8.3. UKB VBM GMD Extraction

Authors: Federico Raimondo

License: BSD 3 clause

2024-02-09 10:11:05,105 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2024-02-09 10:11:05,106 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2024-02-09 10:11:05,106 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber

Dataset created in /home/runner/nilearn_data/oasis1

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

Downloaded 204996608 of 905208634 bytes (22.6%,    3.4s remaining)
Downloaded 423280640 of 905208634 bytes (46.8%,    2.3s remaining)
Downloaded 631185408 of 905208634 bytes (69.7%,    1.3s remaining)
Downloaded 850796544 of 905208634 bytes (94.0%,    0.3s remaining) ...done. (5 seconds, 0 min)
Extracting data from /home/runner/nilearn_data/oasis1/7088b0bf88f5650db26e32ec3afdd589/archive_dartel.tgz..... done.
/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)
2024-02-09 10:11:16,179 - JUNIFER - INFO - Getting element sub-01
2024-02-09 10:11:16,179 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:16,179 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:16,179 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:16,180 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:16,180 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:16,181 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:16,181 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:16,181 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:16,181 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:16,181 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:16,181 - 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)
2024-02-09 10:11:16,244 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:17,077 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:17,287 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:17,288 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:17,288 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:17,288 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:17,288 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:17,288 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:17,288 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:17,291 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:18,087 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:18,284 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:18,285 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:18,285 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:18,285 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:18,285 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:18,285 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:18,285 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:18,288 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:19,129 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:19,328 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:19,328 - JUNIFER - INFO - Getting element sub-02
2024-02-09 10:11:19,328 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:19,328 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:19,328 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:19,329 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:19,329 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:19,329 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:19,329 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:19,329 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:19,329 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:19,329 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:19,332 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:20,169 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:20,366 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:20,366 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:20,366 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:20,366 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:20,366 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:20,366 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:20,366 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:20,368 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:21,202 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:21,399 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:21,399 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:21,400 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:21,400 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:21,400 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:21,400 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:21,400 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:21,402 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:22,325 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:22,523 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:22,524 - JUNIFER - INFO - Getting element sub-03
2024-02-09 10:11:22,524 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:22,524 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:22,524 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:22,525 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:22,525 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:22,525 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:22,525 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:22,525 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:22,525 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:22,525 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:22,528 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:23,408 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:23,600 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:23,600 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:23,600 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:23,601 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:23,601 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:23,601 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:23,601 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:23,603 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:24,435 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:24,629 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:24,629 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:24,629 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:24,629 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:24,629 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:24,629 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:24,629 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:24,632 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:25,497 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:25,693 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:25,693 - JUNIFER - INFO - Getting element sub-04
2024-02-09 10:11:25,693 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:25,693 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:25,694 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:25,694 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:25,695 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:25,695 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:25,695 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:25,695 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:25,695 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:25,695 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:25,697 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:26,567 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:26,762 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:26,762 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:26,762 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:26,763 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:26,763 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:26,763 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:26,763 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:26,765 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:27,652 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:27,854 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:27,854 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:27,854 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:27,855 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:27,855 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:27,855 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:27,855 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:27,857 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:28,817 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:29,016 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:29,016 - JUNIFER - INFO - Getting element sub-05
2024-02-09 10:11:29,017 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:29,017 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:29,017 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:29,018 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:29,018 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:29,018 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:29,018 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:29,018 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:29,018 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:29,018 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:29,021 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:29,951 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:30,144 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:30,145 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:30,145 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:30,145 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:30,145 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:30,145 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:30,145 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:30,148 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:31,002 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:31,197 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:31,197 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:31,198 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:31,198 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:31,198 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:31,198 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:31,198 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:31,200 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:32,039 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:32,237 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:32,237 - JUNIFER - INFO - Getting element sub-06
2024-02-09 10:11:32,237 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:32,237 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:32,237 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:32,238 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:32,238 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:32,238 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:32,238 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:32,238 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:32,238 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:32,239 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:32,241 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:33,097 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:33,288 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:33,288 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:33,288 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:33,288 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:33,288 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:33,288 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:33,288 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:33,291 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:34,141 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:34,335 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:34,335 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:34,336 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:34,336 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:34,336 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:34,336 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:34,336 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:34,338 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:35,205 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:35,404 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:35,404 - JUNIFER - INFO - Getting element sub-07
2024-02-09 10:11:35,404 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:35,405 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:35,405 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:35,406 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:35,406 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:35,406 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:35,406 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:35,406 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:35,406 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:35,406 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:35,408 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:36,280 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:36,469 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:36,469 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:36,470 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:36,470 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:36,470 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:36,470 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:36,470 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:36,472 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:37,316 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:37,510 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:37,511 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:37,511 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:37,511 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:37,511 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:37,511 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:37,511 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:37,513 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:38,366 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:38,565 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:38,566 - JUNIFER - INFO - Getting element sub-08
2024-02-09 10:11:38,566 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:38,566 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:38,566 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:38,567 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:38,567 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:38,567 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:38,567 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:38,567 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:38,567 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:38,567 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:38,570 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:39,485 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:39,677 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:39,678 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:39,678 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:39,678 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:39,678 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:39,678 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:39,678 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:39,680 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:40,570 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:40,766 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:40,766 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:40,767 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:40,767 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:40,767 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:40,767 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:40,767 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:40,769 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:41,683 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:41,882 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:41,882 - JUNIFER - INFO - Getting element sub-09
2024-02-09 10:11:41,883 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:41,883 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:41,883 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:41,884 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:41,884 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:41,884 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:41,884 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:41,884 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:41,884 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:41,884 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:41,886 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:42,851 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:43,042 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:43,042 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:43,042 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:43,042 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:43,042 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:43,042 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:43,042 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:43,045 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:43,900 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:44,093 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:44,093 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:44,094 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:44,094 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:44,094 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:44,094 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:44,094 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:44,096 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:44,935 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:45,144 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:11:45,144 - JUNIFER - INFO - Getting element sub-10
2024-02-09 10:11:45,144 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:11:45,144 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:11:45,144 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:11:45,146 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:11:45,146 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:45,146 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:45,146 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:45,146 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:45,146 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:45,146 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:45,148 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:45,994 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:47,903 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:11:47,903 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:47,903 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:47,903 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:47,903 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:47,903 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:47,903 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:47,905 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:48,733 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:48,929 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:11:48,929 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:11:48,929 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:11:48,930 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:11:48,930 - JUNIFER - INFO -      resolution: 2.0
2024-02-09 10:11:48,930 - JUNIFER - INFO -      n_rois: 1000
2024-02-09 10:11:48,930 - JUNIFER - INFO -      yeo_networks: 7
2024-02-09 10:11:48,932 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:11:49,771 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpdxrqyk2e/test.sqlite (multiple output)>
2024-02-09 10:11:49,970 - 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,
    )