Note

Click here to download the full example code

8.4. UKB VBM GMD Extraction#

Authors: Federico Raimondo

License: BSD 3 clause

2023-07-24 05:09:09,842 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2023-07-24 05:09:09,842 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2023-07-24 05:09:09,843 - 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)
2023-07-24 05:09:09,851 - JUNIFER - INFO - Getting element sub-01
2023-07-24 05:09:09,851 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:09,851 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:09,851 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:09,852 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:09,853 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:09,853 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:09,853 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:09,853 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:09,853 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:09,853 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:09,853 - 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)
2023-07-24 05:09:10,007 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:11,396 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:12,024 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:12,024 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:12,025 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:12,025 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:12,025 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:12,025 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:12,025 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:12,029 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:13,173 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:13,788 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:13,788 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:13,788 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:13,788 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:13,789 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:13,789 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:13,789 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:13,793 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:14,988 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:15,604 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:15,604 - JUNIFER - INFO - Getting element sub-02
2023-07-24 05:09:15,604 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:15,604 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:15,604 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:15,606 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:15,606 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:15,606 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:15,606 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:15,606 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:15,606 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:15,606 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:15,610 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:16,823 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:17,423 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:17,423 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:17,424 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:17,424 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:17,424 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:17,424 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:17,424 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:17,428 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:18,621 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:19,229 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:19,229 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:19,229 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:19,229 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:19,229 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:19,229 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:19,230 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:19,233 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:20,420 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:21,044 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:21,044 - JUNIFER - INFO - Getting element sub-03
2023-07-24 05:09:21,044 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:21,045 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:21,045 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:21,046 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:21,046 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:21,046 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:21,046 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:21,046 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:21,046 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:21,047 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:21,050 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:22,266 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:22,880 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:22,880 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:22,880 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:22,880 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:22,881 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:22,881 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:22,881 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:22,885 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:24,076 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:24,694 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:24,694 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:24,695 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:24,695 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:24,695 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:24,695 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:24,695 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:24,699 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:25,894 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:26,516 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:26,517 - JUNIFER - INFO - Getting element sub-04
2023-07-24 05:09:26,517 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:26,517 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:26,517 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:26,518 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:26,518 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:26,519 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:26,519 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:26,519 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:26,519 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:26,519 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:26,523 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:27,735 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:28,342 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:28,343 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:28,343 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:28,343 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:28,343 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:28,343 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:28,343 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:28,347 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:29,525 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:30,134 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:30,134 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:30,134 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:30,134 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:30,134 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:30,135 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:30,135 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:30,138 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:31,335 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:31,949 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:31,950 - JUNIFER - INFO - Getting element sub-05
2023-07-24 05:09:31,950 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:31,950 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:31,950 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:31,952 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:31,952 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:31,953 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:31,953 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:31,953 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:31,953 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:31,953 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:31,957 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:33,192 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:33,797 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:33,797 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:33,797 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:33,797 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:33,797 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:33,797 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:33,798 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:33,801 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:34,990 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:35,605 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:35,605 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:35,605 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:35,606 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:35,606 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:35,606 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:35,606 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:35,610 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:36,826 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:37,457 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:37,458 - JUNIFER - INFO - Getting element sub-06
2023-07-24 05:09:37,458 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:37,458 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:37,458 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:37,459 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:37,459 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:37,460 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:37,460 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:37,460 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:37,460 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:37,460 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:37,464 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:38,664 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:39,257 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:39,258 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:39,258 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:39,258 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:39,258 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:39,258 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:39,258 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:39,262 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:40,404 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:41,000 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:41,000 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:41,001 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:41,001 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:41,001 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:41,001 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:41,001 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:41,005 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:42,193 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:42,808 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:42,808 - JUNIFER - INFO - Getting element sub-07
2023-07-24 05:09:42,808 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:42,809 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:42,809 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:42,811 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:42,811 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:42,811 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:42,812 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:42,812 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:42,812 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:42,812 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:42,817 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:44,042 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:44,647 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:44,648 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:44,648 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:44,648 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:44,649 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:44,649 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:44,649 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:44,655 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:45,823 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:46,436 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:46,436 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:46,436 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:46,436 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:46,436 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:46,436 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:46,437 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:46,440 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:47,628 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:48,236 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:48,237 - JUNIFER - INFO - Getting element sub-08
2023-07-24 05:09:48,237 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:48,237 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:48,237 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:48,238 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:48,238 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:48,239 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:48,239 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:48,239 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:48,239 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:48,239 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:48,242 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:49,424 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:50,022 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:50,022 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:50,023 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:50,023 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:50,023 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:50,023 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:50,023 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:50,027 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:51,171 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:51,767 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:51,767 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:51,768 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:51,768 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:51,768 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:51,768 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:51,768 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:51,771 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:52,945 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:53,557 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:53,557 - JUNIFER - INFO - Getting element sub-09
2023-07-24 05:09:53,557 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:53,557 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:53,557 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:53,559 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:53,559 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:53,559 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:53,559 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:53,559 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:53,559 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:53,559 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:53,563 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:54,779 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:55,385 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:09:55,385 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:55,386 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:55,386 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:55,386 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:55,386 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:55,387 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:55,391 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:56,553 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:57,156 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:09:57,156 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:57,156 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:57,156 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:57,156 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:57,156 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:57,156 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:57,160 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:09:58,322 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:09:58,926 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:09:58,926 - JUNIFER - INFO - Getting element sub-10
2023-07-24 05:09:58,927 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:09:58,927 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:09:58,927 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:09:58,929 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-07-24 05:09:58,929 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:09:58,930 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:09:58,930 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:09:58,930 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:09:58,930 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:09:58,930 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:09:58,934 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:00,106 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:10:00,699 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-07-24 05:10:00,699 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:00,700 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:00,700 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:00,700 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:10:00,700 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:10:00,700 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:10:00,704 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:01,884 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:10:02,497 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-07-24 05:10:02,497 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:02,497 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:02,497 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:02,498 - JUNIFER - INFO -      resolution: 2.0
2023-07-24 05:10:02,498 - JUNIFER - INFO -      n_rois: 1000
2023-07-24 05:10:02,498 - JUNIFER - INFO -      yeo_networks: 7
2023-07-24 05:10:02,501 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:03,697 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5vgn648r/test.sqlite (multiple output)>
2023-07-24 05:10:04,322 - 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 54.482 seconds)

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