Note

Click here to download the full example code

8.4. UKB VBM GMD Extraction#

Authors: Federico Raimondo

License: BSD 3 clause

2023-09-06 09:38:05,826 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2023-09-06 09:38:05,826 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2023-09-06 09:38:05,826 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:733: 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)
2023-09-06 09:38:05,834 - JUNIFER - INFO - Getting element sub-01
2023-09-06 09:38:05,834 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:05,834 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:05,834 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:05,835 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:05,835 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:05,835 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:05,835 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:05,835 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:05,835 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:05,835 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:05,835 - 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)
2023-09-06 09:38:05,985 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:07,030 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:07,522 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:07,523 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:07,523 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:07,523 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:07,523 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:07,523 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:07,523 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:07,527 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:08,487 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:08,975 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:08,975 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:08,975 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:08,975 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:08,976 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:08,976 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:08,976 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:08,979 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:09,957 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:10,449 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:10,449 - JUNIFER - INFO - Getting element sub-02
2023-09-06 09:38:10,449 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:10,449 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:10,449 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:10,450 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:10,450 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:10,450 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:10,450 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:10,451 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:10,451 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:10,451 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:10,454 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:11,490 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:11,969 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:11,970 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:11,970 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:11,970 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:11,970 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:11,970 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:11,970 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:11,973 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:13,031 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:13,517 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:13,517 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:13,518 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:13,518 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:13,518 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:13,518 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:13,518 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:13,521 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:14,502 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:14,993 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:14,993 - JUNIFER - INFO - Getting element sub-03
2023-09-06 09:38:14,993 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:14,993 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:14,993 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:14,994 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:14,994 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:14,995 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:14,995 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:14,995 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:14,995 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:14,995 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:14,998 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:16,016 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:16,494 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:16,494 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:16,495 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:16,495 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:16,495 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:16,495 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:16,495 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:16,498 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:17,436 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:17,927 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:17,927 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:17,927 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:17,927 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:17,928 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:17,928 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:17,928 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:17,931 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:18,926 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:19,417 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:19,417 - JUNIFER - INFO - Getting element sub-04
2023-09-06 09:38:19,417 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:19,417 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:19,417 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:19,418 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:19,418 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:19,418 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:19,419 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:19,419 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:19,419 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:19,419 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:19,422 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:20,398 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:20,874 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:20,875 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:20,875 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:20,875 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:20,875 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:20,875 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:20,875 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:20,878 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:21,821 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:22,310 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:22,310 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:22,311 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:22,311 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:22,311 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:22,311 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:22,311 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:22,314 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:23,306 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:23,802 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:23,802 - JUNIFER - INFO - Getting element sub-05
2023-09-06 09:38:23,802 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:23,802 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:23,802 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:23,803 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:23,804 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:23,804 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:23,804 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:23,804 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:23,804 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:23,804 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:23,807 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:24,780 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:25,259 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:25,259 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:25,260 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:25,260 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:25,260 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:25,260 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:25,260 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:25,263 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:26,209 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:26,698 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:26,698 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:26,698 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:26,698 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:26,698 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:26,698 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:26,698 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:26,702 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:27,658 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:28,149 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:28,149 - JUNIFER - INFO - Getting element sub-06
2023-09-06 09:38:28,149 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:28,149 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:28,149 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:28,150 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:28,150 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:28,151 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:28,151 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:28,151 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:28,151 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:28,151 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:28,154 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:29,143 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:29,619 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:29,619 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:29,620 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:29,620 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:29,620 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:29,620 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:29,620 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:29,623 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:30,550 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:31,037 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:31,037 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:31,037 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:31,037 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:31,038 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:31,038 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:31,038 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:31,041 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:31,991 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:32,484 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:32,484 - JUNIFER - INFO - Getting element sub-07
2023-09-06 09:38:32,485 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:32,485 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:32,485 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:32,486 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:32,486 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:32,486 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:32,486 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:32,486 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:32,486 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:32,486 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:32,489 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:33,459 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:33,940 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:33,940 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:33,940 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:33,940 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:33,940 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:33,940 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:33,941 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:33,944 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:34,918 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:35,406 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:35,406 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:35,407 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:35,407 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:35,407 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:35,407 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:35,407 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:35,410 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:36,383 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:36,873 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:36,874 - JUNIFER - INFO - Getting element sub-08
2023-09-06 09:38:36,874 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:36,874 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:36,874 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:36,875 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:36,875 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:36,875 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:36,875 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:36,875 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:36,875 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:36,875 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:36,878 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:37,842 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:38,319 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:38,320 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:38,320 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:38,320 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:38,320 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:38,320 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:38,320 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:38,323 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:39,278 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:39,764 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:39,765 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:39,765 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:39,765 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:39,765 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:39,765 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:39,765 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:39,768 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:40,733 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:41,224 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:41,224 - JUNIFER - INFO - Getting element sub-09
2023-09-06 09:38:41,225 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:41,225 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:41,225 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:41,226 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:41,226 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:41,226 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:41,226 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:41,226 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:41,227 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:41,227 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:41,230 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:42,233 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:42,715 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:42,715 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:42,715 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:42,715 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:42,716 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:42,716 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:42,716 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:42,719 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:43,678 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:44,173 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:44,173 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:44,174 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:44,174 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:44,174 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:44,174 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:44,174 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:44,177 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:45,183 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:45,675 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:45,676 - JUNIFER - INFO - Getting element sub-10
2023-09-06 09:38:45,676 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:45,676 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:45,676 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:45,677 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-09-06 09:38:45,677 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:45,677 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:45,677 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:45,677 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:45,677 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:45,678 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:45,681 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:46,659 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:47,139 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-09-06 09:38:47,139 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:47,139 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:47,139 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:47,139 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:47,139 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:47,139 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:47,142 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:48,085 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:48,577 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-09-06 09:38:48,578 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:48,578 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:48,578 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:48,578 - JUNIFER - INFO -      resolution: 2.0
2023-09-06 09:38:48,578 - JUNIFER - INFO -      n_rois: 1000
2023-09-06 09:38:48,578 - JUNIFER - INFO -      yeo_networks: 7
2023-09-06 09:38:48,581 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:49,560 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmppqbygzum/test.sqlite (multiple output)>
2023-09-06 09:38:50,053 - 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 44.229 seconds)

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