Note

Go to the end to download the full example code

8.4. UKB VBM GMD Extraction#

Authors: Federico Raimondo

License: BSD 3 clause

2023-10-17 10:31:29,282 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2023-10-17 10:31:29,283 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2023-10-17 10:31:29,283 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/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)
2023-10-17 10:31:29,291 - JUNIFER - INFO - Getting element sub-01
2023-10-17 10:31:29,291 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:29,291 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:29,291 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:29,292 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:29,292 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:29,292 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:29,292 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:29,292 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:29,292 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:29,292 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:29,293 - JUNIFER - INFO - At least one of the parcellation files are missing. Fetching using nilearn.
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)
2023-10-17 10:31:29,447 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:30,503 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:30,833 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:30,834 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:30,834 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:30,834 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:30,834 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:30,834 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:30,834 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:30,838 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:31,868 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:32,118 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:32,119 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:32,119 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:32,119 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:32,119 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:32,119 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:32,119 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:32,122 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:33,165 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:33,415 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:33,415 - JUNIFER - INFO - Getting element sub-02
2023-10-17 10:31:33,416 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:33,416 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:33,416 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:33,417 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:33,417 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:33,417 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:33,417 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:33,417 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:33,417 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:33,417 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:33,421 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:34,472 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:34,716 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:34,717 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:34,717 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:34,717 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:34,717 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:34,717 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:34,717 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:34,721 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:35,756 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:36,006 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:36,006 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:36,006 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:36,006 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:36,007 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:36,007 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:36,007 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:36,010 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:37,067 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:37,324 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:37,324 - JUNIFER - INFO - Getting element sub-03
2023-10-17 10:31:37,325 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:37,325 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:37,325 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:37,326 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:37,326 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:37,326 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:37,326 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:37,326 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:37,326 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:37,326 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:37,330 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:38,388 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:38,633 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:38,633 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:38,634 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:38,634 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:38,634 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:38,634 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:38,634 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:38,638 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:39,672 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:39,917 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:39,918 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:39,918 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:39,918 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:39,918 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:39,918 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:39,918 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:39,921 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:40,986 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:41,239 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:41,240 - JUNIFER - INFO - Getting element sub-04
2023-10-17 10:31:41,240 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:41,240 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:41,240 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:41,241 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:41,241 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:41,241 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:41,241 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:41,242 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:41,242 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:41,242 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:41,245 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:42,329 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:42,574 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:42,575 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:42,575 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:42,575 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:42,575 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:42,575 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:42,575 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:42,579 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:43,665 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:44,700 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:44,700 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:44,701 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:44,701 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:44,701 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:44,701 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:44,701 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:44,704 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:45,737 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:45,990 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:45,990 - JUNIFER - INFO - Getting element sub-05
2023-10-17 10:31:45,990 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:45,990 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:45,990 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:45,991 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:45,991 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:45,992 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:45,992 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:45,992 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:45,992 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:45,992 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:45,995 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:47,095 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:47,335 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:47,335 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:47,336 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:47,336 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:47,336 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:47,336 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:47,336 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:47,339 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:48,425 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:48,675 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:48,675 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:48,675 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:48,675 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:48,675 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:48,675 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:48,675 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:48,679 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:49,756 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:50,009 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:50,009 - JUNIFER - INFO - Getting element sub-06
2023-10-17 10:31:50,009 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:50,009 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:50,009 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:50,011 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:50,011 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:50,011 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:50,011 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:50,011 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:50,011 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:50,011 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:50,014 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:51,123 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:51,363 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:51,363 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:51,364 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:51,364 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:51,364 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:51,364 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:51,364 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:51,367 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:52,500 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:52,745 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:52,745 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:52,745 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:52,745 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:52,745 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:52,745 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:52,745 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:52,749 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:53,884 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:54,138 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:54,138 - JUNIFER - INFO - Getting element sub-07
2023-10-17 10:31:54,138 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:54,138 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:54,138 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:54,139 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:54,140 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:54,140 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:54,140 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:54,140 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:54,140 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:54,140 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:54,143 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:55,269 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:55,514 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:55,514 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:55,514 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:55,514 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:55,515 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:55,515 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:55,515 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:55,518 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:56,577 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:56,826 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:31:56,826 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:56,826 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:56,826 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:56,826 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:56,827 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:56,827 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:56,830 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:57,960 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:58,221 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:31:58,221 - JUNIFER - INFO - Getting element sub-08
2023-10-17 10:31:58,222 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:31:58,222 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:31:58,222 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:31:58,223 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:31:58,223 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:58,223 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:58,223 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:58,223 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:58,224 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:58,224 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:58,227 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:31:59,337 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:31:59,583 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:31:59,584 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:31:59,584 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:31:59,584 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:31:59,584 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:31:59,584 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:31:59,584 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:31:59,588 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:00,729 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:00,979 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:32:00,979 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:00,979 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:00,979 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:00,979 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:00,979 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:00,979 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:00,983 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:02,138 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:02,388 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:32:02,388 - JUNIFER - INFO - Getting element sub-09
2023-10-17 10:32:02,388 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:32:02,388 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:32:02,388 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:32:02,390 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:32:02,390 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:02,390 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:02,390 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:02,390 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:02,390 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:02,390 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:02,393 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:03,583 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:03,825 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:32:03,826 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:03,826 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:03,826 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:03,826 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:03,826 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:03,826 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:03,830 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:05,008 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:05,256 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:32:05,256 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:05,257 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:05,257 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:05,257 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:05,257 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:05,257 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:05,260 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:06,398 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:06,651 - JUNIFER - INFO - Marker collection fitting done
2023-10-17 10:32:06,652 - JUNIFER - INFO - Getting element sub-10
2023-10-17 10:32:06,652 - JUNIFER - INFO - Fitting pipeline
2023-10-17 10:32:06,652 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-10-17 10:32:06,652 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-10-17 10:32:06,654 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-10-17 10:32:06,654 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:06,654 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:06,654 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:06,654 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:06,654 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:06,654 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:06,657 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:07,792 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:08,037 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-10-17 10:32:08,037 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:08,038 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:08,038 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:08,038 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:08,038 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:08,038 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:08,042 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:09,168 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:09,414 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-10-17 10:32:09,414 - JUNIFER - INFO - Computing VBM_GM
2023-10-17 10:32:09,415 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-10-17 10:32:09,415 - JUNIFER - INFO - Parcellation parameters:
2023-10-17 10:32:09,415 - JUNIFER - INFO -      resolution: 2.0
2023-10-17 10:32:09,415 - JUNIFER - INFO -      n_rois: 1000
2023-10-17 10:32:09,415 - JUNIFER - INFO -      yeo_networks: 7
2023-10-17 10:32:09,418 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-10-17 10:32:10,554 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpal82r104/test.sqlite (multiple output)>
2023-10-17 10:32:10,804 - 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: (0 minutes 41.524 seconds)

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