Note
Click here to download the full example code
7.4. UKB VBM GMD Extraction#
Authors: Federico Raimondo
License: BSD 3 clause
2022-12-20 14:33:33,502 - JUNIFER - INFO - Registering OasisVBMTestingDatagrabber in datagrabber
2022-12-20 14:33:33,502 - JUNIFER - INFO - Registering SPMAuditoryTestingDatagrabber in datagrabber
/opt/hostedtoolcache/Python/3.10.9/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:774: 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)
2022-12-20 14:33:33,510 - JUNIFER - INFO - Getting element sub-01
2022-12-20 14:33:33,510 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:33:33,510 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:33:33,510 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:33:33,511 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:33:33,511 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:33,511 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:33,512 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:33,512 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:33,512 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:33,512 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:33,512 - 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)
2022-12-20 14:33:33,684 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:34,804 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:35,380 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:33:35,380 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:35,381 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:35,381 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:35,381 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:35,381 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:35,381 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:35,385 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:36,498 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:37,027 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:33:37,027 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:37,028 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:37,028 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:37,028 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:37,028 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:37,028 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:37,031 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:38,141 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:38,672 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:33:38,672 - JUNIFER - INFO - Getting element sub-02
2022-12-20 14:33:38,672 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:33:38,673 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:33:38,673 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:33:38,674 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:33:38,674 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:38,674 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:38,674 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:38,674 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:38,674 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:38,674 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:38,677 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:39,811 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:40,333 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:33:40,333 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:40,333 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:40,333 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:40,333 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:40,333 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:40,333 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:40,337 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:41,434 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:41,963 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:33:41,963 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:41,963 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:41,963 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:41,963 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:41,963 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:41,963 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:41,967 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:43,071 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:43,604 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:33:43,604 - JUNIFER - INFO - Getting element sub-03
2022-12-20 14:33:43,604 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:33:43,604 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:33:43,605 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:33:43,606 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:33:43,606 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:43,606 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:43,606 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:43,606 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:43,606 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:43,606 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:43,610 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:44,744 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:45,270 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:33:45,271 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:45,271 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:45,271 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:45,271 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:45,271 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:45,271 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:45,275 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:46,354 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:46,883 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:33:46,883 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:46,883 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:46,883 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:46,884 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:46,884 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:46,884 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:46,887 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:48,021 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:48,555 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:33:48,555 - JUNIFER - INFO - Getting element sub-04
2022-12-20 14:33:48,555 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:33:48,555 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:33:48,555 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:33:48,556 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:33:48,557 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:48,557 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:48,557 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:48,557 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:48,557 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:48,557 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:48,560 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:49,696 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:50,217 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:33:50,217 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:50,217 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:50,217 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:50,217 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:50,218 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:50,218 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:50,221 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:51,312 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:51,839 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:33:51,839 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:51,840 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:51,840 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:51,840 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:51,840 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:51,840 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:51,843 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:52,944 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:54,508 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:33:54,508 - JUNIFER - INFO - Getting element sub-05
2022-12-20 14:33:54,508 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:33:54,509 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:33:54,509 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:33:54,510 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:33:54,510 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:54,510 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:54,510 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:54,510 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:54,510 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:54,510 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:54,514 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:55,619 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:56,143 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:33:56,143 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:56,143 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:56,143 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:56,143 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:56,143 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:56,143 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:56,147 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:57,246 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:57,776 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:33:57,776 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:57,776 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:57,776 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:57,776 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:57,776 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:57,777 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:57,780 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:33:58,892 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:33:59,423 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:33:59,423 - JUNIFER - INFO - Getting element sub-06
2022-12-20 14:33:59,423 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:33:59,423 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:33:59,423 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:33:59,424 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:33:59,425 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:33:59,425 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:33:59,425 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:33:59,425 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:33:59,425 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:33:59,425 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:33:59,429 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:00,571 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:01,091 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:34:01,091 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:01,092 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:01,092 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:01,092 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:01,092 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:01,092 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:01,096 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:02,223 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:02,756 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:34:02,756 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:02,756 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:02,756 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:02,756 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:02,756 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:02,756 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:02,760 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:03,893 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:04,427 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:04,427 - JUNIFER - INFO - Getting element sub-07
2022-12-20 14:34:04,427 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:04,427 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:04,427 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:04,428 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:34:04,428 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:04,429 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:04,429 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:04,429 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:04,429 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:04,429 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:04,432 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:05,573 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:06,095 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:34:06,096 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:06,096 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:06,096 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:06,096 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:06,096 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:06,096 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:06,100 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:07,236 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:07,765 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:34:07,766 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:07,766 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:07,766 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:07,766 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:07,766 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:07,766 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:07,770 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:08,894 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:09,427 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:09,427 - JUNIFER - INFO - Getting element sub-08
2022-12-20 14:34:09,427 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:09,427 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:09,428 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:09,429 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:34:09,429 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:09,429 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:09,429 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:09,429 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:09,429 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:09,429 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:09,433 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:10,551 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:11,073 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:34:11,074 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:11,074 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:11,074 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:11,074 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:11,074 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:11,074 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:11,078 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:12,193 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:12,723 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:34:12,723 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:12,723 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:12,723 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:12,723 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:12,723 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:12,723 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:12,727 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:13,832 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:14,365 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:14,366 - JUNIFER - INFO - Getting element sub-09
2022-12-20 14:34:14,366 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:14,366 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:14,366 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:14,367 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:34:14,367 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:14,367 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:14,367 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:14,367 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:14,367 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:14,368 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:14,371 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:15,530 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:16,055 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:34:16,055 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:16,055 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:16,055 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:16,056 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:16,056 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:16,056 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:16,059 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:17,201 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:17,735 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:34:17,735 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:17,735 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:17,736 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:17,736 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:17,736 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:17,736 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:17,740 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:18,875 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:19,407 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:19,408 - JUNIFER - INFO - Getting element sub-10
2022-12-20 14:34:19,408 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:19,408 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:19,408 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:19,409 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2022-12-20 14:34:19,409 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:19,409 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:19,410 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:19,410 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:19,410 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:19,410 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:19,413 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:20,557 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:21,080 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2022-12-20 14:34:21,080 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:21,080 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:21,081 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:21,081 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:21,081 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:21,081 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:21,084 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:22,187 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:22,720 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2022-12-20 14:34:22,720 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:22,721 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:22,721 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:22,721 - JUNIFER - INFO - n_rois: 1000
2022-12-20 14:34:22,721 - JUNIFER - INFO - yeo_networks: 7
2022-12-20 14:34:22,721 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:22,724 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:23,839 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpsucgesfs/test.sqlite (multiple output)>
2022-12-20 14:34:24,374 - 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 50.875 seconds)