Note
Click here to download the full example code
8.4. UKB VBM GMD Extraction#
Authors: Federico Raimondo
License: BSD 3 clause
2023-03-31 13:29:01,650 - JUNIFER - INFO - Registering OasisVBMTestingDatagrabber in datagrabber
2023-03-31 13:29:01,651 - JUNIFER - INFO - Registering SPMAuditoryTestingDatagrabber in datagrabber
2023-03-31 13:29:01,651 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
/opt/hostedtoolcache/Python/3.10.10/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)
2023-03-31 13:29:01,658 - JUNIFER - INFO - Getting element sub-01
2023-03-31 13:29:01,658 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:01,658 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:01,658 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:01,659 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:01,659 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:01,659 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:01,659 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:01,659 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:01,660 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:01,660 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:01,660 - 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)
2023-03-31 13:29:02,262 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:03,264 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:03,752 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:03,752 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:03,753 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:03,753 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:03,753 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:03,753 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:03,753 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:03,756 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:04,732 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:05,216 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:05,216 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:05,217 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:05,217 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:05,217 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:05,217 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:05,217 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:05,220 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:06,219 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:06,704 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:06,705 - JUNIFER - INFO - Getting element sub-02
2023-03-31 13:29:06,705 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:06,705 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:06,705 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:06,706 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:06,706 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:06,706 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:06,706 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:06,706 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:06,706 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:06,706 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:06,710 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:07,724 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:08,203 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:08,204 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:08,204 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:08,204 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:08,204 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:08,204 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:08,204 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:08,207 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:09,196 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:09,682 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:09,682 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:09,682 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:09,682 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:09,682 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:09,682 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:09,682 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:09,686 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:10,686 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:11,176 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:11,176 - JUNIFER - INFO - Getting element sub-03
2023-03-31 13:29:11,176 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:11,176 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:11,177 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:11,177 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:11,178 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:11,178 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:11,178 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:11,178 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:11,178 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:11,178 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:11,181 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:12,199 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:12,675 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:12,675 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:12,675 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:12,675 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:12,675 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:12,675 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:12,675 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:12,679 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:13,692 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:14,175 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:14,175 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:14,176 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:14,176 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:14,176 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:14,176 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:14,176 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:14,179 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:15,179 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:15,671 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:15,671 - JUNIFER - INFO - Getting element sub-04
2023-03-31 13:29:15,671 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:15,671 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:15,671 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:15,672 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:15,672 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:15,672 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:15,672 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:15,673 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:15,673 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:15,673 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:15,676 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:16,700 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:17,174 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:17,175 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:17,175 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:17,175 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:17,175 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:17,175 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:17,175 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:17,178 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:18,154 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:18,639 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:18,639 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:18,639 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:18,639 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:18,639 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:18,640 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:18,640 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:18,643 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:19,648 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:20,138 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:20,138 - JUNIFER - INFO - Getting element sub-05
2023-03-31 13:29:20,138 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:20,138 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:20,138 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:20,139 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:20,139 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:20,139 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:20,139 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:20,140 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:20,140 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:20,140 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:20,143 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:21,162 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:22,079 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:22,079 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:22,079 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:22,080 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:22,080 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:22,080 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:22,080 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:22,083 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:23,055 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:23,539 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:23,540 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:23,540 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:23,540 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:23,540 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:23,540 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:23,540 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:23,543 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:24,558 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:25,048 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:25,049 - JUNIFER - INFO - Getting element sub-06
2023-03-31 13:29:25,049 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:25,049 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:25,049 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:25,050 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:25,050 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:25,050 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:25,050 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:25,050 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:25,050 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:25,050 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:25,054 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:26,074 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:26,553 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:26,554 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:26,554 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:26,554 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:26,554 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:26,554 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:26,554 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:26,557 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:27,556 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:28,041 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:28,041 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:28,042 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:28,042 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:28,042 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:28,042 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:28,042 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:28,045 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:29,038 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:29,528 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:29,528 - JUNIFER - INFO - Getting element sub-07
2023-03-31 13:29:29,528 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:29,529 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:29,529 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:29,530 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:29,530 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:29,530 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:29,530 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:29,530 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:29,530 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:29,530 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:29,533 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:30,551 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:31,030 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:31,030 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:31,031 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:31,031 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:31,031 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:31,031 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:31,031 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:31,034 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:32,040 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:32,527 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:32,527 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:32,528 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:32,528 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:32,528 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:32,528 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:32,528 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:32,531 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:33,534 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:34,023 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:34,023 - JUNIFER - INFO - Getting element sub-08
2023-03-31 13:29:34,024 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:34,024 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:34,024 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:34,025 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:34,025 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:34,025 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:34,025 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:34,025 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:34,025 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:34,025 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:34,028 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:35,036 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:35,512 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:35,512 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:35,512 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:35,513 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:35,513 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:35,513 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:35,513 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:35,516 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:36,494 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:36,980 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:36,980 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:36,980 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:36,980 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:36,980 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:36,980 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:36,980 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:36,984 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:37,970 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:38,461 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:38,461 - JUNIFER - INFO - Getting element sub-09
2023-03-31 13:29:38,461 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:38,461 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:38,461 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:38,462 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:38,462 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:38,462 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:38,462 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:38,462 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:38,463 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:38,463 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:38,466 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:39,499 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:39,974 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:39,974 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:39,974 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:39,974 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:39,974 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:39,974 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:39,974 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:39,978 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:40,996 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:41,485 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:41,485 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:41,485 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:41,485 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:41,485 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:41,485 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:41,485 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:41,488 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:42,482 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:42,973 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:42,973 - JUNIFER - INFO - Getting element sub-10
2023-03-31 13:29:42,973 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:42,973 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:42,973 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:42,974 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-03-31 13:29:42,974 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:42,974 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:42,975 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:42,975 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:42,975 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:42,975 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:42,978 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:43,981 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:44,458 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-03-31 13:29:44,458 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:44,459 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:44,459 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:44,459 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:44,459 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:44,459 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:44,462 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:45,454 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:45,938 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-03-31 13:29:45,938 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:45,939 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:45,939 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:45,939 - JUNIFER - INFO - n_rois: 1000
2023-03-31 13:29:45,939 - JUNIFER - INFO - yeo_networks: 7
2023-03-31 13:29:45,939 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:45,942 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:46,953 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpvsr2eb6i/test.sqlite (multiple output)>
2023-03-31 13:29:47,442 - 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 45.794 seconds)