Note
Click here to download the full example code
8.4. UKB VBM GMD Extraction#
Authors: Federico Raimondo
License: BSD 3 clause
2023-05-16 14:14:43,227 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2023-05-16 14:14:43,228 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2023-05-16 14:14:43,228 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
/opt/hostedtoolcache/Python/3.10.11/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:733: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
warnings.warn(_LEGACY_FORMAT_MSG)
2023-05-16 14:14:43,236 - JUNIFER - INFO - Getting element sub-01
2023-05-16 14:14:43,237 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:14:43,237 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:14:43,237 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:14:43,238 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:14:43,238 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:43,238 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:43,238 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:43,238 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:43,239 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:43,239 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:43,239 - JUNIFER - INFO - At least one of the parcellation files are missing. Fetching using nilearn.
Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_7Networks_order.txt ...
...done. (0 seconds, 0 min)
Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz ...
...done. (0 seconds, 0 min)
2023-05-16 14:14:43,698 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:44,942 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:45,556 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:14:45,556 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:45,557 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:45,557 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:45,557 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:45,557 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:45,557 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:45,561 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:46,756 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:47,365 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:14:47,365 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:47,366 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:47,366 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:47,366 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:47,366 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:47,366 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:47,372 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:48,579 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:49,191 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:14:49,191 - JUNIFER - INFO - Getting element sub-02
2023-05-16 14:14:49,191 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:14:49,192 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:14:49,192 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:14:49,194 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:14:49,194 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:49,194 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:49,194 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:49,194 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:49,194 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:49,194 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:49,198 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:50,384 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:51,003 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:14:51,003 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:51,004 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:51,004 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:51,004 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:51,004 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:51,004 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:51,009 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:52,183 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:52,784 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:14:52,784 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:52,785 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:52,785 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:52,785 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:52,785 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:52,785 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:52,789 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:53,979 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:54,588 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:14:54,588 - JUNIFER - INFO - Getting element sub-03
2023-05-16 14:14:54,588 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:14:54,588 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:14:54,588 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:14:54,589 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:14:54,589 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:54,590 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:54,590 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:54,590 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:54,590 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:54,590 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:54,594 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:55,779 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:56,383 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:14:56,383 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:56,383 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:56,383 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:56,383 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:56,384 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:56,384 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:56,387 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:57,570 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:58,170 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:14:58,171 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:58,171 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:58,171 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:58,171 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:58,171 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:58,171 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:58,175 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:14:59,352 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:14:59,962 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:14:59,962 - JUNIFER - INFO - Getting element sub-04
2023-05-16 14:14:59,962 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:14:59,962 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:14:59,962 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:14:59,964 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:14:59,964 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:14:59,964 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:14:59,964 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:14:59,964 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:14:59,964 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:14:59,964 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:14:59,968 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:01,228 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:01,827 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:01,827 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:01,828 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:01,828 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:01,828 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:01,828 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:01,828 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:01,832 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:03,033 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:03,634 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:03,635 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:03,635 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:03,635 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:03,635 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:03,635 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:03,636 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:03,640 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:04,831 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:05,435 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:15:05,435 - JUNIFER - INFO - Getting element sub-05
2023-05-16 14:15:05,435 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:15:05,435 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:15:05,435 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:15:05,436 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:15:05,437 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:05,437 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:05,437 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:05,437 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:05,437 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:05,437 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:05,441 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:06,665 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:07,259 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:07,260 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:07,260 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:07,260 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:07,260 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:07,260 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:07,260 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:07,265 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:08,450 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:09,053 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:09,053 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:09,053 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:09,054 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:09,054 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:09,054 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:09,054 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:09,058 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:10,258 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:10,870 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:15:10,870 - JUNIFER - INFO - Getting element sub-06
2023-05-16 14:15:10,870 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:15:10,870 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:15:10,870 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:15:10,871 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:15:10,872 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:10,872 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:10,872 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:10,872 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:10,872 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:10,872 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:10,876 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:12,104 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:12,701 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:12,702 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:12,702 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:12,702 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:12,702 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:12,702 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:12,703 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:12,707 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:13,896 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:14,500 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:14,500 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:14,501 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:14,501 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:14,501 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:14,501 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:14,501 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:14,505 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:15,707 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:16,354 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:15:16,354 - JUNIFER - INFO - Getting element sub-07
2023-05-16 14:15:16,354 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:15:16,355 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:15:16,355 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:15:16,356 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:15:16,356 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:16,356 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:16,356 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:16,356 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:16,356 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:16,356 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:16,360 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:17,571 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:18,164 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:18,165 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:18,165 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:18,165 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:18,165 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:18,165 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:18,165 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:18,169 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:19,348 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:19,948 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:19,949 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:19,949 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:19,949 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:19,949 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:19,949 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:19,950 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:19,954 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:21,175 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:21,787 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:15:21,787 - JUNIFER - INFO - Getting element sub-08
2023-05-16 14:15:21,788 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:15:21,788 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:15:21,788 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:15:21,789 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:15:21,789 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:21,789 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:21,789 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:21,790 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:21,790 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:21,790 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:21,794 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:23,001 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:23,602 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:23,603 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:23,603 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:23,603 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:23,603 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:23,603 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:23,603 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:23,607 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:24,780 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:25,379 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:25,380 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:25,380 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:25,380 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:25,380 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:25,380 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:25,380 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:25,384 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:26,578 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:27,204 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:15:27,204 - JUNIFER - INFO - Getting element sub-09
2023-05-16 14:15:27,204 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:15:27,204 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:15:27,204 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:15:27,205 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:15:27,206 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:27,206 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:27,206 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:27,206 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:27,206 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:27,206 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:27,210 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:28,449 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:29,041 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:29,042 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:29,042 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:29,042 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:29,042 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:29,042 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:29,042 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:29,046 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:30,229 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:30,832 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:30,833 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:30,833 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:30,833 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:30,834 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:30,834 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:30,834 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:30,839 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:32,034 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:32,642 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:15:32,643 - JUNIFER - INFO - Getting element sub-10
2023-05-16 14:15:32,643 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:15:32,643 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:15:32,643 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:15:32,644 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2023-05-16 14:15:32,644 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:32,645 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:32,645 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:32,645 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:32,645 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:32,645 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:32,649 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:33,871 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:34,472 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2023-05-16 14:15:34,472 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:34,473 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:34,473 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:34,473 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:34,473 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:34,473 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:34,478 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:35,646 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:36,248 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2023-05-16 14:15:36,248 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:15:36,249 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:15:36,249 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:15:36,249 - JUNIFER - INFO - n_rois: 1000
2023-05-16 14:15:36,249 - JUNIFER - INFO - yeo_networks: 7
2023-05-16 14:15:36,249 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:15:36,253 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:15:37,454 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpycqiqz_i/test.sqlite (multiple output)>
2023-05-16 14:15:38,064 - 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 54.839 seconds)