
[Job 36] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
260310-04:02:19,352 nipype.workflow INFO:
[Job 41] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
260310-04:02:19,355 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:02:19,446 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260310-04:02:19,451 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260310-04:02:19,451 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".
260310-04:02:19,453 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260310-04:02:19,456 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".
260310-04:02:19,458 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260310-04:02:19,464 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
260310-04:02:19,472 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
260310-04:02:21,358 nipype.workflow INFO:
[MultiProc] Running 6 tasks, and 6 jobs ready. Free memory (GB): 68.53/113.21, Free processors: 2/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* 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
260310-04:03:02,462 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 42.98706s.
260310-04:03:02,837 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 43.370148s.
260310-04:03:03,399 nipype.workflow INFO:
[Job 46] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
260310-04:03:03,401 nipype.workflow INFO:
[Job 50] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
260310-04:03:03,404 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:03:03,512 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260310-04:03:03,516 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260310-04:03:03,516 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".
260310-04:03:03,518 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260310-04:03:03,519 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".
260310-04:03:03,520 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260310-04:03:03,533 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
260310-04:03:03,541 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
260310-04:03:03,786 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.243555s.
260310-04:03:03,792 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.25651s.
260310-04:03:05,401 nipype.workflow INFO:
[Job 53] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
260310-04:03:05,403 nipype.workflow INFO:
[Job 55] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
260310-04:03:05,405 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 6 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:04:28,782 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 137.226862s.
260310-04:04:29,496 nipype.workflow INFO:
[Job 11] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
260310-04:04:29,498 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 6 jobs ready. Free memory (GB): 81.21/113.21, Free processors: 10/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:04:29,669 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260310-04:04:29,677 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".
260310-04:04:29,678 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260310-04:04:29,695 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260310-04:04:31,501 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 5 jobs ready. Free memory (GB): 69.21/113.21, Free processors: 2/32.
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
* 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
260310-04:06:46,869 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 277.078671s.
260310-04:06:49,669 nipype.workflow INFO:
[Job 5] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
260310-04:06:49,671 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 77.21/113.21, Free processors: 8/32.
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
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:06:49,747 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260310-04:06:49,753 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".
260310-04:06:49,755 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260310-04:06:49,761 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260310-04:06:51,672 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 4 jobs ready. Free memory (GB): 69.21/113.21, Free processors: 2/32.
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
* 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
260310-04:10:06,798 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 476.92323s.
260310-04:10:07,888 nipype.workflow INFO:
[Job 10] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
260310-04:10:07,892 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 81.21/113.21, Free processors: 10/32.
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
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:10:07,972 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260310-04:10:07,975 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260310-04:10:07,981 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".
260310-04:10:07,983 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260310-04:10:07,987 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260310-04:10:07,981 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".
260310-04:10:08,34 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260310-04:10:08,50 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260310-04:10:08,325 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.335315s.
260310-04:10:09,889 nipype.workflow INFO:
[Job 28] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
260310-04:10:09,892 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 5 jobs ready. Free memory (GB): 69.21/113.21, Free processors: 2/32.
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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:10:09,971 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:10:09,977 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".
260310-04:10:09,978 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:10:10,7 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260310-04:10:09,978 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260310-04:10:10,36 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".
260310-04:10:10,38 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260310-04:10:10,87 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260310-04:10:11,99 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 1.01061s.
260310-04:10:11,890 nipype.workflow INFO:
[Job 38] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
260310-04:10:11,892 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 4 jobs ready. Free memory (GB): 67.21/113.21, Free processors: 1/32.
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-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* 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
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:10:11,960 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260310-04:10:11,963 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".
260310-04:10:11,965 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260310-04:10:11,969 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
260310-04:10:11,972 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.000971s.
260310-04:10:12,83 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 482.296928s.
260310-04:10:13,894 nipype.workflow INFO:
[Job 4] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
260310-04:10:13,896 nipype.workflow INFO:
[Job 47] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
260310-04:10:13,899 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 4 jobs ready. Free memory (GB): 79.21/113.21, Free processors: 9/32.
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-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* 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
260310-04:10:13,982 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260310-04:10:13,986 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260310-04:10:13,989 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".
260310-04:10:13,991 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260310-04:10:13,991 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".
260310-04:10:13,992 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260310-04:10:13,996 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260310-04:10:13,997 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260310-04:10:14,337 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.338191s.
260310-04:10:15,895 nipype.workflow INFO:
[Job 25] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
260310-04:10:15,896 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 4 jobs ready. Free memory (GB): 71.21/113.21, Free processors: 3/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:10:15,967 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:10:15,972 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".
260310-04:10:15,973 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:10:15,975 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260310-04:10:15,981 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".
260310-04:10:15,983 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260310-04:10:15,993 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260310-04:10:16,77 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260310-04:10:17,897 nipype.workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 67.21/113.21, Free processors: 1/32.
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-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:10:19,194 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 3.11479s.
260310-04:10:19,899 nipype.workflow INFO:
[Job 35] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
260310-04:10:19,903 nipype.workflow INFO:
[MultiProc] Running 6 tasks, and 2 jobs ready. Free memory (GB): 69.21/113.21, Free processors: 2/32.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:10:20,213 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 10.203415s.
260310-04:10:21,901 nipype.workflow INFO:
[Job 37] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
260310-04:10:21,902 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 2 jobs ready. Free memory (GB): 71.21/113.21, Free processors: 3/32.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* 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
* 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
260310-04:10:25,850 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 9.855162s.
260310-04:10:25,906 nipype.workflow INFO:
[Job 34] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
260310-04:10:25,910 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 3 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:10:25,994 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260310-04:10:25,999 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".
260310-04:10:26,1 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260310-04:10:26,7 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260310-04:10:26,657 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.647775s.
260310-04:10:27,906 nipype.workflow INFO:
[Job 44] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
260310-04:10:27,908 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 73.21/113.21, Free processors: 4/32.
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
* 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
260310-04:11:33,131 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 283.368283s.
260310-04:11:33,976 nipype.workflow INFO:
[Job 17] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
260310-04:11:33,979 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 81.21/113.21, Free processors: 10/32.
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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:11:34,60 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260310-04:11:34,65 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".
260310-04:11:34,66 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260310-04:11:34,69 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
260310-04:11:35,979 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 79.21/113.21, Free processors: 2/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:11:38,450 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 4.380335s.
260310-04:11:39,983 nipype.workflow INFO:
[Job 45] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
260310-04:11:39,986 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 81.21/113.21, Free processors: 10/32.
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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:11:40,76 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260310-04:11:40,80 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".
260310-04:11:40,81 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".
260310-04:11:40,82 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260310-04:11:40,85 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".
260310-04:11:40,86 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
260310-04:11:40,87 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".
260310-04:11:40,92 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
260310-04:11:41,69 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.974913s.
260310-04:11:41,985 nipype.workflow INFO:
[Job 52] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
260310-04:11:41,988 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 79.21/113.21, Free processors: 2/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:11:42,69 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260310-04:11:42,75 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".
260310-04:11:42,76 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260310-04:11:42,94 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
260310-04:11:43,701 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 3.612605s.
260310-04:11:43,986 nipype.workflow INFO:
[Job 49] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
260310-04:11:43,989 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 79.21/113.21, Free processors: 8/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:11:44,70 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".
260310-04:11:44,74 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".
260310-04:11:44,75 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".
260310-04:11:44,77 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
260310-04:11:44,638 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.559449s.
260310-04:11:45,989 nipype.workflow INFO:
[Job 54] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
260310-04:11:45,994 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 79.21/113.21, Free processors: 8/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:11:46,107 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260310-04:11:46,111 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".
260310-04:11:46,113 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260310-04:11:46,133 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
260310-04:11:47,992 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 77.21/113.21, Free processors: 6/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:12:08,503 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 26.40625s.
260310-04:12:10,13 nipype.workflow INFO:
[Job 56] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
260310-04:12:10,16 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 79.21/113.21, Free processors: 8/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
* 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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:12:10,101 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260310-04:12:10,107 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".
260310-04:12:10,108 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260310-04:12:10,117 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
260310-04:12:12,16 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 76.80/113.21, Free processors: 6/32.
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_vsharp
* 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
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:12:12,681 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 26.545558s.
260310-04:12:14,18 nipype.workflow INFO:
[Job 57] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
260310-04:12:14,22 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 78.80/113.21, Free processors: 8/32.
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.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260310-04:12:14,109 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260310-04:12:14,118 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".
260310-04:12:14,120 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260310-04:12:14,139 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
260310-04:12:14,826 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 465.129461s.
260310-04:12:16,19 nipype.workflow INFO:
[Job 16] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
260310-04:12:16,23 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 88.39/113.21, Free processors: 14/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* 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
260310-04:12:16,109 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260310-04:12:16,115 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".
260310-04:12:16,118 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260310-04:12:16,124 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260310-04:12:16,460 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.332875s.
260310-04:12:18,21 nipype.workflow INFO:
[Job 30] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
260310-04:12:18,25 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 88.39/113.21, Free processors: 14/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* 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
260310-04:12:18,110 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:12:18,114 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260310-04:12:18,117 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".
260310-04:12:18,120 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:12:18,120 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".
260310-04:12:18,122 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260310-04:12:18,153 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260310-04:12:18,278 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260310-04:12:20,25 nipype.workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 84.39/113.21, Free processors: 12/32.
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-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* 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
260310-04:12:20,590 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 2.3086130000000002s.
260310-04:12:22,26 nipype.workflow INFO:
[Job 40] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
260310-04:12:22,29 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 86.39/113.21, Free processors: 13/32.
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.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* 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
260310-04:12:28,65 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 9.909708s.
260310-04:12:29,340 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 135.341226s.
260310-04:12:30,35 nipype.workflow INFO:
[Job 23] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
260310-04:12:30,37 nipype.workflow INFO:
[Job 39] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
260310-04:12:30,41 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 96.39/113.21, Free processors: 20/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:30,133 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260310-04:12:30,139 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".
260310-04:12:30,142 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260310-04:12:30,149 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260310-04:12:30,816 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.664779s.
260310-04:12:32,37 nipype.workflow INFO:
[Job 48] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
260310-04:12:32,42 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 96.39/113.21, Free processors: 20/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:43,738 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 29.595673s.
260310-04:12:44,51 nipype.workflow INFO:
[Job 59] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
260310-04:12:44,55 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 98.80/113.21, Free processors: 22/32.
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
260310-04:12:44,137 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260310-04:12:44,142 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".
260310-04:12:44,144 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260310-04:12:44,147 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
260310-04:12:44,149 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000359s.
260310-04:12:44,611 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 34.493064s.
260310-04:12:46,53 nipype.workflow INFO:
[Job 58] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
260310-04:12:46,56 nipype.workflow INFO:
[Job 61] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
260310-04:12:46,59 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:46,144 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260310-04:12:46,150 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260310-04:12:46,151 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".
260310-04:12:46,155 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260310-04:12:46,156 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".
260310-04:12:46,158 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260310-04:12:46,160 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
260310-04:12:46,163 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260310-04:12:46,164 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000716s.
260310-04:12:46,171 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.005895s.
260310-04:12:48,54 nipype.workflow INFO:
[Job 60] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
260310-04:12:48,56 nipype.workflow INFO:
[Job 63] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
260310-04:12:48,59 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:48,148 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260310-04:12:48,151 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260310-04:12:48,155 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260310-04:12:48,155 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".
260310-04:12:48,157 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260310-04:12:48,160 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".
260310-04:12:48,163 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260310-04:12:48,171 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.005939s.
260310-04:12:48,160 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".
260310-04:12:48,213 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260310-04:12:48,163 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260310-04:12:48,217 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
260310-04:12:48,221 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.001305s.
260310-04:12:48,228 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
260310-04:12:48,808 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.556055s.
260310-04:12:50,56 nipype.workflow INFO:
[Job 62] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
260310-04:12:50,59 nipype.workflow INFO:
[Job 66] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
260310-04:12:50,61 nipype.workflow INFO:
[Job 67] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
260310-04:12:50,65 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:50,153 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260310-04:12:50,157 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260310-04:12:50,158 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".
260310-04:12:50,159 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260310-04:12:50,160 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260310-04:12:50,160 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".
260310-04:12:50,162 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260310-04:12:50,164 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".
260310-04:12:50,166 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260310-04:12:50,177 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
260310-04:12:50,179 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
260310-04:12:50,179 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
260310-04:12:50,183 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.001549s.
260310-04:12:50,184 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.001922s.
260310-04:12:50,747 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.568219s.
260310-04:12:52,58 nipype.workflow INFO:
[Job 64] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
260310-04:12:52,60 nipype.workflow INFO:
[Job 65] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
260310-04:12:52,62 nipype.workflow INFO:
[Job 70] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
260310-04:12:52,65 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:52,160 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260310-04:12:52,165 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260310-04:12:52,165 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".
260310-04:12:52,167 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260310-04:12:52,168 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".
260310-04:12:52,170 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260310-04:12:52,172 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
260310-04:12:52,176 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.001924s.
260310-04:12:52,176 nipype.workflow INFO:
[Node] Executing "create_permutations" <nipype.interfaces.utility.wrappers.Function>
260310-04:12:52,180 nipype.workflow INFO:
[Node] Finished "create_permutations", elapsed time 0.001396s.
260310-04:12:54,60 nipype.workflow INFO:
[Job 68] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
260310-04:12:54,62 nipype.workflow INFO:
[Job 69] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations).
260310-04:12:54,65 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:56,63 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:12:56,155 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260310-04:12:56,161 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".
260310-04:12:56,162 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260310-04:12:56,163 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".
260310-04:12:56,165 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".
260310-04:12:56,164 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".
260310-04:12:56,166 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:12:56,167 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm1" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:12:56,170 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm2" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:12:56,170 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm3" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:12:58,66 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 93.21/113.21, Free processors: 20/32.
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
260310-04:13:41,166 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm2", elapsed time 44.994412s.
260310-04:13:42,61 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm3", elapsed time 45.88934s.
260310-04:13:42,113 nipype.workflow INFO:
[Job 78] Completed (_nibabel_numpy_analyse-qsm2).
260310-04:13:42,115 nipype.workflow INFO:
[Job 79] Completed (_nibabel_numpy_analyse-qsm3).
260310-04:13:42,117 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 97.21/113.21, Free processors: 22/32.
Currently running:
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:13:47,205 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm0", elapsed time 51.037337s.
260310-04:13:48,119 nipype.workflow INFO:
[Job 76] Completed (_nibabel_numpy_analyse-qsm0).
260310-04:13:48,121 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 99.21/113.21, Free processors: 23/32.
Currently running:
* _nibabel_numpy_analyse-qsm1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:13:49,708 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm1", elapsed time 53.539474s.
260310-04:13:50,121 nipype.workflow INFO:
[Job 77] Completed (_nibabel_numpy_analyse-qsm1).
260310-04:13:50,125 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:13:50,205 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260310-04:13:50,213 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260310-04:13:50,221 nipype.workflow INFO:
[Node] Setting-up "_nibabel_numpy_analyse-qsm0" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-1/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/nibabel_numpy_analyse-qsm/mapflow/_nibabel_numpy_analyse-qsm0".
260310-04:13:50,225 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm0" - collecting precomputed outputs
260310-04:13:50,226 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm0" found cached.
260310-04:13:50,228 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".
260310-04:13:50,230 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm1" - collecting precomputed outputs
260310-04:13:50,230 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm1" found cached.
260310-04:13:50,232 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".
260310-04:13:50,234 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm2" - collecting precomputed outputs
260310-04:13:50,235 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm2" found cached.
260310-04:13:50,237 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".
260310-04:13:50,239 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm3" - collecting precomputed outputs
260310-04:13:50,239 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm3" found cached.
260310-04:13:52,123 nipype.workflow INFO:
[Job 72] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm).
260310-04:13:52,126 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:13:52,209 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260310-04:13:52,214 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".
260310-04:13:52,216 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260310-04:13:52,221 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260310-04:13:52,520 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.297508s.
260310-04:13:54,125 nipype.workflow INFO:
[Job 74] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile).
260310-04:13:54,130 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 101.21/113.21, Free processors: 24/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260310-04:16:45,462 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 397.409207s.
260310-04:16:46,317 nipype.workflow INFO:
[Job 22] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
260310-04:16:46,319 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 113.21/113.21, Free processors: 32/32.
260310-04:16:46,399 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260310-04:16:46,405 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".
260310-04:16:46,406 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260310-04:16:46,409 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260310-04:16:46,702 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.291549s.
260310-04:16:48,319 nipype.workflow INFO:
[Job 33] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
260310-04:16:48,321 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 113.21/113.21, Free processors: 32/32.
260310-04:16:48,399 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:16:48,403 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".
260310-04:16:48,403 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260310-04:16:48,407 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".
260310-04:16:48,407 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260310-04:16:48,421 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260310-04:16:48,404 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260310-04:16:48,476 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260310-04:16:49,989 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 1.5667659999999999s.
260310-04:16:50,320 nipype.workflow INFO:
[Job 43] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
260310-04:16:50,322 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 111.21/113.21, Free processors: 31/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
260310-04:16:50,385 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260310-04:16:50,388 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".
260310-04:16:50,389 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260310-04:16:50,393 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
260310-04:16:50,395 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.001169s.
260310-04:16:52,322 nipype.workflow INFO:
[Job 51] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
260310-04:16:52,324 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 111.21/113.21, Free processors: 31/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
260310-04:16:52,399 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260310-04:16:52,404 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".
260310-04:16:52,406 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260310-04:16:52,420 nipype.workflow INFO:
[Node] Executing "create_permutations" <nipype.interfaces.utility.wrappers.Function>
260310-04:16:52,422 nipype.workflow INFO:
[Node] Finished "create_permutations", elapsed time 0.00066s.
260310-04:16:54,324 nipype.workflow INFO:
[Job 71] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations).
260310-04:16:54,326 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 111.21/113.21, Free processors: 31/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
260310-04:16:56,329 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 111.21/113.21, Free processors: 31/32.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
260310-04:16:56,415 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260310-04:16:56,425 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".
260310-04:16:56,425 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260310-04:16:56,428 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:16:56,437 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".
260310-04:16:56,440 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm1" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:16:56,441 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".
260310-04:16:56,445 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".
260310-04:16:56,448 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm3" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:16:56,449 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm2" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260310-04:16:57,593 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 9.1164s.
260310-04:16:58,330 nipype.workflow INFO:
[Job 42] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
260310-04:16:58,332 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 105.21/113.21, Free processors: 28/32.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
260310-04:17:47,584 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm0", elapsed time 51.155017s.
260310-04:17:48,427 nipype.workflow INFO:
[Job 80] Completed (_nibabel_numpy_analyse-qsm0).
260310-04:17:48,429 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 107.21/113.21, Free processors: 29/32.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
260310-04:17:48,959 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm3", elapsed time 52.509971s.
260310-04:17:49,36 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm1", elapsed time 52.594187s.
260310-04:17:50,171 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm2", elapsed time 53.720953s.
260310-04:17:50,428 nipype.workflow INFO:
[Job 81] Completed (_nibabel_numpy_analyse-qsm1).
260310-04:17:50,429 nipype.workflow INFO:
[Job 82] Completed (_nibabel_numpy_analyse-qsm2).
260310-04:17:50,430 nipype.workflow INFO:
[Job 83] Completed (_nibabel_numpy_analyse-qsm3).
260310-04:17:50,432 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 113.21/113.21, Free processors: 32/32.
260310-04:17:50,511 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260310-04:17:50,516 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260310-04:17:50,520 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".
260310-04:17:50,521 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm0" - collecting precomputed outputs
260310-04:17:50,522 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm0" found cached.
260310-04:17:50,522 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".
260310-04:17:50,523 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm1" - collecting precomputed outputs
260310-04:17:50,524 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm1" found cached.
260310-04:17:50,524 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".
260310-04:17:50,525 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm2" - collecting precomputed outputs
260310-04:17:50,526 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm2" found cached.
260310-04:17:50,526 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".
260310-04:17:50,527 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm3" - collecting precomputed outputs
260310-04:17:50,528 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm3" found cached.
260310-04:17:52,430 nipype.workflow INFO:
[Job 73] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm).
260310-04:17:52,432 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 113.21/113.21, Free processors: 32/32.
260310-04:17:52,496 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260310-04:17:52,499 nipype.workflow INFO:
[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".
260310-04:17:52,500 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260310-04:17:52,505 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260310-04:17:52,709 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.20175s.
260310-04:17:54,432 nipype.workflow INFO:
[Job 75] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile).
260310-04:17:54,434 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 113.21/113.21, Free processors: 32/32.
[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-2026-03-10-033227
├── 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-2026-03-10-040207
├── 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-2026-03-10-033227_Chimap_sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-03-10-033227_dseg_analysis.csv
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-03-10-033227_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-03-10-040207_dseg_analysis.csv
│ │ ├── sub-1_ses-20170705_desc-qsmxt-2026-03-10-040207_Chimap_sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-03-10-033227_dseg_analysis.csv
│ │ └── sub-1_ses-20170705_desc-qsmxt-2026-03-10-040207_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-03-10-040207_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-2026-03-10-033227_Chimap_sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-03-10-033227_dseg_analysis.csv
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-03-10-033227_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-03-10-040207_dseg_analysis.csv
│ │ ├── sub-2_ses-20170705_desc-qsmxt-2026-03-10-040207_Chimap_sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-03-10-033227_dseg_analysis.csv
│ │ └── sub-2_ses-20170705_desc-qsmxt-2026-03-10-040207_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-03-10-040207_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 | 588 | -0.234321 | 0.124799 | -0.018375 | -0.022032 | 0.034551 |
| 1 | 4th-Ventricle | 1545 | -0.126117 | 0.052944 | -0.044446 | -0.044738 | 0.030515 |
| 2 | Brain-Stem | 18759 | -0.279382 | 0.184913 | -0.046081 | -0.042250 | 0.028613 |
| 3 | CSF | 868 | -1.393693 | 0.945752 | 0.026954 | 0.031358 | 0.142805 |
| 4 | Left-Accumbens-area | 512 | -0.141920 | 0.128334 | 0.021749 | 0.020072 | 0.030743 |
| ... | ... | ... | ... | ... | ... | ... | ... |
| 91 | ctx-rh-superiorfrontal | 29614 | -0.133274 | 0.251870 | -0.004509 | -0.009532 | 0.024327 |
| 92 | ctx-rh-superiorparietal | 12074 | -0.084225 | 0.306628 | -0.015666 | -0.014670 | 0.022258 |
| 93 | ctx-rh-superiortemporal | 16371 | -0.090982 | 0.248737 | 0.005474 | 0.012545 | 0.024069 |
| 94 | ctx-rh-supramarginal | 12124 | -0.056940 | 0.239688 | 0.018219 | 0.019439 | 0.022529 |
| 95 | ctx-rh-transversetemporal | 1245 | -0.004704 | 0.132365 | 0.034663 | 0.035511 | 0.014424 |
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 | ||
| CSF | -0.040 | 0.030 |
| Thalamus | -0.010 | 0.022 |
| Brain stem | -0.004 | 0.017 |
| Putamen | -0.003 | 0.012 |
| White matter | -0.003 | 0.027 |
| Caudate | -0.002 | 0.013 |
| Pallidum | -0.001 | 0.008 |
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
%load_ext watermark
%watermark
%watermark --iversions
Last updated: 2026-03-10T04:18:02.121688+00:00
Python implementation: CPython
Python version : 3.13.11
IPython version : 9.9.0
Compiler : GCC 14.3.0
OS : Linux
Release : 5.15.0-170-generic
Machine : x86_64
Processor : x86_64
CPU cores : 32
Architecture: 64bit
ipyniivue : 2.4.4
json : 2.0.9
matplotlib: 3.10.8
nibabel : 5.3.3
nilearn : 0.13.1
numpy : 2.4.2
pandas : 2.3.3
seaborn : 0.13.2