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 11.22 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 0.496714 seconds (0.496145 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 0.123471 seconds (0.121113 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 0.117968 seconds (0.117927 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 0.490654 seconds (0.490593 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 0.117689 seconds (0.117646 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 0.116779 seconds (0.116740 for core code).
[INFO]: Scanning for multi-coil data to merge...
[INFO]: Scanning for multi-coil runs to combine...
[INFO]: Checking for complex or polar data requiring fixing...
Loading NIfTIs: 100%|█████████████████████████| 46/46 [00:00<00:00, 1735.26it/s]
[INFO]: Finished
!tree bids
bids
├── derivatives
│ ├── qsmxt-2026-08-27-224935
│ │ ├── 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
│ │ │ │ ├── _0x10e37e0d23f836237717b9997a3446b0.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
│ │ │ │ ├── _0x667ecea91ffeb5e4a1a89652202c47dc.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
│ │ │ │ ├── _0xa2906c7f252188c1c1100085b5fdccf9.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_copyfile.pklz
│ │ │ ├── fastsurfer_segment-t1
│ │ │ │ ├── _0xe864f7dc8df7984a1f76cf1ad4137ed9.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
│ │ │ │ ├── _0xf23339ac437d4a43d111dc58b75860b7.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ │ ├── func_read-json-me
│ │ │ │ ├── _0x6aa7f740fe933329299de30b15476d9f.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_read-json-me.pklz
│ │ │ ├── func_read-json-se
│ │ │ │ ├── _0xf9b8b38a7d0301701df42b9b7ae9b88b.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_func_read-json-se.pklz
│ │ │ ├── nibabel_as-canonical
│ │ │ │ ├── _0x2597017492f5b4a292dccd94c744e8d0.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_nibabel_as-canonical.pklz
│ │ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ │ ├── _0x5bf8f22d5240f6bca1364f5e81c7b9b0.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
│ │ │ │ ├── _0x318b9d066366795d7a1371bc14fa7f47.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ └── result_nibabel_read-nii.pklz
│ │ │ └── numpy_numpy_nibabel_mgz2nii
│ │ │ ├── _0x222d3b97d359c96b1eeb9763d8554625.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ │ └── qsm_acq-acqqsmp21mmisote20_T2starw
│ │ ├── ants_register-t1-to-qsm
│ │ │ ├── _0xdb581fef299e8b2cfadbeb52d9a8fe07.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
│ │ │ ├── _0x2e477b391dbc5e501aae7b4264176d66.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
│ │ │ ├── _0xdd53910b6fef6b4d0a5f6a4daecff823.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_combine_lists1.pklz
│ │ ├── combine_lists2
│ │ │ ├── _0xe979148fd3db08f2a13cb1a2c7c9b1fa.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_combine_lists2.pklz
│ │ ├── copy_qsm_json_sidecar
│ │ │ ├── _0x17717c722599bce633b138ee6b7a4f0d.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copy_qsm_json_sidecar.pklz
│ │ ├── copyfile
│ │ │ ├── _0x98b4ddaa885091f0f842d7a41a2dfd3e.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copyfile.pklz
│ │ ├── create_permutations
│ │ │ ├── _0xbc595714d39776b6eeb547f06be4c1d7.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_create_permutations.pklz
│ │ ├── fastsurfer_segment-t1
│ │ │ ├── _0xe864f7dc8df7984a1f76cf1ad4137ed9.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
│ │ │ ├── _0xc17ebec2f8593525babc9ef2829283ea.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ ├── func_read-json-me
│ │ │ ├── _0x7fa39ac6fcbd314c1ea0c5f466b23506.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-me.pklz
│ │ ├── func_read-json-se
│ │ │ ├── _0x94aaee356ae540b3cfafea11afbadae0.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-se.pklz
│ │ ├── mask_workflow
│ │ │ ├── fsl-bet
│ │ │ │ ├── _0xb1411913c331e99444fb4df58437a6aa.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
│ │ │ ├── _0xe36fdcebddf67e927b5312b4eb240451.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
│ │ │ ├── _0xb7a8211cfbdf20b8b660157c8728f787.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_as-canonical.pklz
│ │ ├── nibabel_numpy_analyse-qsm
│ │ │ ├── _0x41b5873bf810a691a278f74d5f452a2a.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── mapflow
│ │ │ │ └── _nibabel_numpy_analyse-qsm0
│ │ │ │ ├── _0x3554ede26d8caa38f1322f32cfaab372.json
│ │ │ │ ├── _inputs.pklz
│ │ │ │ ├── _node.pklz
│ │ │ │ ├── _report
│ │ │ │ │ └── report.rst
│ │ │ │ ├── result__nibabel_numpy_analyse-qsm0.pklz
│ │ │ │ └── sub-1_ses-20170705_desc-qsmxt-2026-08-27-224935_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-08-27-224935_dseg_analysis.csv
│ │ │ └── result_nibabel_numpy_analyse-qsm.pklz
│ │ ├── nibabel_numpy_nilearn_axial-resampling
│ │ │ ├── _0xda88f4c507f36695984e5de213270e2c.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_nilearn_axial-resampling.pklz
│ │ ├── nibabel_numpy_nilearn_qsm-resampled
│ │ │ ├── _0x90a3e99709e04c955316473cf49975a9.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_nilearn_qsm-resampled.pklz
│ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ ├── _0x74c9cff00e2c5cd38f66a0604bbcc4c5.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
│ │ │ ├── _0x4f6e5730081e817b853d7e78762db92a.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_numpy_qsm-average.pklz
│ │ ├── nibabel_numpy_qsm-referenced
│ │ │ ├── _0x7389848d13044d9245c5061a00778b0c.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
│ │ │ ├── _0xc0264bbb5cc92eaa936d965a851aec14.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
│ │ │ ├── _0xd2847885f8f20987e99cbbdd887227d4.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_read-nii.pklz
│ │ ├── numpy_numpy_nibabel_mgz2nii
│ │ │ ├── _0x9f5477d8ca352e156762b45535b3a1be.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ │ └── qsm_workflow
│ │ ├── mrt_romeo
│ │ │ ├── _0xbf2197ea124711e7e45f44130eb4fd5f.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
│ │ │ ├── _0x510958ece2383bee79ee22e5c74d9b59.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
│ │ │ ├── _0x2d8f47039d8f22b38e6009a350974c2a.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
│ │ ├── _0xafbc5bd8585f24cd61a3333f0a7a5a87.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
│ │ │ ├── _0x7ba311dc0d6ece03e28b1c9fe9e81ece.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
│ │ │ ├── _0x9e8f9e3290f7b9a40cb536608a63710c.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
│ │ │ ├── _0x2c2aba51a12b894918f366acd7ebc05a.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_copyfile.pklz
│ │ ├── fastsurfer_segment-t1
│ │ │ ├── _0x3984c40fee1bf1cbbd31179b0986181a.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
│ │ │ ├── _0x7f6cc66cb3785b5425ebc3898342c207.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_getfirst-canonical-magnitude.pklz
│ │ ├── func_read-json-me
│ │ │ ├── _0xd5b2a59b41121c2266a528779919da52.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-me.pklz
│ │ ├── func_read-json-se
│ │ │ ├── _0xb8579247d70577643b9dfa2ca1c3dc27.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_func_read-json-se.pklz
│ │ ├── nibabel_as-canonical
│ │ │ ├── _0xff0d489bff0bf534a145a7cabee5c2b2.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_as-canonical.pklz
│ │ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ │ ├── _0xc8a0442d768095a6de66d9340177cb6c.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
│ │ │ ├── _0xc42879c41b90b5375394dcc74f89169f.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ └── result_nibabel_read-nii.pklz
│ │ └── numpy_numpy_nibabel_mgz2nii
│ │ ├── _0x228d9ea554d4d8c76f0ea06c8dba1bd3.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ └── qsm_acq-acqqsmp21mmisote20_T2starw
│ ├── ants_register-t1-to-qsm
│ │ ├── _0xed9452e813a159200881b954328a217e.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
│ │ ├── _0xb49ebd8ec3e82b3dfc077af1c375e6b8.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
│ │ ├── _0xe1bb2b18da94f6fec888572eb6a21744.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_combine_lists1.pklz
│ ├── combine_lists2
│ │ ├── _0x09485436e484f1b86ea9d1d8a5e8548c.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_combine_lists2.pklz
│ ├── copy_qsm_json_sidecar
│ │ ├── _0x73407c727e77d194881ef86d204d5a42.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_copy_qsm_json_sidecar.pklz
│ ├── copyfile
│ │ ├── _0xd015068b2ebf2c86c6ce2f5ecf4c260a.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_copyfile.pklz
│ ├── create_permutations
│ │ ├── _0x21fdaefab5cc67478ff6c090ddeafdf6.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_create_permutations.pklz
│ ├── fastsurfer_segment-t1
│ │ ├── _0x3984c40fee1bf1cbbd31179b0986181a.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
│ │ ├── _0x2f30019d8766fe3c827c0c0871324ad4.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_getfirst-canonical-magnitude.pklz
│ ├── func_read-json-me
│ │ ├── _0x69a23adbb433c15f95b2c4782a12ffc6.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_read-json-me.pklz
│ ├── func_read-json-se
│ │ ├── _0xe3f41a31d3d32a0d0fc23bfb1afaff07.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_func_read-json-se.pklz
│ ├── mask_workflow
│ │ ├── fsl-bet
│ │ │ ├── _0x46edefbc40f326c7c127450acbcc6d2c.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
│ │ ├── _0xc420c9371c08df6975d5d64cf016d019.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
│ │ ├── _0x9f79df459a0f0e9b28651dc31a2b1cd6.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_as-canonical.pklz
│ ├── nibabel_numpy_analyse-qsm
│ │ ├── _0x5d632e0aa03936ab04a254e48623ce11.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ ├── mapflow
│ │ │ └── _nibabel_numpy_analyse-qsm0
│ │ │ ├── _0x04c536b8b0239b043c8ae30e246c3a93.json
│ │ │ ├── _inputs.pklz
│ │ │ ├── _node.pklz
│ │ │ ├── _report
│ │ │ │ └── report.rst
│ │ │ ├── result__nibabel_numpy_analyse-qsm0.pklz
│ │ │ └── sub-2_ses-20170705_desc-qsmxt-2026-08-27-224935_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-08-27-224935_dseg_analysis.csv
│ │ └── result_nibabel_numpy_analyse-qsm.pklz
│ ├── nibabel_numpy_nilearn_axial-resampling
│ │ ├── _0x88653dad8a32da543ad21d85da2610a9.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_nilearn_axial-resampling.pklz
│ ├── nibabel_numpy_nilearn_qsm-resampled
│ │ ├── _0x6196cb809ceef76751a6f285483b6c95.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_nilearn_qsm-resampled.pklz
│ ├── nibabel_numpy_nilearn_t1w-seg-resampled
│ │ ├── _0x691ab00220f042a6acaf59fe4431cf77.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
│ │ ├── _0x9f2300d86636ba8f1ce8e1a6ec80bc28.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_numpy_qsm-average.pklz
│ ├── nibabel_numpy_qsm-referenced
│ │ ├── _0x38025aee28f9f7b2cbcdf7d33289f1f3.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
│ │ ├── _0x4ea0ec1d0fdb6902d83867b83aa85123.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
│ │ ├── _0x804796709769d01e7a4699306201b94c.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_nibabel_read-nii.pklz
│ ├── numpy_numpy_nibabel_mgz2nii
│ │ ├── _0x0432932d232a3768ce81a3b58f48664a.json
│ │ ├── _inputs.pklz
│ │ ├── _node.pklz
│ │ ├── _report
│ │ │ └── report.rst
│ │ └── result_numpy_numpy_nibabel_mgz2nii.pklz
│ └── qsm_workflow
│ ├── mrt_romeo
│ │ ├── _0xc916e3e6335564f7d0cafbfd93eaaede.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
│ │ ├── _0xa87b8f3f8d31cd5cf7f2db1d6753d2d6.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
│ │ ├── _0xb6999aa4ce5b4a108a047e4d1eb0e2a3.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
│ ├── _0xa765e9414a1a7c80a97a7ee5609952e5.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_2026-08-27_22-49-07429734.txt
├── log_2026-08-27_23-10-33932276.txt
├── references.txt
├── sub-1
│ └── ses-20170705
│ └── anat
│ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.json
│ ├── sub-1_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.nii
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.json
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.nii
│ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.json
│ └── sub-1_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.nii
└── sub-2
└── ses-20170705
└── anat
├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.json
├── sub-2_ses-20170705_acq-acqmp2ragehighres0p5isoslab_part-mag_T1w.nii
├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.json
├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-mag_T2starw.nii
├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.json
└── sub-2_ses-20170705_acq-acqqsmp21mmisote20_part-phase_T2starw.nii
205 directories, 494 files
Inspect input data#
Here we define a function we will use to visualise NIfTI images so we can view some of the input data:
%%capture
!pip install seaborn==0.13.2 numpy==2.3.5 nibabel==5.3.3 pandas==2.3.3 nilearn==0.13.1
from glob import glob
from matplotlib import pyplot as plt
import numpy as np
import nibabel as nib
def show_nii(nii_path, title=None, figsize=(4,5), cmap='gray', **imshow_args):
# load data\n",
data_1 = nib.load(nii_path).get_fdata()
# get middle slices\n",
slc_data1 = np.rot90(data_1[np.shape(data_1)[0]//2,:,:])
slc_data2 = np.rot90(data_1[:,np.shape(data_1)[1]//2,:])
slc_data3 = np.rot90(data_1[:,:,np.shape(data_1)[2]//2])
# show slices\n",
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=figsize)
if title: plt.suptitle(title)
axes[0].imshow(slc_data1, cmap=cmap, **imshow_args)
axes[1].imshow(slc_data2, cmap=cmap, **imshow_args)
axes[2].imshow(slc_data3, cmap=cmap, **imshow_args)
axes[0].axis('off')
axes[1].axis('off')
axes[2].axis('off')
fig.tight_layout()
fig.subplots_adjust(top=1.55)
plt.show()
show_nii(glob("bids/sub-*/ses-*/anat/*mag*T2starw*nii*")[0], title="Magnitude", vmax=500)
show_nii(glob("bids/sub-*/ses-*/anat/*phase*T2starw*nii*")[0], title="Phase")
show_nii(glob("bids/sub-*/ses-*/anat/*T1w*nii*")[0], title="T1-weighted")
Interactive Display using Niivue#
from ipyniivue import NiiVue
nv_T1 = NiiVue()
nv_T1.load_volumes([{"path": glob("bids/sub-*/ses-*/anat/*T1w*nii*")[0]}])
nv_T1
[HF-patcher] sub-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: 54.351 GB
[INFO]: Creating QSMxT workflow for sub-1.ses-20170705.acq-acqmp2ragehighres0p5isoslab.T1w...
[INFO]: Creating QSMxT workflow for sub-1.ses-20170705.acq-acqqsmp21mmisote20.T2starw...
[INFO]: Creating QSMxT workflow for sub-2.ses-20170705.acq-acqmp2ragehighres0p5isoslab.T1w...
[INFO]: Creating QSMxT workflow for sub-2.ses-20170705.acq-acqqsmp21mmisote20.T2starw...
[INFO]: Running using MultiProc plugin with n_procs=16
260827-23:10:54,683 nipype.workflow INFO:
Workflow qsmxt-workflow settings: ['check', 'execution', 'logging', 'monitoring']
260827-23:10:54,713 nipype.workflow INFO:
Running in parallel.
260827-23:10:54,715 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 24 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260827-23:10:54,753 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260827-23:10:54,824 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260827-23:10:54,825 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".
260827-23:10:54,826 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260827-23:10:54,826 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260827-23:10:54,827 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260827-23:10:54,827 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".
260827-23:10:54,828 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260827-23:10:54,828 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260827-23:10:54,828 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,829 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260827-23:10:54,829 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".
260827-23:10:54,830 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260827-23:10:54,831 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260827-23:10:54,832 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260827-23:10:54,832 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,833 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260827-23:10:54,833 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".
260827-23:10:54,833 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".
260827-23:10:54,834 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260827-23:10:54,834 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260827-23:10:54,835 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.000991s.
260827-23:10:54,835 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,835 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".
260827-23:10:54,836 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260827-23:10:54,837 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,837 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,839 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,840 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.001048s.
260827-23:10:54,840 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.00346s.
260827-23:10:54,841 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.002834s.
260827-23:10:54,846 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.005403s.
260827-23:10:54,829 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".
260827-23:10:54,831 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.00083s.
260827-23:10:54,881 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260827-23:10:54,832 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".
260827-23:10:54,883 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260827-23:10:54,833 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".
260827-23:10:54,884 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260827-23:10:54,886 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,888 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000834s.
260827-23:10:54,895 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260827-23:10:54,884 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:54,943 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.006428s.
260827-23:10:56,718 nipype.workflow INFO:
[Job 0] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
260827-23:10:56,719 nipype.workflow INFO:
[Job 1] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
260827-23:10:56,720 nipype.workflow INFO:
[Job 2] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
260827-23:10:56,721 nipype.workflow INFO:
[Job 3] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
260827-23:10:56,722 nipype.workflow INFO:
[Job 6] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
260827-23:10:56,722 nipype.workflow INFO:
[Job 7] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
260827-23:10:56,723 nipype.workflow INFO:
[Job 8] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
260827-23:10:56,724 nipype.workflow INFO:
[Job 9] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
260827-23:10:56,725 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 18 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:10:56,786 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260827-23:10:56,788 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260827-23:10:56,789 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260827-23:10:56,790 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".
260827-23:10:56,790 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".
260827-23:10:56,791 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260827-23:10:56,791 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me".
260827-23:10:56,791 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".
260827-23:10:56,792 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se".
260827-23:10:56,794 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:56,794 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260827-23:10:56,795 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:56,796 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000797s.
260827-23:10:56,797 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.000772s.
260827-23:10:58,719 nipype.workflow INFO:
[Job 12] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-me).
260827-23:10:58,721 nipype.workflow INFO:
[Job 13] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_read-json-se).
260827-23:10:58,722 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 15 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:10:58,766 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260827-23:10:58,767 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260827-23:10:58,769 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".
260827-23:10:58,770 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical".
260827-23:10:58,773 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:58,779 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.00392s.
260827-23:10:58,769 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".
260827-23:10:58,820 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii".
260827-23:10:58,823 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260827-23:10:58,828 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.002963s.
260827-23:11:00,722 nipype.workflow INFO:
[Job 14] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_read-nii).
260827-23:11:00,723 nipype.workflow INFO:
[Job 15] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_as-canonical).
260827-23:11:00,725 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 14 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:00,780 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260827-23:11:00,781 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260827-23:11:00,782 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".
260827-23:11:00,783 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me".
260827-23:11:00,786 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".
260827-23:11:00,786 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se".
260827-23:11:00,787 nipype.workflow INFO:
[Node] Executing "func_read-json-me" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:00,789 nipype.workflow INFO:
[Node] Executing "func_read-json-se" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:00,790 nipype.workflow INFO:
[Node] Finished "func_read-json-me", elapsed time 0.000832s.
260827-23:11:00,791 nipype.workflow INFO:
[Node] Finished "func_read-json-se", elapsed time 0.00078s.
260827-23:11:02,723 nipype.workflow INFO:
[Job 18] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-me).
260827-23:11:02,724 nipype.workflow INFO:
[Job 19] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_read-json-se).
260827-23:11:02,726 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:02,781 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260827-23:11:02,783 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260827-23:11:02,783 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".
260827-23:11:02,784 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii".
260827-23:11:02,786 nipype.workflow INFO:
[Node] Executing "nibabel_read-nii" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:02,786 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".
260827-23:11:02,787 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical".
260827-23:11:02,789 nipype.workflow INFO:
[Node] Executing "nibabel_as-canonical" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:02,789 nipype.workflow INFO:
[Node] Finished "nibabel_read-nii", elapsed time 0.002317s.
260827-23:11:02,796 nipype.workflow INFO:
[Node] Finished "nibabel_as-canonical", elapsed time 0.004571s.
260827-23:11:04,726 nipype.workflow INFO:
[Job 20] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_read-nii).
260827-23:11:04,727 nipype.workflow INFO:
[Job 21] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_as-canonical).
260827-23:11:04,728 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:04,802 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260827-23:11:04,804 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260827-23:11:04,806 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".
260827-23:11:04,806 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260827-23:11:04,809 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".
260827-23:11:04,809 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260827-23:11:04,820 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
260827-23:11:04,809 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:04,864 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000357s.
260827-23:11:05,135 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.313882s.
260827-23:11:06,729 nipype.workflow INFO:
[Job 24] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
260827-23:11:06,733 nipype.workflow INFO:
[Job 26] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
260827-23:11:06,735 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 11 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:06,816 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260827-23:11:06,818 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260827-23:11:06,820 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".
260827-23:11:06,820 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260827-23:11:06,820 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".
260827-23:11:06,821 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude".
260827-23:11:06,822 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:06,823 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000279s.
260827-23:11:06,823 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:06,827 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000288s.
260827-23:11:08,732 nipype.workflow INFO:
[Job 27] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
260827-23:11:08,740 nipype.workflow INFO:
[Job 29] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.func_getfirst-canonical-magnitude).
260827-23:11:08,741 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:08,798 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260827-23:11:08,800 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260827-23:11:08,802 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".
260827-23:11:08,803 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase".
260827-23:11:08,803 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".
260827-23:11:08,803 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude".
260827-23:11:08,805 nipype.workflow INFO:
[Node] Executing "func_getfirst-canonical-magnitude" <nipype.interfaces.utility.wrappers.Function>
260827-23:11:08,807 nipype.workflow INFO:
[Node] Finished "func_getfirst-canonical-magnitude", elapsed time 0.000343s.
260827-23:11:08,811 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_scale-phase" <qsmxt.interfaces.nipype_interface_processphase.ScalePhaseInterface>
260827-23:11:09,167 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_scale-phase", elapsed time 0.354876s.
260827-23:11:10,734 nipype.workflow INFO:
[Job 31] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_scale-phase).
260827-23:11:10,736 nipype.workflow INFO:
[Job 32] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.func_getfirst-canonical-magnitude).
260827-23:11:10,737 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:10,807 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260827-23:11:10,809 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".
260827-23:11:10,810 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260827-23:11:10,815 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
260827-23:11:10,822 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.006357s.
260827-23:11:10,809 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260827-23:11:10,862 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".
260827-23:11:10,863 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling".
260827-23:11:10,865 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_axial-resampling" <qsmxt.interfaces.nipype_interface_axialsampling.AxialSamplingInterface>
260827-23:11:10,876 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_axial-resampling", elapsed time 0.009769s.
260827-23:11:12,738 nipype.workflow INFO:
[Job 36] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
260827-23:11:12,739 nipype.workflow INFO:
[Job 41] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_axial-resampling).
260827-23:11:12,744 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 10 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:12,814 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260827-23:11:12,816 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260827-23:11:12,819 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".
260827-23:11:12,819 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".
260827-23:11:12,823 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260827-23:11:12,837 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
260827-23:11:12,819 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo".
260827-23:11:12,882 nipype.workflow INFO:
[Node] Executing "mrt_romeo" <qsmxt.interfaces.nipype_interface_romeo.RomeoB0Interface>
260827-23:11:14,742 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 31.84/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:42,248 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 29.410018s.
260827-23:11:42,398 nipype.workflow INFO:
[Node] Finished "mrt_romeo", elapsed time 29.515149s.
260827-23:11:42,782 nipype.workflow INFO:
[Job 46] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
260827-23:11:42,783 nipype.workflow INFO:
[Job 50] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.mrt_romeo).
260827-23:11:42,785 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 10 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:42,847 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260827-23:11:42,849 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".
260827-23:11:42,850 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260827-23:11:42,866 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
260827-23:11:42,954 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.087114s.
260827-23:11:44,783 nipype.workflow INFO:
[Job 53] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
260827-23:11:44,787 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:11:44,855 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260827-23:11:44,857 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".
260827-23:11:44,857 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase".
260827-23:11:44,867 nipype.workflow INFO:
[Node] Executing "nibabel-numpy_normalize-phase" <qsmxt.interfaces.nipype_interface_processphase.PhaseToNormalizedInterface>
260827-23:11:44,947 nipype.workflow INFO:
[Node] Finished "nibabel-numpy_normalize-phase", elapsed time 0.079215s.
260827-23:11:46,785 nipype.workflow INFO:
[Job 55] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.nibabel-numpy_normalize-phase).
260827-23:11:46,791 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:14:10,342 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 193.54652s.
260827-23:14:12,929 nipype.workflow INFO:
[Job 5] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
260827-23:14:12,931 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:14:12,999 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260827-23:14:13,1 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".
260827-23:14:13,2 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260827-23:14:13,12 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260827-23:14:14,932 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 32.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:15:49,485 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 294.588911s.
260827-23:15:51,60 nipype.workflow INFO:
[Job 4] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
260827-23:15:51,62 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:15:51,133 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260827-23:15:51,135 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260827-23:15:51,136 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".
260827-23:15:51,137 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".
260827-23:15:51,140 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260827-23:15:51,143 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260827-23:15:51,140 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260827-23:15:51,197 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260827-23:15:51,393 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.195116s.
260827-23:15:53,64 nipype.workflow INFO:
[Job 25] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
260827-23:15:53,66 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:15:53,113 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:15:53,116 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".
260827-23:15:53,116 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:15:53,118 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260827-23:15:53,123 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".
260827-23:15:53,123 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260827-23:15:53,146 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260827-23:15:53,213 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260827-23:15:55,69 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 6 jobs ready. Free memory (GB): 32.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:15:55,325 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 2.110897s.
260827-23:15:56,339 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 3.192084s.
260827-23:15:57,70 nipype.workflow INFO:
[Job 34] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
260827-23:15:57,71 nipype.workflow INFO:
[Job 35] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
260827-23:15:57,73 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:15:57,136 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260827-23:15:57,138 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".
260827-23:15:57,139 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260827-23:15:57,142 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260827-23:15:57,620 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.477602s.
260827-23:15:59,72 nipype.workflow INFO:
[Job 44] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
260827-23:15:59,74 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:17:15,995 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 84.850773s.
260827-23:17:17,156 nipype.workflow INFO:
[Job 11] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
260827-23:17:17,158 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:17:17,209 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260827-23:17:17,212 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".
260827-23:17:17,215 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1".
260827-23:17:17,228 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260827-23:17:19,160 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 32.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:19:20,671 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 307.658036s.
260827-23:19:21,327 nipype.workflow INFO:
[Job 10] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
260827-23:19:21,329 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:19:21,380 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260827-23:19:21,383 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".
260827-23:19:21,383 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260827-23:19:21,383 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm".
260827-23:19:21,385 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".
260827-23:19:21,386 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260827-23:19:21,386 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260827-23:19:21,388 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260827-23:19:21,591 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.202383s.
260827-23:19:23,329 nipype.workflow INFO:
[Job 28] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
260827-23:19:23,331 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:19:23,385 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:19:23,388 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260827-23:19:23,389 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".
260827-23:19:23,389 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:19:23,390 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".
260827-23:19:23,391 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260827-23:19:23,412 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260827-23:19:23,414 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260827-23:19:24,113 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.700128s.
260827-23:19:25,331 nipype.workflow INFO:
[Job 38] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
260827-23:19:25,333 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 34.51/56.51, Free processors: 1/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:19:25,402 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260827-23:19:25,407 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".
260827-23:19:25,408 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260827-23:19:25,414 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
260827-23:19:25,416 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.000656s.
260827-23:19:26,722 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 3.3066969999999998s.
260827-23:19:27,334 nipype.workflow INFO:
[Job 37] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
260827-23:19:27,338 nipype.workflow INFO:
[Job 47] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
260827-23:19:27,339 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1
260827-23:22:16,575 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 299.346487s.
260827-23:22:17,491 nipype.workflow INFO:
[Job 16] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.fastsurfer_segment-t1).
260827-23:22:17,492 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 48.51/56.51, Free processors: 10/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260827-23:22:17,538 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260827-23:22:17,540 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".
260827-23:22:17,540 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1".
260827-23:22:17,541 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260827-23:22:17,546 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".
260827-23:22:17,546 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii".
260827-23:22:17,548 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260827-23:22:17,552 nipype.workflow INFO:
[Node] Executing "fastsurfer_segment-t1" <qsmxt.interfaces.nipype_interface_fastsurfer.FastSurferInterface>
260827-23:22:17,741 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.192324s.
260827-23:22:19,493 nipype.workflow INFO:
[Job 30] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.numpy_numpy_nibabel_mgz2nii).
260827-23:22:19,494 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260827-23:22:19,534 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:22:19,536 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".
260827-23:22:19,536 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:22:19,558 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260827-23:22:21,495 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 34.51/56.51, Free processors: 1/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260827-23:22:22,467 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 2.908211s.
260827-23:22:23,495 nipype.workflow INFO:
[Job 39] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.nibabel_numpy_nilearn_t1w-seg-resampled).
260827-23:22:23,496 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm
260827-23:22:36,839 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 195.451676s.
260827-23:22:37,505 nipype.workflow INFO:
[Job 17] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_register-t1-to-qsm).
260827-23:22:37,508 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:22:37,574 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260827-23:22:37,576 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".
260827-23:22:37,577 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm".
260827-23:22:37,577 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260827-23:22:37,579 nipype.workflow INFO:
[Node] Executing "ants_register-t1-to-qsm" <nipype.interfaces.ants.registration.RegistrationSynQuick>
260827-23:22:37,580 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".
260827-23:22:37,580 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm".
260827-23:22:37,679 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260827-23:22:39,508 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 34.51/56.51, Free processors: 1/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:22:39,726 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 2.045109s.
260827-23:22:41,510 nipype.workflow INFO:
[Job 40] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.ants_transform-segmentation-to-qsm).
260827-23:22:41,511 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:22:41,565 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260827-23:22:41,567 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".
260827-23:22:41,568 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile".
260827-23:22:41,570 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260827-23:22:41,996 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.424436s.
260827-23:22:43,512 nipype.workflow INFO:
[Job 48] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqmp2ragehighres0p5isoslab_T1w.copyfile).
260827-23:22:43,514 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 2/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:23:59,535 nipype.workflow INFO:
[Node] Finished "ants_register-t1-to-qsm", elapsed time 81.955019s.
260827-23:24:01,590 nipype.workflow INFO:
[Job 23] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_register-t1-to-qsm).
260827-23:24:01,592 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:01,658 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260827-23:24:01,660 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".
260827-23:24:01,663 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260827-23:24:01,665 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
260827-23:24:03,593 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:04,916 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 3.245795s.
260827-23:24:05,593 nipype.workflow INFO:
[Job 45] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
260827-23:24:05,594 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:05,642 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260827-23:24:05,644 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".
260827-23:24:05,644 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet".
260827-23:24:05,646 nipype.workflow INFO:
[Node] Executing "fsl-bet" <qsmxt.interfaces.nipype_interface_bet2.Bet2Interface>
260827-23:24:07,595 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 42.51/56.51, Free processors: 0/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:08,386 nipype.workflow INFO:
[Node] Finished "fsl-bet", elapsed time 2.738862s.
260827-23:24:09,597 nipype.workflow INFO:
[Job 49] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.fsl-bet).
260827-23:24:09,599 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:09,650 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".
260827-23:24:09,652 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".
260827-23:24:09,653 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".
260827-23:24:09,654 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".
260827-23:24:09,656 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
260827-23:24:09,653 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".
260827-23:24:09,704 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".
260827-23:24:09,706 nipype.workflow INFO:
[Node] Executing "scipy_numpy_nibabel_bet_erode" <qsmxt.interfaces.nipype_interface_erode.ErosionInterface>
260827-23:24:10,64 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.407314s.
260827-23:24:10,116 nipype.workflow INFO:
[Node] Finished "scipy_numpy_nibabel_bet_erode", elapsed time 0.408632s.
260827-23:24:11,597 nipype.workflow INFO:
[Job 52] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
260827-23:24:11,599 nipype.workflow INFO:
[Job 54] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.mask_workflow.scipy_numpy_nibabel_bet_erode).
260827-23:24:11,600 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:11,658 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260827-23:24:11,661 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".
260827-23:24:11,661 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260827-23:24:11,663 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".
260827-23:24:11,663 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260827-23:24:11,680 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
260827-23:24:11,661 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp".
260827-23:24:11,734 nipype.workflow INFO:
[Node] Executing "qsmjl_vsharp" <qsmxt.interfaces.nipype_interface_qsmjl.VsharpInterface>
260827-23:24:13,601 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 40.51/56.51, Free processors: 4/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
* qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:28,746 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 17.064384s.
260827-23:24:29,322 nipype.workflow INFO:
[Node] Finished "qsmjl_vsharp", elapsed time 17.585924s.
260827-23:24:29,616 nipype.workflow INFO:
[Job 56] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
260827-23:24:29,618 nipype.workflow INFO:
[Job 57] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_vsharp).
260827-23:24:29,619 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:29,679 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260827-23:24:29,682 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260827-23:24:29,682 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".
260827-23:24:29,686 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260827-23:24:29,688 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".
260827-23:24:29,689 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts".
260827-23:24:29,699 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
260827-23:24:29,704 nipype.workflow INFO:
[Node] Executing "qsmjl_rts" <qsmxt.interfaces.nipype_interface_qsmjl.RtsQsmInterface>
260827-23:24:31,616 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 39.70/56.51, Free processors: 4/16.
Currently running:
* qsmxt-workflow.sub-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
260827-23:24:51,734 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 22.0336s.
260827-23:24:51,788 nipype.workflow INFO:
[Node] Finished "qsmjl_rts", elapsed time 22.081547s.
260827-23:24:53,632 nipype.workflow INFO:
[Job 58] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
260827-23:24:53,633 nipype.workflow INFO:
[Job 59] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.qsm_workflow.qsmjl_rts).
260827-23:24:53,635 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:53,688 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260827-23:24:53,691 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260827-23:24:53,691 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".
260827-23:24:53,692 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260827-23:24:53,692 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".
260827-23:24:53,692 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average".
260827-23:24:53,694 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
260827-23:24:53,694 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-average" <qsmxt.interfaces.nipype_interface_nonzeroaverage.NonzeroAverageInterface>
260827-23:24:53,695 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000169s.
260827-23:24:53,695 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-average", elapsed time 0.000201s.
260827-23:24:55,634 nipype.workflow INFO:
[Job 60] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
260827-23:24:55,637 nipype.workflow INFO:
[Job 61] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-average).
260827-23:24:55,638 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:55,686 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260827-23:24:55,688 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".
260827-23:24:55,688 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260827-23:24:55,689 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".
260827-23:24:55,690 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260827-23:24:55,692 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260827-23:24:55,695 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.001803s.
260827-23:24:55,688 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled".
260827-23:24:55,740 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_qsm-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260827-23:24:55,742 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_qsm-resampled", elapsed time 0.001498s.
260827-23:24:57,635 nipype.workflow INFO:
[Job 62] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
260827-23:24:57,637 nipype.workflow INFO:
[Job 63] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_qsm-resampled).
260827-23:24:57,638 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:57,683 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260827-23:24:57,685 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".
260827-23:24:57,686 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260827-23:24:57,695 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
260827-23:24:57,685 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260827-23:24:57,738 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".
260827-23:24:57,738 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260827-23:24:57,741 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
260827-23:24:57,742 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.00039s.
260827-23:24:57,738 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260827-23:24:57,790 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".
260827-23:24:57,791 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced".
260827-23:24:57,805 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_qsm-referenced" <qsmxt.interfaces.nipype_interface_qsm_referencing.ReferenceQSMInterface>
260827-23:24:57,791 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260827-23:24:57,848 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".
260827-23:24:57,849 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1".
260827-23:24:57,855 nipype.workflow INFO:
[Node] Executing "combine_lists1" <nipype.interfaces.utility.wrappers.Function>
260827-23:24:57,856 nipype.workflow INFO:
[Node] Finished "combine_lists1", elapsed time 0.000427s.
260827-23:24:58,48 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.352312s.
260827-23:24:58,158 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_qsm-referenced", elapsed time 0.352556s.
260827-23:24:59,638 nipype.workflow INFO:
[Job 64] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
260827-23:24:59,639 nipype.workflow INFO:
[Job 65] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
260827-23:24:59,640 nipype.workflow INFO:
[Job 66] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_qsm-referenced).
260827-23:24:59,641 nipype.workflow INFO:
[Job 67] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists1).
260827-23:24:59,642 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:24:59,697 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260827-23:24:59,699 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".
260827-23:24:59,700 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260827-23:24:59,701 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
260827-23:24:59,703 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.000504s.
260827-23:24:59,699 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260827-23:24:59,752 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260827-23:24:59,752 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".
260827-23:24:59,755 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".
260827-23:24:59,755 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260827-23:24:59,757 nipype.workflow INFO:
[Node] Executing "create_permutations" <nipype.interfaces.utility.wrappers.Function>
260827-23:24:59,758 nipype.workflow INFO:
[Node] Finished "create_permutations", elapsed time 0.000418s.
260827-23:24:59,755 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar".
260827-23:24:59,808 nipype.workflow INFO:
[Node] Executing "copy_qsm_json_sidecar" <qsmxt.interfaces.nipype_interface_copy_json_sidecar.CopyJsonSidecarInterface>
260827-23:24:59,809 nipype.workflow INFO:
[Node] Finished "copy_qsm_json_sidecar", elapsed time 0.000484s.
260827-23:25:01,640 nipype.workflow INFO:
[Job 68] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
260827-23:25:01,641 nipype.workflow INFO:
[Job 69] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations).
260827-23:25:01,643 nipype.workflow INFO:
[Job 70] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copy_qsm_json_sidecar).
260827-23:25:01,644 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:25:03,642 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:25:03,720 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260827-23:25:03,723 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".
260827-23:25:03,723 nipype.workflow INFO:
[Node] Outdated cache found for "_nibabel_numpy_analyse-qsm0".
260827-23:25:03,724 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".
260827-23:25:03,725 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".
260827-23:25:03,725 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm0" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260827-23:25:03,726 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm2" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260827-23:25:03,726 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm3" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260827-23:25:03,723 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".
260827-23:25:03,776 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm1" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
260827-23:25:05,645 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 36.51/56.51, Free processors: 4/16.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:25:50,669 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm2", elapsed time 46.941021s.
260827-23:25:51,688 nipype.workflow INFO:
[Job 78] Completed (_nibabel_numpy_analyse-qsm2).
260827-23:25:51,690 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 38.51/56.51, Free processors: 5/16.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:26:00,116 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm0", elapsed time 56.389651s.
260827-23:26:00,492 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm1", elapsed time 56.711264s.
260827-23:26:00,510 nipype.workflow INFO:
[Node] Finished "_nibabel_numpy_analyse-qsm3", elapsed time 56.782021s.
260827-23:26:01,698 nipype.workflow INFO:
[Job 76] Completed (_nibabel_numpy_analyse-qsm0).
260827-23:26:01,699 nipype.workflow INFO:
[Job 77] Completed (_nibabel_numpy_analyse-qsm1).
260827-23:26:01,699 nipype.workflow INFO:
[Job 79] Completed (_nibabel_numpy_analyse-qsm3).
260827-23:26:01,700 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:26:01,773 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260827-23:26:01,776 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm".
260827-23:26:01,779 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".
260827-23:26:01,781 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm0" - collecting precomputed outputs
260827-23:26:01,781 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm0" found cached.
260827-23:26:01,782 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".
260827-23:26:01,783 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm1" - collecting precomputed outputs
260827-23:26:01,783 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm1" found cached.
260827-23:26:01,784 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".
260827-23:26:01,784 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm2" - collecting precomputed outputs
260827-23:26:01,785 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm2" found cached.
260827-23:26:01,785 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".
260827-23:26:01,786 nipype.workflow INFO:
[Node] Cached "_nibabel_numpy_analyse-qsm3" - collecting precomputed outputs
260827-23:26:01,787 nipype.workflow INFO:
[Node] "_nibabel_numpy_analyse-qsm3" found cached.
260827-23:26:03,700 nipype.workflow INFO:
[Job 72] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_analyse-qsm).
260827-23:26:03,702 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:26:03,752 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260827-23:26:03,754 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".
260827-23:26:03,755 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile".
260827-23:26:03,757 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
260827-23:26:03,937 nipype.workflow INFO:
[Node] Finished "copyfile", elapsed time 0.179193s.
260827-23:26:05,701 nipype.workflow INFO:
[Job 74] Completed (qsmxt-workflow.sub-1.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile).
260827-23:26:05,704 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 44.51/56.51, Free processors: 8/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1
260827-23:27:14,515 nipype.workflow INFO:
[Node] Finished "fastsurfer_segment-t1", elapsed time 296.962336s.
260827-23:27:15,762 nipype.workflow INFO:
[Job 22] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.fastsurfer_segment-t1).
260827-23:27:15,763 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260827-23:27:15,810 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260827-23:27:15,812 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".
260827-23:27:15,812 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii".
260827-23:27:15,814 nipype.workflow INFO:
[Node] Executing "numpy_numpy_nibabel_mgz2nii" <qsmxt.interfaces.nipype_interface_mgz2nii.Mgz2NiiInterface>
260827-23:27:15,997 nipype.workflow INFO:
[Node] Finished "numpy_numpy_nibabel_mgz2nii", elapsed time 0.181509s.
260827-23:27:17,764 nipype.workflow INFO:
[Job 33] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.numpy_numpy_nibabel_mgz2nii).
260827-23:27:17,765 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260827-23:27:17,808 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:27:17,810 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".
260827-23:27:17,812 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled".
260827-23:27:17,812 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260827-23:27:17,814 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".
260827-23:27:17,815 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm".
260827-23:27:17,832 nipype.workflow INFO:
[Node] Executing "ants_transform-segmentation-to-qsm" <nipype.interfaces.ants.resampling.ApplyTransforms>
260827-23:27:17,835 nipype.workflow INFO:
[Node] Executing "nibabel_numpy_nilearn_t1w-seg-resampled" <qsmxt.interfaces.nipype_interface_resample_like.ResampleLikeInterface>
260827-23:27:18,466 nipype.workflow INFO:
[Node] Finished "ants_transform-segmentation-to-qsm", elapsed time 0.633047s.
260827-23:27:19,766 nipype.workflow INFO:
[Job 43] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.ants_transform-segmentation-to-qsm).
260827-23:27:19,768 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 54.51/56.51, Free processors: 15/16.
Currently running:
* qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled
260827-23:27:19,816 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260827-23:27:19,818 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".
260827-23:27:19,818 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2".
260827-23:27:19,820 nipype.workflow INFO:
[Node] Executing "combine_lists2" <nipype.interfaces.utility.wrappers.Function>
260827-23:27:19,821 nipype.workflow INFO:
[Node] Finished "combine_lists2", elapsed time 0.000318s.
260827-23:27:20,879 nipype.workflow INFO:
[Node] Finished "nibabel_numpy_nilearn_t1w-seg-resampled", elapsed time 3.043042s.
260827-23:27:21,768 nipype.workflow INFO:
[Job 42] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.nibabel_numpy_nilearn_t1w-seg-resampled).
260827-23:27:21,769 nipype.workflow INFO:
[Job 51] Completed (qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.combine_lists2).
260827-23:27:21,770 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
260827-23:27:21,812 nipype.workflow INFO:
[Node] Outdated cache found for "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.create_permutations".
260827-23:27:21,813 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".
260827-23:27:21,814 nipype.workflow INFO:
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260827-23:27:25,821 nipype.workflow INFO:
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[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".
260827-23:27:25,822 nipype.workflow INFO:
[Node] Executing "_nibabel_numpy_analyse-qsm1" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
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[Node] Executing "_nibabel_numpy_analyse-qsm2" <qsmxt.interfaces.nipype_interface_analyse.AnalyseInterface>
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260827-23:27:27,776 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 48.51/56.51, Free processors: 12/16.
Currently running:
* _nibabel_numpy_analyse-qsm3
* _nibabel_numpy_analyse-qsm2
* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
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* _nibabel_numpy_analyse-qsm1
* _nibabel_numpy_analyse-qsm0
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Currently running:
* _nibabel_numpy_analyse-qsm0
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260827-23:28:15,878 nipype.workflow INFO:
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260827-23:28:15,884 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".
260827-23:28:15,885 nipype.workflow INFO:
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[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".
260827-23:28:15,887 nipype.workflow INFO:
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260827-23:28:15,888 nipype.workflow INFO:
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260827-23:28:15,889 nipype.workflow INFO:
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260827-23:28:15,890 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".
260827-23:28:15,891 nipype.workflow INFO:
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[Node] Setting-up "qsmxt-workflow.sub-2.ses-20170705.qsm_acq-acqqsmp21mmisote20_T2starw.copyfile" in "/home/jovyan/workspace/books/examples/quantitative_imaging/bids/derivatives/workflow/qsmxt-workflow/sub-2/ses-20170705/qsm_acq-acqqsmp21mmisote20_T2starw/copyfile".
260827-23:28:17,887 nipype.workflow INFO:
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260827-23:28:17,889 nipype.workflow INFO:
[Node] Executing "copyfile" <qsmxt.interfaces.nipype_interface_copyfile.DynamicCopyFiles>
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260827-23:28:19,829 nipype.workflow INFO:
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260827-23:28:19,831 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 56.51/56.51, Free processors: 16/16.
[INFO]: Warnings occurred!
[INFO]: Finished
View results#
Let’s have a look at the generated qsm folder:
!tree bids/derivatives/qsmxt-*-* --dirsfirst
bids/derivatives/qsmxt-2026-08-27-224935
├── 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-2026-08-27-231053
├── 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-2026-08-27-224935_Chimap_sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-08-27-224935_dseg_analysis.csv
│ │ ├── sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-08-27-224935_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-08-27-231053_dseg_analysis.csv
│ │ ├── sub-1_ses-20170705_desc-qsmxt-2026-08-27-231053_Chimap_sub-1_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-08-27-224935_dseg_analysis.csv
│ │ └── sub-1_ses-20170705_desc-qsmxt-2026-08-27-231053_Chimap_sub-1_ses-20170705_space-qsm_desc-qsmxt-2026-08-27-231053_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-2026-08-27-224935_Chimap_sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-08-27-224935_dseg_analysis.csv
│ │ ├── sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_desc-qsmxt-2026-08-27-224935_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-08-27-231053_dseg_analysis.csv
│ │ ├── sub-2_ses-20170705_desc-qsmxt-2026-08-27-231053_Chimap_sub-2_ses-20170705_acq-acqqsmp21mmisote20_T2starw_space-qsm_desc-qsmxt-2026-08-27-224935_dseg_analysis.csv
│ │ └── sub-2_ses-20170705_desc-qsmxt-2026-08-27-231053_Chimap_sub-2_ses-20170705_space-qsm_desc-qsmxt-2026-08-27-231053_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 | 593 | -0.234321 | 0.124799 | -0.018955 | -0.022252 | 0.034571 |
| 1 | 4th-Ventricle | 1541 | -0.126117 | 0.052944 | -0.045795 | -0.045746 | 0.030755 |
| 2 | Brain-Stem | 18699 | -0.279382 | 0.102235 | -0.045174 | -0.041312 | 0.028731 |
| 3 | CSF | 864 | -1.393693 | 0.945752 | 0.027255 | 0.031507 | 0.142815 |
| 4 | Left-Accumbens-area | 520 | -0.141920 | 0.128334 | 0.023897 | 0.021386 | 0.031151 |
| ... | ... | ... | ... | ... | ... | ... | ... |
| 91 | ctx-rh-superiorfrontal | 29677 | -0.133274 | 0.251870 | -0.003990 | -0.009347 | 0.024487 |
| 92 | ctx-rh-superiorparietal | 12053 | -0.084225 | 0.306628 | -0.015600 | -0.014690 | 0.022030 |
| 93 | ctx-rh-superiortemporal | 16318 | -0.090982 | 0.248737 | 0.006749 | 0.012938 | 0.024256 |
| 94 | ctx-rh-supramarginal | 12050 | -0.056940 | 0.239688 | 0.018507 | 0.019464 | 0.022786 |
| 95 | ctx-rh-transversetemporal | 1252 | -0.004825 | 0.129559 | 0.034270 | 0.035046 | 0.014374 |
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, alongside the Neurodesktop version extracted from the
JUPYTER_IMAGEorNEURODESKTOP_VERSIONenvironment variables.
import os
%load_ext watermark
%watermark
%watermark --iversions
neurodesktop_version = (
os.environ.get('JUPYTER_IMAGE', '').split(':')[-1] or
os.environ.get('NEURODESKTOP_VERSION', 'unknown')
)
print(f"Neurodesktop version: {neurodesktop_version}")
Last updated: 2026-08-27T23:28:25.335722+00:00
Python implementation: CPython
Python version : 3.13.14
IPython version : 9.12.0
Compiler : GCC 14.3.0
OS : Linux
Release : 6.8.0-111-generic
Machine : x86_64
Processor : x86_64
CPU cores : 16
Architecture: 64bit
ipyniivue : 2.4.4
json : 2.0.9
matplotlib: 3.11.0
nibabel : 5.3.3
nilearn : 0.13.1
numpy : 2.3.5
pandas : 2.3.3
seaborn : 0.13.2
Neurodesktop version: 2026-07-11