Note

Click here to download the full example code

8.4. UKB VBM GMD Extraction#

Authors: Federico Raimondo

License: BSD 3 clause

2023-05-16 14:02:10,037 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2023-05-16 14:02:10,037 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2023-05-16 14:02:10,037 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
/opt/hostedtoolcache/Python/3.10.11/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)
2023-05-16 14:02:10,044 - JUNIFER - INFO - Getting element sub-01
2023-05-16 14:02:10,045 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:10,045 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:10,045 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:10,046 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:10,046 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:10,046 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:10,046 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:10,046 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:10,046 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:10,046 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:10,046 - 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)
2023-05-16 14:02:10,193 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:11,267 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:11,762 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:11,762 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:11,763 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:11,763 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:11,763 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:11,763 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:11,763 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:11,766 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:12,714 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:13,202 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:13,203 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:13,203 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:13,203 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:13,203 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:13,203 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:13,203 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:13,206 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:14,183 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:14,680 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:14,680 - JUNIFER - INFO - Getting element sub-02
2023-05-16 14:02:14,680 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:14,680 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:14,680 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:14,681 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:14,681 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:14,681 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:14,681 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:14,681 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:14,681 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:14,682 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:14,685 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:15,649 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:16,133 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:16,133 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:16,133 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:16,133 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:16,133 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:16,133 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:16,133 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:16,137 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:17,076 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:17,564 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:17,565 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:17,565 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:17,565 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:17,565 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:17,565 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:17,565 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:17,568 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:18,535 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:19,031 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:19,032 - JUNIFER - INFO - Getting element sub-03
2023-05-16 14:02:19,032 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:19,032 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:19,032 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:19,033 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:19,033 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:19,033 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:19,033 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:19,033 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:19,033 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:19,033 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:19,036 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:20,030 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:20,514 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:20,514 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:20,515 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:20,515 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:20,515 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:20,515 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:20,515 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:20,518 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:21,513 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:22,013 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:22,013 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:22,013 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:22,013 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:22,014 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:22,014 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:22,014 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:22,017 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:22,984 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:23,479 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:23,479 - JUNIFER - INFO - Getting element sub-04
2023-05-16 14:02:23,479 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:23,479 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:23,479 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:23,481 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:23,481 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:23,481 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:23,482 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:23,482 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:23,482 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:23,482 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:23,485 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:24,444 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:24,931 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:24,931 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:24,932 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:24,932 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:24,932 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:24,932 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:24,932 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:24,935 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:25,905 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:26,396 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:26,396 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:26,396 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:26,396 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:26,396 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:26,396 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:26,396 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:26,400 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:27,352 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:27,847 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:27,847 - JUNIFER - INFO - Getting element sub-05
2023-05-16 14:02:27,847 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:27,847 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:27,848 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:27,849 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:27,849 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:27,849 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:27,849 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:27,849 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:27,849 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:27,849 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:27,852 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:28,821 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:29,305 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:29,305 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:29,305 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:29,305 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:29,305 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:29,305 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:29,305 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:29,309 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:30,254 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:30,746 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:30,746 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:30,746 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:30,746 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:30,746 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:30,746 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:30,746 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:30,750 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:31,724 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:32,226 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:32,226 - JUNIFER - INFO - Getting element sub-06
2023-05-16 14:02:32,226 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:32,226 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:32,226 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:32,227 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:32,227 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:32,227 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:32,227 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:32,227 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:32,227 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:32,228 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:32,232 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:33,269 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:33,752 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:33,752 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:33,752 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:33,752 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:33,752 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:33,752 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:33,753 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:33,756 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:34,731 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:35,222 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:35,222 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:35,223 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:35,223 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:35,223 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:35,223 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:35,223 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:35,226 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:36,214 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:36,712 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:36,713 - JUNIFER - INFO - Getting element sub-07
2023-05-16 14:02:36,713 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:36,713 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:36,713 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:36,714 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:36,714 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:36,714 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:36,714 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:36,714 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:36,714 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:36,714 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:36,717 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:37,671 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:38,161 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:38,161 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:38,161 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:38,161 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:38,161 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:38,161 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:38,161 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:38,164 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:39,119 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:39,614 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:39,614 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:39,615 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:39,615 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:39,615 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:39,615 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:39,615 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:39,618 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:40,564 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:41,059 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:41,060 - JUNIFER - INFO - Getting element sub-08
2023-05-16 14:02:41,060 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:41,060 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:41,060 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:41,061 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:41,061 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:41,061 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:41,061 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:41,061 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:41,061 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:41,061 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:41,064 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:42,046 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:42,528 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:42,528 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:42,529 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:42,529 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:42,529 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:42,529 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:42,529 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:42,532 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:43,472 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:43,965 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:43,965 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:43,965 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:43,965 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:43,965 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:43,965 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:43,966 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:43,969 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:44,922 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:45,420 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:45,420 - JUNIFER - INFO - Getting element sub-09
2023-05-16 14:02:45,420 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:45,420 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:45,420 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:45,421 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:45,421 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:45,422 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:45,422 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:45,422 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:45,422 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:45,422 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:45,425 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:46,441 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:46,925 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:46,925 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:46,926 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:46,926 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:46,926 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:46,926 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:46,926 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:46,929 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:47,902 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:48,397 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:48,397 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:48,397 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:48,397 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:48,397 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:48,397 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:48,397 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:48,401 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:49,374 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:49,873 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:02:49,874 - JUNIFER - INFO - Getting element sub-10
2023-05-16 14:02:49,874 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:02:49,874 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:02:49,874 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:02:49,875 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:02:49,875 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:49,875 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:49,875 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:49,875 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:49,875 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:49,875 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:49,879 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:50,873 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:51,355 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:02:51,356 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:51,356 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:51,356 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:51,356 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:51,356 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:51,356 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:51,359 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:52,316 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:52,807 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:02:52,807 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:02:52,807 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:02:52,807 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:02:52,807 - JUNIFER - INFO -      n_rois: 1000
2023-05-16 14:02:52,808 - JUNIFER - INFO -      yeo_networks: 7
2023-05-16 14:02:52,808 - JUNIFER - INFO -      resolution: 2.0
2023-05-16 14:02:52,811 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:02:53,790 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp460li_40/test.sqlite (multiple output)>
2023-05-16 14:02:54,289 - 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 44.254 seconds)

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