Note
Go to the end to download the full example code
8.3. UKB VBM GMD Extraction#
Authors: Federico Raimondo
License: BSD 3 clause
2024-02-09 10:27:00,199 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2024-02-09 10:27:00,199 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2024-02-09 10:27:00,199 - 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 235626496 of 905208634 bytes (26.0%, 2.8s remaining)
Downloaded 471269376 of 905208634 bytes (52.1%, 1.8s remaining)
Downloaded 706445312 of 905208634 bytes (78.0%, 0.8s remaining) ...done. (4 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 10:27:10,928 - JUNIFER - INFO - Getting element sub-01
2024-02-09 10:27:10,928 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:10,928 - 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 10:27:10,928 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:10,929 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:10,929 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:10,929 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:10,929 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:10,929 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:10,929 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:10,929 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:10,930 - 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 10:27:10,991 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:11,859 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:12,079 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:12,080 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:12,080 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:12,080 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:12,080 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:12,080 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:12,080 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:12,083 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:12,975 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:13,181 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:13,181 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:13,181 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:13,181 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:13,181 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:13,181 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:13,181 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:13,184 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:14,088 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:14,291 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:14,291 - JUNIFER - INFO - Getting element sub-02
2024-02-09 10:27:14,291 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:14,291 - 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 10:27:14,291 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:14,292 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:14,292 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:14,292 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:14,292 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:14,292 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:14,293 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:14,293 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:14,295 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:15,180 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:15,443 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:15,443 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:15,443 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:15,443 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:15,443 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:15,443 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:15,443 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:15,446 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:16,342 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:16,545 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:16,546 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:16,546 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:16,546 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:16,546 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:16,546 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:16,546 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:16,548 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:17,443 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:17,645 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:17,646 - JUNIFER - INFO - Getting element sub-03
2024-02-09 10:27:17,646 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:17,646 - 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 10:27:17,646 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:17,647 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:17,647 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:17,647 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:17,647 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:17,647 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:17,647 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:17,647 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:17,650 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:18,554 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:18,752 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:18,753 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:18,753 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:18,753 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:18,753 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:18,753 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:18,753 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:18,756 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:19,676 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:19,877 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:19,877 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:19,878 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:19,878 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:19,878 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:19,878 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:19,878 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:19,880 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:20,750 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:20,952 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:20,952 - JUNIFER - INFO - Getting element sub-04
2024-02-09 10:27:20,952 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:20,952 - 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 10:27:20,952 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:20,953 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:20,953 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:20,954 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:20,954 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:20,954 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:20,954 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:20,954 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:20,956 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:21,862 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:22,065 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:22,065 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:22,065 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:22,065 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:22,065 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:22,066 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:22,066 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:22,068 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:22,957 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:23,155 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:23,155 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:23,156 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:23,156 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:23,156 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:23,156 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:23,156 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:23,158 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:24,025 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:24,228 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:24,228 - JUNIFER - INFO - Getting element sub-05
2024-02-09 10:27:24,228 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:24,228 - 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 10:27:24,228 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:24,229 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:24,230 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:24,230 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:24,230 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:24,230 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:24,230 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:24,230 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:24,232 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:25,167 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:25,363 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:25,363 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:25,363 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:25,363 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:25,363 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:25,364 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:25,364 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:25,366 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:26,235 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:26,434 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:26,434 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:26,434 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:26,434 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:26,434 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:26,434 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:26,434 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:26,437 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:27,327 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:27,532 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:27,533 - JUNIFER - INFO - Getting element sub-06
2024-02-09 10:27:27,533 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:27,533 - 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 10:27:27,533 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:27,534 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:27,534 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:27,534 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:27,534 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:27,534 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:27,534 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:27,534 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:27,537 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:28,424 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:28,617 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:28,617 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:28,618 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:28,618 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:28,618 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:28,618 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:28,618 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:28,620 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:29,463 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:29,664 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:29,665 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:29,665 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:29,665 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:29,665 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:29,665 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:29,665 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:29,667 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:30,513 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:30,718 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:30,718 - JUNIFER - INFO - Getting element sub-07
2024-02-09 10:27:30,718 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:30,718 - 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 10:27:30,718 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:30,719 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:30,719 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:30,720 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:30,720 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:30,720 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:30,720 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:30,720 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:30,722 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:31,636 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:31,832 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:31,832 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:31,832 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:31,832 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:31,832 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:31,832 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:31,832 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:31,835 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:32,717 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:32,914 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:32,914 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:32,914 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:32,914 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:32,915 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:32,915 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:32,915 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:32,917 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:33,773 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:33,978 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:33,978 - JUNIFER - INFO - Getting element sub-08
2024-02-09 10:27:33,978 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:33,978 - 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 10:27:33,978 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:33,979 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:33,979 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:33,980 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:33,980 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:33,980 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:33,980 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:33,980 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:33,982 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:34,886 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:35,083 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:35,083 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:35,083 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:35,083 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:35,083 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:35,083 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:35,083 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:35,086 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:35,966 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:36,173 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:36,173 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:36,173 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:36,173 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:36,173 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:36,173 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:36,173 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:36,176 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:37,096 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:37,302 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:37,302 - JUNIFER - INFO - Getting element sub-09
2024-02-09 10:27:37,302 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:37,303 - 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 10:27:37,303 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:37,304 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:37,304 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:37,304 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:37,304 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:37,304 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:37,304 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:37,304 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:37,307 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:38,253 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:38,449 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:38,449 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:38,449 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:38,449 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:38,449 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:38,449 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:38,449 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:38,451 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:39,289 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:39,488 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:39,488 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:39,488 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:39,489 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:39,489 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:39,489 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:39,489 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:39,491 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:40,346 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:40,549 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:27:40,550 - JUNIFER - INFO - Getting element sub-10
2024-02-09 10:27:40,550 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:27:40,550 - 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 10:27:40,550 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:27:40,551 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-02-09 10:27:40,551 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:40,551 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:40,551 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:40,551 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:40,551 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:40,551 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:40,554 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:41,401 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:43,328 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-02-09 10:27:43,328 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:43,328 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:43,328 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:43,328 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:43,328 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:43,328 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:43,330 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:44,224 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:44,428 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-02-09 10:27:44,428 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:27:44,428 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:27:44,428 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:27:44,428 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:27:44,429 - JUNIFER - INFO - n_rois: 1000
2024-02-09 10:27:44,429 - JUNIFER - INFO - yeo_networks: 7
2024-02-09 10:27:44,431 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:27:45,323 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmph6kac39e/test.sqlite (multiple output)>
2024-02-09 10:27:45,528 - 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 45.332 seconds)