Note

Go to the end to download the full example code

8.3. UKB VBM GMD Extraction#

Authors: Federico Raimondo

License: BSD 3 clause

2024-04-30 12:44:12,557 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2024-04-30 12:44:12,557 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2024-04-30 12:44:12,557 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
2024-04-30 12:44:12,557 - JUNIFER - INFO - Validating Marker Collection
2024-04-30 12:44:12,557 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-04-30 12:44:12,557 - JUNIFER - INFO - Validating Data Reader:
2024-04-30 12:44:12,557 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-04-30 12:44:12,557 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_TrimMean80
2024-04-30 12:44:12,557 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-30 12:44:12,557 - JUNIFER - INFO - Validating storage for Schaefer1000x7_TrimMean80
2024-04-30 12:44:12,557 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_Mean
2024-04-30 12:44:12,557 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-30 12:44:12,557 - JUNIFER - INFO - Validating storage for Schaefer1000x7_Mean
2024-04-30 12:44:12,558 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_Std
2024-04-30 12:44:12,558 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-30 12:44:12,558 - JUNIFER - INFO - Validating storage for Schaefer1000x7_Std

Dataset created in /home/runner/nilearn_data/oasis1

Downloading data from https://www.nitrc.org/frs/download.php/6364/archive_dartel.tgz ...

Downloaded 93601792 of 905208634 bytes (10.3%,    8.7s remaining)
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Downloaded 436232192 of 905208634 bytes (48.2%,    4.3s remaining)
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Downloaded 779575296 of 905208634 bytes (86.1%,    1.1s remaining)
Downloaded 888356864 of 905208634 bytes (98.1%,    0.2s remaining) ...done. (9 seconds, 0 min)
Extracting data from /home/runner/nilearn_data/oasis1/7088b0bf88f5650db26e32ec3afdd589/archive_dartel.tgz..... done.
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nilearn/datasets/struct.py:852: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
  warnings.warn(_LEGACY_FORMAT_MSG)
2024-04-30 12:44:27,523 - JUNIFER - INFO - Getting element sub-01
2024-04-30 12:44:27,523 - JUNIFER - INFO - Fitting pipeline
2024-04-30 12:44:27,523 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 12:44:27,523 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 12:44:27,524 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 12:44:27,524 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 12:44:27,525 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 12:44:27,525 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 12:44:27,525 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 12:44:27,525 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 12:44:27,525 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 12:44:27,525 - JUNIFER - INFO - At least one of the parcellation files are missing. Fetching using nilearn.

Dataset created in /home/runner/junifer/data/parcellations/schaefer_2018

Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_7Networks_order.txt ...
 ...done. (0 seconds, 0 min)
Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz ...
 ...done. (0 seconds, 0 min)
2024-04-30 12:44:27,769 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 12:44:27,806 - JUNIFER - INFO - Downloading xfm file for MNI152NLin6Asym to MNI152Lin from https://gin.g-node.org/juaml/human-template-xfms/raw/main/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:07:27,190 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152Lin/tpl-MNI152Lin_res-02_T1w.nii.gz

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2024-04-30 13:07:28,156 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations5f5m0s3o/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations5f5m0s3o/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpthf59d51/parcellationsgpb1vsur/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:07:35,825 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:07:36,915 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:07:37,072 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:07:37,072 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:07:37,073 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:07:37,073 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:07:37,073 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:07:37,073 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:07:37,073 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:07:37,075 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:07:37,111 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:07:38,269 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:07:38,368 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationswh6lsxgc/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationswh6lsxgc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpthf59d51/parcellations5boknqs8/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:07:45,715 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:07:46,772 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:07:46,928 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:07:46,928 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:07:46,928 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:07:46,929 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:07:46,929 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:07:46,929 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:07:46,929 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:07:46,931 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:07:46,968 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:07:48,140 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:07:48,239 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationslc_qrl8f/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationslc_qrl8f/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpthf59d51/parcellations9egv5nf2/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:07:55,470 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:07:56,592 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:07:56,749 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:07:56,750 - JUNIFER - INFO - Getting element sub-02
2024-04-30 13:07:56,750 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:07:56,750 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:07:56,750 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:07:56,751 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:07:56,751 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:07:56,752 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:07:56,752 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:07:56,752 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:07:56,752 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:07:56,752 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:07:56,754 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:07:56,790 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:07:57,938 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:07:58,037 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsb0yieyn0/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsb0yieyn0/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj1yfghc0/parcellations4a92y5dq/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:08:05,290 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:08:06,383 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:08:06,535 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:08:06,536 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:08:06,536 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:08:06,536 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:08:06,536 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:08:06,536 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:08:06,536 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:08:06,538 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:08:06,576 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:08:07,760 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:08:07,860 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations700sil4h/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations700sil4h/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj1yfghc0/parcellationsvf4kx67n/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:08:15,114 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:08:16,163 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:08:16,319 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:08:16,319 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:08:16,320 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:08:16,320 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:08:16,320 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:08:16,320 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:08:16,320 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:08:16,322 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:08:16,358 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:08:17,523 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:08:17,622 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsbq0wgbdj/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsbq0wgbdj/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj1yfghc0/parcellations8sa_g12p/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:08:24,896 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:08:25,965 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:08:26,124 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:08:26,125 - JUNIFER - INFO - Getting element sub-03
2024-04-30 13:08:26,125 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:08:26,125 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:08:26,125 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:08:26,126 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:08:26,126 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:08:26,126 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:08:26,127 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:08:26,127 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:08:26,127 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:08:26,127 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:08:26,129 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:08:26,165 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:08:27,336 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:08:27,436 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsfna_u_5z/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsfna_u_5z/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp13ty0dcs/parcellationstqdbfuxv/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:08:34,687 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:08:35,827 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:08:35,987 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:08:35,988 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:08:35,988 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:08:35,988 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:08:35,988 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:08:35,988 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:08:35,988 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:08:35,990 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:08:36,027 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:08:37,212 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:08:37,311 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsrnu3w3dx/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsrnu3w3dx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp13ty0dcs/parcellationsp5g95hdx/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:08:44,603 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:08:45,670 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:08:45,827 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:08:45,827 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:08:45,827 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:08:45,828 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:08:45,828 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:08:45,828 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:08:45,828 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:08:45,830 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:08:45,869 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:08:47,024 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:08:47,123 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations7d6x9qp6/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations7d6x9qp6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp13ty0dcs/parcellationse2m6z4p6/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:08:54,360 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:08:55,454 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:08:55,616 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:08:55,617 - JUNIFER - INFO - Getting element sub-04
2024-04-30 13:08:55,617 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:08:55,617 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:08:55,617 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:08:55,618 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:08:55,618 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:08:55,618 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:08:55,618 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:08:55,618 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:08:55,618 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:08:55,618 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:08:55,620 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:08:55,657 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:08:56,856 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:08:56,955 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsssq1e510/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsssq1e510/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpdcztok4r/parcellationszwwfk6dd/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:09:04,379 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:09:05,488 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:09:05,638 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:09:05,638 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:09:05,639 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:09:05,639 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:09:05,639 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:09:05,639 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:09:05,639 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:09:05,641 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:09:05,678 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:09:06,862 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:09:06,962 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations5bbzpgl5/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations5bbzpgl5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpdcztok4r/parcellationsqdtolb4c/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:09:14,226 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:09:15,282 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:09:15,440 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:09:15,440 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:09:15,440 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:09:15,440 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:09:15,440 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:09:15,440 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:09:15,440 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:09:15,442 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:09:15,480 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:09:16,653 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:09:16,752 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations2npss_5h/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations2npss_5h/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpdcztok4r/parcellations4qfk6zkr/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:09:24,127 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:09:25,192 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:09:25,350 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:09:25,351 - JUNIFER - INFO - Getting element sub-05
2024-04-30 13:09:25,351 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:09:25,351 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:09:25,351 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:09:25,352 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:09:25,352 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:09:25,352 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:09:25,352 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:09:25,352 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:09:25,352 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:09:25,352 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:09:25,354 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:09:25,390 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:09:26,551 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:09:26,650 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations200gvlxp/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations200gvlxp/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp4lgsi7a9/parcellationsb5f0cu0z/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:09:33,901 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:09:35,040 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:09:35,193 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:09:35,194 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:09:35,194 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:09:35,194 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:09:35,194 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:09:35,194 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:09:35,194 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:09:35,196 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:09:35,234 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:09:36,400 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:09:36,500 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsz7_r2huc/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsz7_r2huc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp4lgsi7a9/parcellations1ex__l1e/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:09:43,794 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:09:44,851 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:09:45,006 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:09:45,006 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:09:45,007 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:09:45,007 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:09:45,007 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:09:45,007 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:09:45,007 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:09:45,009 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:09:45,046 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:09:46,214 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:09:46,313 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsdwdo0d2p/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsdwdo0d2p/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp4lgsi7a9/parcellationsuza8l4r5/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:09:53,547 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:09:54,622 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:09:54,782 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:09:54,783 - JUNIFER - INFO - Getting element sub-06
2024-04-30 13:09:54,783 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:09:54,783 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:09:54,783 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:09:54,784 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:09:54,784 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:09:54,784 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:09:54,784 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:09:54,784 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:09:54,784 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:09:54,784 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:09:54,786 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:09:54,823 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:09:56,011 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:09:56,111 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationso2ar1gx6/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationso2ar1gx6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzi3on885/parcellations9gqd67t8/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:10:03,473 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:10:04,566 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:10:04,719 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:10:04,719 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:10:04,720 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:10:04,720 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:10:04,720 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:10:04,720 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:10:04,720 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:10:04,722 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:10:04,761 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:10:05,938 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:10:06,038 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsio0rdihw/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsio0rdihw/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzi3on885/parcellationspgxkvvuo/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:10:13,196 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:10:14,265 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:10:14,424 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:10:14,424 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:10:14,424 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:10:14,424 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:10:14,424 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:10:14,424 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:10:14,424 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:10:14,427 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:10:14,465 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:10:15,648 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:10:15,747 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationszw8t4mg_/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationszw8t4mg_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzi3on885/parcellations9lnj5uf5/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:10:23,055 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:10:24,159 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:10:24,316 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:10:24,317 - JUNIFER - INFO - Getting element sub-07
2024-04-30 13:10:24,317 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:10:24,317 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:10:24,317 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:10:24,318 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:10:24,318 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:10:24,319 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:10:24,319 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:10:24,319 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:10:24,319 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:10:24,319 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:10:24,321 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:10:24,356 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:10:25,525 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:10:25,624 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsgekfifsq/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsgekfifsq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp_h7d1y2z/parcellationsl7pqru7s/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:10:32,894 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:10:33,984 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:10:34,138 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:10:34,138 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:10:34,138 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:10:34,138 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:10:34,138 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:10:34,138 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:10:34,138 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:10:34,140 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:10:34,177 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:10:35,355 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:10:35,454 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations4oz7olnr/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations4oz7olnr/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp_h7d1y2z/parcellationsrglzj79r/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:10:42,835 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:10:43,939 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:10:44,096 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:10:44,096 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:10:44,097 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:10:44,097 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:10:44,097 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:10:44,097 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:10:44,097 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:10:44,099 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:10:44,136 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:10:45,297 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:10:45,396 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations5dqngpg7/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations5dqngpg7/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp_h7d1y2z/parcellationsqk1esn5o/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:10:52,671 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:10:53,763 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:10:53,921 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:10:53,922 - JUNIFER - INFO - Getting element sub-08
2024-04-30 13:10:53,922 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:10:53,922 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:10:53,922 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:10:53,923 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:10:53,923 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:10:53,923 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:10:53,923 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:10:53,923 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:10:53,923 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:10:53,923 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:10:53,925 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:10:53,962 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:10:55,147 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:10:55,247 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations_i2po1as/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations_i2po1as/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmppr4ygi3k/parcellations92ph4v56/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:11:02,449 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:11:03,531 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:11:03,682 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:11:03,683 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:11:03,683 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:11:03,683 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:11:03,683 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:11:03,683 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:11:03,683 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:11:03,685 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:11:03,722 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:11:04,916 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:11:05,015 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsc1ntdexi/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsc1ntdexi/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmppr4ygi3k/parcellationsgz1ize72/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:11:12,296 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:11:13,363 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:11:13,518 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:11:13,518 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:11:13,518 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:11:13,518 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:11:13,518 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:11:13,518 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:11:13,518 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:11:13,520 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:11:13,558 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:11:14,730 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:11:14,829 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations0tb96dv8/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations0tb96dv8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmppr4ygi3k/parcellationsiy59x_q_/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:11:22,170 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:11:23,290 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:11:23,448 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:11:23,448 - JUNIFER - INFO - Getting element sub-09
2024-04-30 13:11:23,448 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:11:23,448 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:11:23,449 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:11:23,449 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:11:23,449 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:11:23,450 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:11:23,450 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:11:23,450 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:11:23,450 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:11:23,450 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:11:23,452 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:11:23,488 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:11:24,668 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:11:24,767 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsv8no217_/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationsv8no217_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj43528ce/parcellationsdpvbzv_t/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:11:32,026 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:11:33,154 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:11:33,305 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:11:33,305 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:11:33,306 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:11:33,306 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:11:33,306 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:11:33,306 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:11:33,306 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:11:33,308 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:11:33,339 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:11:34,513 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:11:34,613 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationseedqi3qx/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellationseedqi3qx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj43528ce/parcellations9hy0ugh4/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:11:41,848 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:11:42,939 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:11:43,095 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:11:43,095 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:11:43,096 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:11:43,096 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:11:43,096 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:11:43,096 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:11:43,096 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:11:43,098 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:11:43,129 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:11:44,313 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:11:44,413 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations4pxllav7/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations4pxllav7/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj43528ce/parcellationsiev0h6c1/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:11:51,713 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:11:52,795 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:11:52,953 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:11:52,953 - JUNIFER - INFO - Getting element sub-10
2024-04-30 13:11:52,953 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:11:52,953 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:11:52,953 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:11:52,954 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-30 13:11:52,954 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:11:52,955 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:11:52,955 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:11:52,955 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:11:52,955 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:11:52,955 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:11:52,957 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:11:52,988 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:11:54,191 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:11:54,290 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations83ritq4t/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations83ritq4t/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2w5b6__a/parcellationszigo3fsj/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:12:01,576 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:12:02,665 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:12:02,816 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-30 13:12:02,816 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:12:02,816 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:12:02,817 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:12:02,817 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:12:02,817 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:12:02,817 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:12:02,819 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:12:02,850 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:12:04,017 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:12:04,118 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations_5se05em/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations_5se05em/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2w5b6__a/parcellationsf62nx8js/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:12:11,295 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:12:12,364 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:12:12,520 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-30 13:12:12,520 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:12:12,520 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:12:12,520 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:12:12,520 - JUNIFER - INFO -      resolution: 2.0
2024-04-30 13:12:12,520 - JUNIFER - INFO -      n_rois: 1000
2024-04-30 13:12:12,520 - JUNIFER - INFO -      yeo_networks: 7
2024-04-30 13:12:12,522 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:12:12,554 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:12:13,733 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:12:13,831 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations3bn7uprq/Schaefer1000x7.nii.gz -r /tmp/tmp1q1papv3/parcellations3bn7uprq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2w5b6__a/parcellationsrcuik2ti/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:12:21,106 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:12:22,170 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpf98ycw3o/test.sqlite (multiple output)>
2024-04-30 13:12:22,330 - JUNIFER - INFO - Marker collection fitting done


import tempfile

import junifer.testing.registry  # noqa: F401
from junifer.api import run


datagrabber = {
    "kind": "OasisVBMTestingDataGrabber",
}

markers = [
    {
        "name": "Schaefer1000x7_TrimMean80",
        "kind": "ParcelAggregation",
        "parcellation": "Schaefer1000x7",
        "method": "trim_mean",
        "method_params": {"proportiontocut": 0.2},
    },
    {
        "name": "Schaefer1000x7_Mean",
        "kind": "ParcelAggregation",
        "parcellation": "Schaefer1000x7",
        "method": "mean",
    },
    {
        "name": "Schaefer1000x7_Std",
        "kind": "ParcelAggregation",
        "parcellation": "Schaefer1000x7",
        "method": "std",
    },
]

storage = {
    "kind": "SQLiteFeatureStorage",
}

with tempfile.TemporaryDirectory() as tmpdir:
    uri = f"{tmpdir}/test.sqlite"
    storage["uri"] = uri
    run(
        workdir="/tmp",
        datagrabber=datagrabber,
        markers=markers,
        storage=storage,
    )

Total running time of the script: (28 minutes 9.776 seconds)

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