Note

Go to the end to download the full example code

8.3. UKB VBM GMD Extraction#

Authors: Federico Raimondo

License: BSD 3 clause

2024-04-05 15:42:19,187 - JUNIFER - INFO - Registering OasisVBMTestingDataGrabber in datagrabber
2024-04-05 15:42:19,187 - JUNIFER - INFO - Registering SPMAuditoryTestingDataGrabber in datagrabber
2024-04-05 15:42:19,187 - JUNIFER - INFO - Registering PartlyCloudyTestingDataGrabber in datagrabber
2024-04-05 15:42:19,187 - JUNIFER - INFO - Validating Marker Collection
2024-04-05 15:42:19,187 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-04-05 15:42:19,187 - JUNIFER - INFO - Validating Data Reader:
2024-04-05 15:42:19,187 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-04-05 15:42:19,188 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_TrimMean80
2024-04-05 15:42:19,188 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-05 15:42:19,188 - JUNIFER - INFO - Validating storage for Schaefer1000x7_TrimMean80
2024-04-05 15:42:19,188 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_Mean
2024-04-05 15:42:19,188 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-05 15:42:19,188 - JUNIFER - INFO - Validating storage for Schaefer1000x7_Mean
2024-04-05 15:42:19,188 - JUNIFER - INFO - Validating Marker: Schaefer1000x7_Std
2024-04-05 15:42:19,188 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-05 15:42:19,188 - JUNIFER - INFO - Validating storage for Schaefer1000x7_Std

Dataset created in /home/runner/nilearn_data/oasis1

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

Downloaded 87408640 of 905208634 bytes (9.7%,    9.4s remaining)
Downloaded 196149248 of 905208634 bytes (21.7%,    7.2s remaining)
Downloaded 312942592 of 905208634 bytes (34.6%,    5.7s remaining)
Downloaded 432553984 of 905208634 bytes (47.8%,    4.4s remaining)
Downloaded 551346176 of 905208634 bytes (60.9%,    3.2s remaining)
Downloaded 669597696 of 905208634 bytes (74.0%,    2.1s remaining)
Downloaded 785260544 of 905208634 bytes (86.7%,    1.1s remaining)
Downloaded 904560640 of 905208634 bytes (99.9%,    0.0s remaining) ...done. (9 seconds, 0 min)
Extracting data from /home/runner/nilearn_data/oasis1/7088b0bf88f5650db26e32ec3afdd589/archive_dartel.tgz..... done.
/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nilearn/datasets/struct.py:852: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
  warnings.warn(_LEGACY_FORMAT_MSG)
2024-04-05 15:42:34,165 - JUNIFER - INFO - Getting element sub-01
2024-04-05 15:42:34,165 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:42:34,165 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:42:34,165 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:42:34,166 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:42:34,166 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:42:34,167 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:42:34,167 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:42:34,167 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:42:34,167 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:42:34,167 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:42:34,167 - JUNIFER - INFO - At least one of the parcellation files are missing. Fetching using nilearn.

Dataset created in /home/runner/junifer/data/parcellations/schaefer_2018

Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_7Networks_order.txt ...
 ...done. (0 seconds, 0 min)
Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz ...
 ...done. (0 seconds, 0 min)
2024-04-05 15:42:34,230 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:42:34,267 - 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
2024-04-05 15:51:32,813 - 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]
 43%|████▎     | 626k/1.45M [00:00<00:00, 5.20MB/s]
100%|██████████| 1.45M/1.45M [00:00<00:00, 9.81MB/s]
2024-04-05 15:51:33,260 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations2ytr1an1/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations2ytr1an1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj80ev5ue/parcellationsdkczexy0/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:51:40,886 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:51:42,043 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:51:42,199 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:51:42,199 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:51:42,199 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:51:42,200 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:51:42,200 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:51:42,200 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:51:42,200 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:51:42,202 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:51:42,239 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:51:43,432 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:51:43,532 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsvl4tdfuf/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsvl4tdfuf/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj80ev5ue/parcellations9ylbgb5o/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:51:50,828 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:51:52,066 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:51:52,228 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:51:52,228 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:51:52,228 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:51:52,228 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:51:52,228 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:51:52,228 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:51:52,228 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:51:52,230 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:51:52,268 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:51:53,506 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:51:53,607 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations53fl0iq5/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations53fl0iq5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpj80ev5ue/parcellationsl8sk43sc/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:52:00,896 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:52:02,058 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:52:02,221 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:52:02,222 - JUNIFER - INFO - Getting element sub-02
2024-04-05 15:52:02,222 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:52:02,222 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:52:02,222 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:52:02,223 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:52:02,223 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:52:02,223 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:52:02,223 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:52:02,223 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:52:02,223 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:52:02,223 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:52:02,225 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:52:02,261 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:52:03,470 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:52:03,569 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations2at7ysdb/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations2at7ysdb/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpn63kkm6r/parcellationsakupem5l/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:52:10,857 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:52:12,089 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:52:12,243 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:52:12,243 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:52:12,244 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:52:12,244 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:52:12,244 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:52:12,244 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:52:12,244 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:52:12,246 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:52:12,284 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:52:13,537 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:52:13,638 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationswnil7jeh/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationswnil7jeh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpn63kkm6r/parcellationszvj6j6va/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:52:20,978 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:52:22,247 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:52:22,407 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:52:22,407 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:52:22,407 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:52:22,407 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:52:22,407 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:52:22,407 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:52:22,407 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:52:22,410 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:52:22,447 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:52:23,702 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:52:23,802 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations69uopo3w/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations69uopo3w/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpn63kkm6r/parcellations30km1o4f/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:52:31,050 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:52:32,409 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:52:32,575 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:52:32,576 - JUNIFER - INFO - Getting element sub-03
2024-04-05 15:52:32,576 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:52:32,576 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:52:32,576 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:52:32,577 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:52:32,577 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:52:32,577 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:52:32,577 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:52:32,577 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:52:32,577 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:52:32,577 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:52:32,579 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:52:32,616 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:52:33,927 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:52:34,028 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationscy27nu7e/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationscy27nu7e/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5mzpmb0d/parcellationsjressb4y/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:52:41,346 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:52:42,585 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:52:42,743 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:52:42,743 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:52:42,743 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:52:42,743 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:52:42,743 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:52:42,743 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:52:42,744 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:52:42,746 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:52:42,783 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:52:44,074 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:52:44,175 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations29ek3u5d/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations29ek3u5d/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5mzpmb0d/parcellationsb2jjrvqf/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:52:51,401 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:52:52,703 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:52:52,868 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:52:52,868 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:52:52,868 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:52:52,868 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:52:52,868 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:52:52,868 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:52:52,868 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:52:52,870 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:52:52,908 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:52:54,205 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:52:54,305 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations60lf2_n0/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations60lf2_n0/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5mzpmb0d/parcellationsz0ikhr03/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:53:01,647 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:53:02,930 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:53:03,093 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:53:03,094 - JUNIFER - INFO - Getting element sub-04
2024-04-05 15:53:03,094 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:53:03,094 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:53:03,094 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:53:03,095 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:53:03,095 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:53:03,096 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:53:03,096 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:53:03,096 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:53:03,096 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:53:03,096 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:53:03,098 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:53:03,133 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:53:04,373 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:53:04,473 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsclp90v5i/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsclp90v5i/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpogtntbu5/parcellationszcn7sw2n/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:53:11,709 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:53:13,076 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:53:13,232 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:53:13,232 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:53:13,233 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:53:13,233 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:53:13,233 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:53:13,233 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:53:13,233 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:53:13,235 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:53:13,273 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:53:14,555 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:53:14,655 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations7o2jeod5/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations7o2jeod5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpogtntbu5/parcellationsv1wb9r2g/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:53:22,001 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:53:23,327 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:53:23,492 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:53:23,492 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:53:23,493 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:53:23,493 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:53:23,493 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:53:23,493 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:53:23,493 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:53:23,495 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:53:23,533 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:53:24,797 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:53:24,897 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations6j_komkh/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations6j_komkh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpogtntbu5/parcellationshk5l9zei/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:53:32,314 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:53:33,565 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:53:33,728 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:53:33,729 - JUNIFER - INFO - Getting element sub-05
2024-04-05 15:53:33,729 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:53:33,729 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:53:33,729 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:53:33,730 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:53:33,730 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:53:33,730 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:53:33,730 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:53:33,730 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:53:33,730 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:53:33,730 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:53:33,732 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:53:33,769 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:53:34,996 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:53:35,096 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsod1p389w/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsod1p389w/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpbuah4mn5/parcellationsjkg0eds7/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:53:42,389 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:53:43,616 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:53:43,774 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:53:43,774 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:53:43,774 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:53:43,774 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:53:43,774 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:53:43,774 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:53:43,774 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:53:43,776 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:53:43,812 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:53:45,018 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:53:45,117 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations3smtwkhm/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations3smtwkhm/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpbuah4mn5/parcellationsuv512hqi/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:53:52,391 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:53:53,579 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:53:53,736 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:53:53,736 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:53:53,736 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:53:53,736 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:53:53,736 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:53:53,736 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:53:53,736 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:53:53,738 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:53:53,776 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:53:54,981 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:53:55,080 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsvbbe0di4/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsvbbe0di4/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpbuah4mn5/parcellationsofem0c7w/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:54:02,409 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:54:03,647 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:54:03,806 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:54:03,807 - JUNIFER - INFO - Getting element sub-06
2024-04-05 15:54:03,807 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:54:03,807 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:54:03,807 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:54:03,808 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:54:03,808 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:54:03,808 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:54:03,809 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:54:03,809 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:54:03,809 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:54:03,809 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:54:03,811 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:54:03,846 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:54:05,072 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:54:05,171 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationshlyv5mgu/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationshlyv5mgu/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzzgwxup5/parcellationsbdw694yz/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:54:12,407 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:54:13,853 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:54:14,007 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:54:14,007 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:54:14,008 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:54:14,008 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:54:14,008 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:54:14,008 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:54:14,008 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:54:14,010 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:54:14,047 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:54:15,296 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:54:15,395 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations9gakgj5r/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations9gakgj5r/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzzgwxup5/parcellationsp7wdh_t3/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:54:22,813 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:54:24,161 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:54:24,323 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:54:24,323 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:54:24,324 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:54:24,324 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:54:24,324 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:54:24,324 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:54:24,324 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:54:24,326 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:54:24,363 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:54:25,644 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:54:25,747 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsv7tnkyae/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsv7tnkyae/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzzgwxup5/parcellationsy2ffb706/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:54:33,188 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:54:34,393 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:54:34,552 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:54:34,552 - JUNIFER - INFO - Getting element sub-07
2024-04-05 15:54:34,553 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:54:34,553 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:54:34,553 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:54:34,554 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:54:34,554 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:54:34,554 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:54:34,554 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:54:34,554 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:54:34,554 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:54:34,554 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:54:34,556 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:54:34,592 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:54:35,849 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:54:35,948 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsp_vbjoqf/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsp_vbjoqf/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi_v11g7x/parcellations15wb06r7/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:54:43,389 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:54:44,560 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:54:44,714 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:54:44,714 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:54:44,714 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:54:44,714 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:54:44,714 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:54:44,714 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:54:44,714 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:54:44,716 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:54:44,753 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:54:45,969 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:54:46,068 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsbqz0gr3m/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsbqz0gr3m/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi_v11g7x/parcellations3hfadqd4/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:54:53,361 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:54:54,510 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:54:54,667 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:54:54,667 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:54:54,667 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:54:54,667 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:54:54,668 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:54:54,668 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:54:54,668 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:54:54,670 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:54:54,706 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:54:55,905 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:54:56,005 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsapi7qini/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsapi7qini/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi_v11g7x/parcellationsi7xgpvr2/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:55:03,321 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:55:04,476 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:55:04,636 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:55:04,636 - JUNIFER - INFO - Getting element sub-08
2024-04-05 15:55:04,637 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:55:04,637 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:55:04,637 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:55:04,637 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:55:04,637 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:55:04,638 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:55:04,638 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:55:04,638 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:55:04,638 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:55:04,638 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:55:04,640 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:55:04,676 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:55:05,845 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:55:05,943 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations3atnhybh/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations3atnhybh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpt6xdg1e9/parcellationshvq7kmoh/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:55:13,206 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:55:14,413 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:55:14,566 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:55:14,566 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:55:14,566 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:55:14,566 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:55:14,567 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:55:14,567 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:55:14,567 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:55:14,568 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:55:14,605 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:55:15,794 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:55:15,895 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationssz39mwyq/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationssz39mwyq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpt6xdg1e9/parcellations0f28g7ka/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:55:23,275 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:55:24,493 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:55:24,650 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:55:24,650 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:55:24,651 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:55:24,651 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:55:24,651 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:55:24,651 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:55:24,651 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:55:24,653 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:55:24,688 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:55:25,878 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:55:25,977 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations7azjds9f/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations7azjds9f/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpt6xdg1e9/parcellations6zt8ajav/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:55:33,377 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:55:34,578 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:55:34,740 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:55:34,740 - JUNIFER - INFO - Getting element sub-09
2024-04-05 15:55:34,740 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:55:34,740 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:55:34,740 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:55:34,741 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:55:34,741 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:55:34,742 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:55:34,742 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:55:34,742 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:55:34,742 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:55:34,742 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:55:34,744 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:55:34,780 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:55:35,960 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:55:36,060 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations_yz_pn52/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations_yz_pn52/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2wmq688g/parcellations7tcvwz7p/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:55:43,359 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:55:44,538 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:55:44,689 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:55:44,689 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:55:44,690 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:55:44,690 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:55:44,690 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:55:44,690 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:55:44,690 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:55:44,692 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:55:44,724 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:55:45,880 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:55:45,979 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsfq7m4x_1/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsfq7m4x_1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2wmq688g/parcellationsbq14ng1z/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:55:53,314 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:55:54,461 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:55:54,620 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:55:54,620 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:55:54,621 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:55:54,621 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:55:54,621 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:55:54,621 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:55:54,621 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:55:54,623 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:55:54,655 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:55:55,820 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:55:55,919 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsvyi8_jlc/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsvyi8_jlc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2wmq688g/parcellationsxrtzm5yd/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:56:03,228 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:56:04,370 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:56:04,529 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:56:04,529 - JUNIFER - INFO - Getting element sub-10
2024-04-05 15:56:04,529 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:56:04,529 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:56:04,529 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:56:04,530 - JUNIFER - INFO - Fitting marker Schaefer1000x7_TrimMean80
2024-04-05 15:56:04,530 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:56:04,530 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:56:04,530 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:56:04,531 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:56:04,531 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:56:04,531 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:56:04,532 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:56:04,565 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:56:05,726 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:56:05,825 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsoo8ozd5o/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationsoo8ozd5o/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpm7sh5w4j/parcellationsgu0qy4g1/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:56:13,120 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:56:14,394 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:56:14,547 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Mean
2024-04-05 15:56:14,547 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:56:14,547 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:56:14,547 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:56:14,547 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:56:14,547 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:56:14,547 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:56:14,549 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:56:14,581 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:56:15,787 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:56:15,889 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations2eoppgsl/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellations2eoppgsl/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpm7sh5w4j/parcellationsdxr_8iox/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:56:23,183 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:56:24,455 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:56:24,614 - JUNIFER - INFO - Fitting marker Schaefer1000x7_Std
2024-04-05 15:56:24,614 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:56:24,614 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:56:24,614 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:56:24,614 - JUNIFER - INFO -      resolution: 2.0
2024-04-05 15:56:24,614 - JUNIFER - INFO -      n_rois: 1000
2024-04-05 15:56:24,614 - JUNIFER - INFO -      yeo_networks: 7
2024-04-05 15:56:24,616 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:56:24,648 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:56:25,860 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:56:25,960 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationse5f7ctvd/Schaefer1000x7.nii.gz -r /tmp/tmpp56odh8d/parcellationse5f7ctvd/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpm7sh5w4j/parcellationsx5oza2j1/Schaefer1000x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:56:33,210 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:56:34,374 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpeci84okt/test.sqlite (multiple output)>
2024-04-05 15:56:34,534 - 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: (14 minutes 15.350 seconds)

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