8.3. UKB VBM GMD Extraction

Authors: Federico Raimondo

License: BSD 3 clause

2024-07-22 09:22:18,841 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2024-07-22 09:22:18,841 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2024-07-22 09:22:18,841 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
2024-07-22 09:22:18,841 - JUNIFER - INFO - Validating Marker Collection
2024-07-22 09:22:18,841 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-07-22 09:22:18,841 - JUNIFER - INFO - Validating Data Reader:
2024-07-22 09:22:18,841 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-07-22 09:22:18,841 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_TrimMean80
2024-07-22 09:22:18,841 - JUNIFER - INFO - Marker output type: ['vector']
2024-07-22 09:22:18,841 - JUNIFER - INFO - Validating storage for Schaefer1000x7_TrimMean80
2024-07-22 09:22:18,841 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_Mean
2024-07-22 09:22:18,842 - JUNIFER - INFO - Marker output type: ['vector']
2024-07-22 09:22:18,842 - JUNIFER - INFO - Validating storage for Schaefer1000x7_Mean
2024-07-22 09:22:18,842 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_Std
2024-07-22 09:22:18,842 - JUNIFER - INFO - Marker output type: ['vector']
2024-07-22 09:22:18,842 - JUNIFER - INFO - Validating storage for Schaefer1000x7_Std

Added README.md to /home/runner/nilearn_data


Dataset created in /home/runner/nilearn_data/oasis1

Downloading data from https://www.nitrc.org/frs/download.php/6364/archive_dartel.tgz ...

Downloaded 156794880 of 905208634 bytes (17.3%,    4.8s remaining)
Downloaded 352296960 of 905208634 bytes (38.9%,    3.1s remaining)
Downloaded 606584832 of 905208634 bytes (67.0%,    1.5s remaining)
Downloaded 861814784 of 905208634 bytes (95.2%,    0.2s remaining) ...done. (5 seconds, 0 min)
Extracting data from /home/runner/nilearn_data/oasis1/7088b0bf88f5650db26e32ec3afdd589/archive_dartel.tgz..... done.
2024-07-22 09:22:30,246 - JUNIFER - INFO - Getting element sub-01
2024-07-22 09:22:30,246 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:22:30,246 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:22:30,247 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:22:30,247 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:22:30,248 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:22:30,248 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:22:30,248 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:22:30,248 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:22:30,248 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:22:30,248 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:22:30,248 - JUNIFER - INFO - At least one of the parcellation files are missing. Fetching using nilearn.

Added README.md to /home/runner/junifer/data/parcellations


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)
2024-07-22 09:22:30,275 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:22:30,312 - JUNIFER - INFO - Downloading xfm file for MNI152NLin6Asym to MNI152Lin from https://gin.g-node.org/juaml/human-template-xfms/raw/main/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:28:40,151 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152Lin/tpl-MNI152Lin_res-02_T1w.nii.gz

  0%|          | 0.00/1.45M [00:00<?, ?B/s]
100%|██████████| 1.45M/1.45M [00:00<00:00, 68.1MB/s]
2024-07-22 09:28:45,414 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsrjumnxhz/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsrjumnxhz/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa2lsypn2/parcellationsa4a2spts/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:28:53,183 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:28:54,514 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:28:54,675 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:28:54,676 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:28:54,676 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:28:54,676 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:28:54,676 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:28:54,676 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:28:54,676 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:28:54,678 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:28:54,712 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:28:56,006 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:28:56,107 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations_9tjoheo/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellations_9tjoheo/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa2lsypn2/parcellations0cgf9rag/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:29:03,511 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:29:04,737 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:29:04,901 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:29:04,901 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:29:04,901 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:29:04,901 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:29:04,902 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:29:04,902 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:29:04,902 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:29:04,904 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:29:04,937 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:29:06,197 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:29:06,297 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsr2blkvcs/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsr2blkvcs/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa2lsypn2/parcellationsrmdvg_n3/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:29:13,582 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:29:14,944 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:29:15,114 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:29:15,116 - JUNIFER - INFO - Getting element sub-02
2024-07-22 09:29:15,116 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:29:15,116 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:29:15,116 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:29:15,117 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:29:15,117 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:29:15,117 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:29:15,118 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:29:15,118 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:29:15,118 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:29:15,118 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:29:15,120 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:29:15,157 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:29:16,451 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:29:16,552 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsihd9xph2/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsihd9xph2/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpcgptvhhb/parcellationsy_psu36n/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:29:24,023 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:29:25,209 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:29:25,363 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:29:25,363 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:29:25,363 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:29:25,363 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:29:25,363 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:29:25,363 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:29:25,363 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:29:25,365 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:29:25,398 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:29:26,638 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:29:26,738 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations2xt7abij/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellations2xt7abij/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpcgptvhhb/parcellationsm3_fm3t7/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:29:34,129 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:29:35,307 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:29:35,467 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:29:35,467 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:29:35,468 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:29:35,468 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:29:35,468 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:29:35,468 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:29:35,468 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:29:35,470 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:29:35,502 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:29:36,737 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:29:36,836 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsiu7ajwvm/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsiu7ajwvm/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpcgptvhhb/parcellations9ytr0vo8/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:29:44,217 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:29:45,428 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:29:45,590 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:29:45,591 - JUNIFER - INFO - Getting element sub-03
2024-07-22 09:29:45,591 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:29:45,591 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:29:45,591 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:29:45,592 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:29:45,592 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:29:45,592 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:29:45,592 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:29:45,592 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:29:45,592 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:29:45,592 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:29:45,594 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:29:45,627 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:29:46,853 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:29:46,953 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations1vjshipo/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellations1vjshipo/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpaizt67hr/parcellationsu6ltvms6/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:29:54,221 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:29:55,420 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:29:55,576 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:29:55,576 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:29:55,576 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:29:55,576 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:29:55,576 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:29:55,576 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:29:55,576 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:29:55,578 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:29:55,611 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:29:56,848 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:29:56,947 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsz5umvghx/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsz5umvghx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpaizt67hr/parcellationsvtfpj__q/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:30:04,387 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:30:05,608 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:30:05,767 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:30:05,767 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:30:05,768 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:30:05,768 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:30:05,768 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:30:05,768 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:30:05,768 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:30:05,770 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:30:05,803 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:30:07,049 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:30:07,149 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationss91rlhe9/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationss91rlhe9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpaizt67hr/parcellationske9cv33z/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:30:14,471 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:30:15,671 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:30:15,838 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:30:15,838 - JUNIFER - INFO - Getting element sub-04
2024-07-22 09:30:15,838 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:30:15,838 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:30:15,838 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:30:15,839 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:30:15,839 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:30:15,840 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:30:15,840 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:30:15,840 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:30:15,840 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:30:15,840 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:30:15,842 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:30:15,875 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:30:17,088 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:30:17,187 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsjys7li3g/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsjys7li3g/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvrxjmw3_/parcellations9ox6x6__/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:30:24,539 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:30:25,745 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:30:25,900 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:30:25,900 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:30:25,900 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:30:25,900 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:30:25,900 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:30:25,900 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:30:25,900 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:30:25,902 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:30:25,935 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:30:27,172 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:30:27,273 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsigee491u/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsigee491u/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvrxjmw3_/parcellations6fygf8kw/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:30:34,708 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:30:35,881 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:30:36,043 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:30:36,043 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:30:36,044 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:30:36,044 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:30:36,044 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:30:36,044 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:30:36,044 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:30:36,046 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:30:36,078 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:30:37,311 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:30:37,411 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations6l6npxdg/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellations6l6npxdg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvrxjmw3_/parcellationsq4ktt7e0/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:30:44,834 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:30:46,019 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:30:46,183 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:30:46,184 - JUNIFER - INFO - Getting element sub-05
2024-07-22 09:30:46,184 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:30:46,185 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:30:46,185 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:30:46,185 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:30:46,185 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:30:46,186 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:30:46,186 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:30:46,186 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:30:46,186 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:30:46,186 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:30:46,188 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:30:46,225 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:30:47,456 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:30:47,555 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationswrpmuj_h/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationswrpmuj_h/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptsz1q3qq/parcellationsbobfx_2f/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:30:54,952 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:30:56,161 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:30:56,318 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:30:56,318 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:30:56,318 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:30:56,318 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:30:56,318 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:30:56,318 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:30:56,318 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:30:56,320 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:30:56,354 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:30:57,585 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:30:57,684 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsoxbb6bqr/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsoxbb6bqr/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptsz1q3qq/parcellationshjoi03bt/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:31:05,091 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:31:06,278 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:31:06,437 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:31:06,437 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:31:06,437 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:31:06,437 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:31:06,437 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:31:06,437 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:31:06,437 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:31:06,439 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:31:06,472 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:31:07,717 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:31:07,816 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsu8jwhg5o/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsu8jwhg5o/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptsz1q3qq/parcellationsp9wcf05b/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:31:15,290 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:31:16,480 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:31:16,643 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:31:16,645 - JUNIFER - INFO - Getting element sub-06
2024-07-22 09:31:16,645 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:31:16,645 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:31:16,645 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:31:16,646 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:31:16,646 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:31:16,646 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:31:16,646 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:31:16,646 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:31:16,646 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:31:16,646 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:31:16,648 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:31:16,685 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:31:17,926 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:31:18,026 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsbn1tav50/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsbn1tav50/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpq75ns403/parcellations98tz0p69/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:31:25,482 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:31:26,677 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:31:26,832 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:31:26,832 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:31:26,833 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:31:26,833 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:31:26,833 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:31:26,833 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:31:26,833 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:31:26,835 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:31:26,868 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:31:28,104 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:31:28,206 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsqdaxtkcx/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsqdaxtkcx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpq75ns403/parcellationsskh1k0i3/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:31:35,622 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:31:36,794 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:31:36,955 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:31:36,955 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:31:36,956 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:31:36,956 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:31:36,956 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:31:36,956 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:31:36,956 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:31:36,958 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:31:36,990 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:31:38,236 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:31:38,336 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationshpbvxkgx/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationshpbvxkgx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpq75ns403/parcellationsxt2cjve4/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:31:45,809 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:31:46,984 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:31:47,144 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:31:47,146 - JUNIFER - INFO - Getting element sub-07
2024-07-22 09:31:47,146 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:31:47,146 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:31:47,146 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:31:47,147 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:31:47,147 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:31:47,147 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:31:47,147 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:31:47,148 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:31:47,148 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:31:47,148 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:31:47,149 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:31:47,186 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:31:48,417 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:31:48,516 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationshj3l55v5/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationshj3l55v5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2ds5nexa/parcellationsg0mujxq5/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:31:55,997 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:31:57,222 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:31:57,375 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:31:57,375 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:31:57,375 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:31:57,375 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:31:57,375 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:31:57,375 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:31:57,376 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:31:57,377 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:31:57,410 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:31:58,673 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:31:58,773 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationstm7mzu17/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationstm7mzu17/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2ds5nexa/parcellationstr0i_ang/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:32:06,173 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:32:07,363 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:32:07,521 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:32:07,521 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:32:07,521 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:32:07,521 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:32:07,521 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:32:07,521 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:32:07,521 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:32:07,523 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:32:07,556 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:32:08,785 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:32:08,884 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations664ckd3_/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellations664ckd3_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2ds5nexa/parcellations5spxotz_/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:32:16,265 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:32:17,461 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:32:17,623 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:32:17,625 - JUNIFER - INFO - Getting element sub-08
2024-07-22 09:32:17,625 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:32:17,625 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:32:17,625 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:32:17,626 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:32:17,626 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:32:17,626 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:32:17,626 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:32:17,626 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:32:17,626 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:32:17,626 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:32:17,628 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:32:17,665 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:32:18,903 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:32:19,002 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationskdu_051s/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationskdu_051s/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpssbazhyd/parcellations8plk0nz9/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:32:26,441 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:32:27,633 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:32:27,788 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:32:27,788 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:32:27,789 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:32:27,789 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:32:27,789 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:32:27,789 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:32:27,789 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:32:27,791 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:32:27,824 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:32:29,051 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:32:29,150 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsz6_3t56q/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsz6_3t56q/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpssbazhyd/parcellationsduna0qia/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:32:36,554 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:32:37,729 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:32:37,890 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:32:37,890 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:32:37,890 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:32:37,890 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:32:37,890 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:32:37,890 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:32:37,890 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:32:37,892 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:32:37,925 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:32:39,159 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:32:39,259 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsj_v2s3_g/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsj_v2s3_g/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpssbazhyd/parcellationsjw986nzs/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:32:46,642 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:32:47,825 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:32:47,986 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:32:47,988 - JUNIFER - INFO - Getting element sub-09
2024-07-22 09:32:47,988 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:32:47,988 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:32:47,988 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:32:47,989 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:32:47,989 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:32:47,990 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:32:47,990 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:32:47,990 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:32:47,990 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:32:47,990 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:32:47,992 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:32:48,030 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:32:49,258 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:32:49,357 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsdbfpn95b/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsdbfpn95b/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpfplu5o17/parcellations2cmnvine/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:32:56,805 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:32:58,011 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:32:58,166 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:32:58,166 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:32:58,166 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:32:58,166 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:32:58,166 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:32:58,166 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:32:58,167 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:32:58,168 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:32:58,200 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:32:59,410 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:32:59,510 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsipaxrb0y/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsipaxrb0y/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpfplu5o17/parcellationsomacyegd/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:33:07,025 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:33:08,201 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:33:08,360 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:33:08,360 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:33:08,360 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:33:08,360 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:33:08,360 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:33:08,360 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:33:08,360 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:33:08,362 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:33:08,395 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:33:09,607 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:33:09,706 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsfwzp0vjd/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsfwzp0vjd/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpfplu5o17/parcellationsrgulig7h/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:33:17,271 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:33:18,448 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:33:18,609 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:33:18,610 - JUNIFER - INFO - Getting element sub-10
2024-07-22 09:33:18,610 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:33:18,610 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:33:18,610 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:33:18,611 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-07-22 09:33:18,611 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:33:18,611 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:33:18,611 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:33:18,611 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:33:18,612 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:33:18,612 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:33:18,613 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:33:18,646 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:33:19,843 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:33:19,943 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsgdpdctoc/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsgdpdctoc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpnhk8q2d8/parcellationsa8t298wk/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:33:27,368 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:33:28,552 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:33:28,706 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-07-22 09:33:28,706 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:33:28,706 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:33:28,706 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:33:28,706 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:33:28,706 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:33:28,707 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:33:28,708 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:33:28,740 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:33:29,948 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:33:30,046 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations5da6l8sc/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellations5da6l8sc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpnhk8q2d8/parcellationscz1_400k/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:33:37,510 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:33:38,665 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:33:38,824 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-07-22 09:33:38,824 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:33:38,824 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:33:38,824 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:33:38,824 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:33:38,824 - JUNIFER - INFO -      n_rois: 1000
2024-07-22 09:33:38,824 - JUNIFER - INFO -      yeo_networks: 7
2024-07-22 09:33:38,826 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:33:38,858 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:33:40,063 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:33:40,162 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsxsce4rez/Schaefer1000x7.nii.gz -r /tmp/tmpcysmnw4q/parcellationsxsce4rez/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpnhk8q2d8/parcellations7o0o9wou/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:33:47,643 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:33:48,798 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpjkm0wiac/test.sqlite (multiple output)>
2024-07-22 09:33:48,961 - 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,
    )