.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/run_junifer_julearn.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_run_junifer_julearn.py: Run junifer and julearn. ======================== This example uses a ParcelAggregation marker to compute the mean of each parcel using the Schaefer parcellation (100 rois, 7 Yeo networks) for a 3D nifti to extract some features for machine learning using julearn to predict some other data. Authors: Leonard Sasse, Sami Hamdan, Nicolas Nieto, Synchon Mandal License: BSD 3 clause .. GENERATED FROM PYTHON SOURCE LINES 14-27 .. code-block:: Python import tempfile import nilearn import pandas as pd from julearn import run_cross_validation, PipelineCreator import junifer.testing.registry # noqa: F401 from junifer.api import collect, run from junifer.storage.sqlite import SQLiteFeatureStorage from junifer.utils import configure_logging .. GENERATED FROM PYTHON SOURCE LINES 28-29 Set the logging level to info to see extra information: .. GENERATED FROM PYTHON SOURCE LINES 29-32 .. code-block:: Python configure_logging(level="INFO") .. rst-class:: sphx-glr-script-out .. code-block:: none 2024-07-22 09:34:23,163 - JUNIFER - INFO - ===== Lib Versions ===== 2024-07-22 09:34:23,164 - JUNIFER - INFO - numpy: 1.26.4 2024-07-22 09:34:23,164 - JUNIFER - INFO - scipy: 1.14.0 2024-07-22 09:34:23,164 - JUNIFER - INFO - pandas: 2.1.4 2024-07-22 09:34:23,164 - JUNIFER - INFO - nilearn: 0.10.4 2024-07-22 09:34:23,164 - JUNIFER - INFO - nibabel: 5.2.1 2024-07-22 09:34:23,164 - JUNIFER - INFO - junifer: 0.0.5 2024-07-22 09:34:23,164 - JUNIFER - INFO - ======================== .. GENERATED FROM PYTHON SOURCE LINES 33-34 Define the markers you want: .. GENERATED FROM PYTHON SOURCE LINES 34-52 .. code-block:: Python marker_dicts = [ { "name": "Schaefer100x17_TrimMean80", "kind": "ParcelAggregation", "parcellation": "Schaefer100x17", "method": "trim_mean", "method_params": {"proportiontocut": 0.2}, }, { "name": "Schaefer200x17_Mean", "kind": "ParcelAggregation", "parcellation": "Schaefer200x17", "method": "mean", }, ] .. GENERATED FROM PYTHON SOURCE LINES 53-54 Define target and confounds for julearn machine learning: .. GENERATED FROM PYTHON SOURCE LINES 54-58 .. code-block:: Python y = "age" confound = "sex" .. GENERATED FROM PYTHON SOURCE LINES 59-61 Load the VBM phenotype data for machine learning data: - Fetch the Oasis dataset .. GENERATED FROM PYTHON SOURCE LINES 61-70 .. code-block:: Python oasis_dataset = nilearn.datasets.fetch_oasis_vbm() age = oasis_dataset.ext_vars[y][:10] sex = ( pd.Series(oasis_dataset.ext_vars["mf"][:10]) .map(lambda x: 1 if x == "F" else 0) .values ) .. GENERATED FROM PYTHON SOURCE LINES 71-72 Create a temporary directory for junifer feature extraction: .. GENERATED FROM PYTHON SOURCE LINES 72-92 .. code-block:: Python with tempfile.TemporaryDirectory() as tmpdir: storage = {"kind": "SQLiteFeatureStorage", "uri": f"{tmpdir}/test.sqlite"} # run the defined junifer feature extraction pipeline run( workdir="/tmp", datagrabber={"kind": "OasisVBMTestingDataGrabber"}, markers=marker_dicts, storage=storage, ) # read in extracted features and add confounds and targets # for julearn run cross validation collect(storage) db = SQLiteFeatureStorage(uri=storage["uri"]) df_vbm = db.read_df(feature_name="VBM_GM_Schaefer200x17_Mean_aggregation") oasis_subjects = [x[0] for x in df_vbm.index] df_vbm.index = oasis_subjects .. rst-class:: sphx-glr-script-out .. code-block:: none 2024-07-22 09:34:23,177 - JUNIFER - INFO - Validating Marker Collection 2024-07-22 09:34:23,177 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM'] 2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating Data Reader: 2024-07-22 09:34:23,178 - JUNIFER - INFO - Data Reader output type: ['VBM_GM'] 2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80 2024-07-22 09:34:23,178 - JUNIFER - INFO - Marker output type: ['vector'] 2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80 2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean 2024-07-22 09:34:23,178 - JUNIFER - INFO - Marker output type: ['vector'] 2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean 2024-07-22 09:34:23,182 - JUNIFER - INFO - Getting element sub-01 2024-07-22 09:34:23,182 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:34:23,182 - 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 09:34:23,182 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:34:23,183 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:34:23,183 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:23,183 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:23,183 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:23,183 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:23,183 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:34:23,183 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:23,184 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:23,214 - 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 09:34:24,282 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:24,379 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationst3i99eyp/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationst3i99eyp/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprihz_ri0/parcellationsioo3p7fp/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:25,773 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:26,795 - JUNIFER - INFO - Storing in 2024-07-22 09:34:26,825 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:34:26,826 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:26,826 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:26,826 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:26,826 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:26,826 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:34:26,826 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:26,827 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:26,857 - 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 09:34:27,940 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:28,037 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsa0qxppoa/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsa0qxppoa/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprihz_ri0/parcellationsauqfh99k/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:30,095 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:31,146 - JUNIFER - INFO - Storing in 2024-07-22 09:34:31,192 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:34:31,193 - JUNIFER - INFO - Getting element sub-02 2024-07-22 09:34:31,193 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:34:31,193 - 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 09:34:31,193 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:34:31,194 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:34:31,194 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:31,194 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:31,194 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:31,194 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:31,194 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:34:31,194 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:31,196 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:31,225 - 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 09:34:32,293 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:32,390 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations38z3e0vc/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations38z3e0vc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvh0jl4rb/parcellations2eh9zimq/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:33,781 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:34,800 - JUNIFER - INFO - Storing in 2024-07-22 09:34:34,829 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:34:34,830 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:34,830 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:34,830 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:34,830 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:34,830 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:34:34,830 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:34,831 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:34,861 - 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 09:34:35,933 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:36,030 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsu8e4_09l/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsu8e4_09l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvh0jl4rb/parcellationsmfkw14ca/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:38,066 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:39,090 - JUNIFER - INFO - Storing in 2024-07-22 09:34:39,136 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:34:39,137 - JUNIFER - INFO - Getting element sub-03 2024-07-22 09:34:39,137 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:34:39,137 - 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 09:34:39,137 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:34:39,138 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:34:39,138 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:39,138 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:39,138 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:39,138 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:39,138 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:34:39,138 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:39,140 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:39,169 - 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 09:34:40,250 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:40,347 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations_abyizpw/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations_abyizpw/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprfbrs_rk/parcellations8vtf54p8/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:41,737 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:42,768 - JUNIFER - INFO - Storing in 2024-07-22 09:34:42,798 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:34:42,798 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:42,798 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:42,798 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:42,798 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:42,798 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:34:42,798 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:42,800 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:42,830 - 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 09:34:43,910 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:44,007 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsd9nbha6y/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsd9nbha6y/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprfbrs_rk/parcellationsxudy6a8i/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:46,039 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:47,090 - JUNIFER - INFO - Storing in 2024-07-22 09:34:47,137 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:34:47,137 - JUNIFER - INFO - Getting element sub-04 2024-07-22 09:34:47,137 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:34:47,137 - 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 09:34:47,137 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:34:47,138 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:34:47,138 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:47,139 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:47,139 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:47,139 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:47,139 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:34:47,139 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:47,140 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:47,169 - 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 09:34:48,263 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:48,360 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations2osr48o9/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations2osr48o9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7bcbf8ui/parcellationskvyurlow/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:49,757 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:50,793 - JUNIFER - INFO - Storing in 2024-07-22 09:34:50,822 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:34:50,822 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:50,823 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:50,823 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:50,823 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:50,823 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:34:50,823 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:50,824 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:50,854 - 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 09:34:51,929 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:52,026 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations0f77c4c5/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations0f77c4c5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7bcbf8ui/parcellationserodyis8/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:54,067 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:55,095 - JUNIFER - INFO - Storing in 2024-07-22 09:34:55,141 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:34:55,141 - JUNIFER - INFO - Getting element sub-05 2024-07-22 09:34:55,142 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:34:55,142 - 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 09:34:55,142 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:34:55,142 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:34:55,143 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:55,143 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:55,143 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:55,143 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:55,143 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:34:55,143 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:55,144 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:55,174 - 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 09:34:56,244 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:56,341 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsnr_vaiv1/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsnr_vaiv1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprq8u3ecq/parcellationszdj1gr5a/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:34:57,736 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:34:58,744 - JUNIFER - INFO - Storing in 2024-07-22 09:34:58,774 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:34:58,774 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:34:58,774 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:34:58,775 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:34:58,775 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:34:58,775 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:34:58,775 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:34:58,776 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:34:58,806 - 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 09:34:59,863 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:34:59,960 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsj8n2ncv8/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsj8n2ncv8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprq8u3ecq/parcellationsaxn99s4z/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:01,990 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:03,016 - JUNIFER - INFO - Storing in 2024-07-22 09:35:03,062 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:35:03,063 - JUNIFER - INFO - Getting element sub-06 2024-07-22 09:35:03,063 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:35:03,063 - 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 09:35:03,063 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:35:03,064 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:35:03,064 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:03,064 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:03,064 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:03,064 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:03,064 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:35:03,064 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:03,065 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:03,095 - 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 09:35:04,154 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:04,251 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations43z30hom/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations43z30hom/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgocnkhqz/parcellationsf6mfaxmv/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:05,646 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:06,698 - JUNIFER - INFO - Storing in 2024-07-22 09:35:06,727 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:35:06,727 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:06,728 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:06,728 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:06,728 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:06,728 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:35:06,728 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:06,729 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:06,759 - 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 09:35:07,842 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:07,940 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationswj36usot/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationswj36usot/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgocnkhqz/parcellations3lepy87z/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:09,966 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:11,001 - JUNIFER - INFO - Storing in 2024-07-22 09:35:11,047 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:35:11,048 - JUNIFER - INFO - Getting element sub-07 2024-07-22 09:35:11,048 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:35:11,048 - 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 09:35:11,048 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:35:11,049 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:35:11,049 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:11,049 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:11,049 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:11,049 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:11,049 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:35:11,049 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:11,050 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:11,080 - 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 09:35:12,140 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:12,237 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationszolq70hr/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationszolq70hr/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpsqs6vci8/parcellationsebiml_5n/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:13,628 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:14,653 - JUNIFER - INFO - Storing in 2024-07-22 09:35:14,683 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:35:14,683 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:14,684 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:14,684 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:14,684 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:14,684 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:35:14,684 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:14,685 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:14,715 - 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 09:35:15,772 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:15,869 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations6ikeall8/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations6ikeall8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpsqs6vci8/parcellationsqj5dhrm4/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:17,906 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:18,924 - JUNIFER - INFO - Storing in 2024-07-22 09:35:18,970 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:35:18,970 - JUNIFER - INFO - Getting element sub-08 2024-07-22 09:35:18,971 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:35:18,971 - 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 09:35:18,971 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:35:18,971 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:35:18,971 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:18,972 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:18,972 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:18,972 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:18,972 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:35:18,972 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:18,973 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:19,003 - 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 09:35:20,065 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:20,162 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationspivijrv_/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationspivijrv_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpwgohhjqg/parcellations0wtjix8i/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:21,561 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:22,583 - JUNIFER - INFO - Storing in 2024-07-22 09:35:22,612 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:35:22,612 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:22,613 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:22,613 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:22,613 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:22,613 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:35:22,613 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:22,614 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:22,644 - 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 09:35:23,707 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:23,804 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsr0p5c7qg/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsr0p5c7qg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpwgohhjqg/parcellationsy6sxnsni/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:25,844 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:26,873 - JUNIFER - INFO - Storing in 2024-07-22 09:35:26,919 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:35:26,919 - JUNIFER - INFO - Getting element sub-09 2024-07-22 09:35:26,920 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:35:26,920 - 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 09:35:26,920 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:35:26,920 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:35:26,921 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:26,921 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:26,921 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:26,921 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:26,921 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:35:26,921 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:26,922 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:26,952 - 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 09:35:28,010 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:28,107 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations49yg_375/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations49yg_375/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi3c49glk/parcellationszbdb6u6q/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:29,501 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:30,603 - JUNIFER - INFO - Storing in 2024-07-22 09:35:30,633 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:35:30,633 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:30,633 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:30,633 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:30,633 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:30,633 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:35:30,633 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:30,635 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:30,665 - 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 09:35:31,722 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:31,820 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsviu1_u5d/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsviu1_u5d/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi3c49glk/parcellations6ah_6w9b/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:33,857 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:34,888 - JUNIFER - INFO - Storing in 2024-07-22 09:35:34,934 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:35:34,935 - JUNIFER - INFO - Getting element sub-10 2024-07-22 09:35:34,935 - JUNIFER - INFO - Fitting pipeline 2024-07-22 09:35:34,935 - 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 09:35:34,935 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-07-22 09:35:34,936 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-07-22 09:35:34,936 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:34,936 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:34,936 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:34,936 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:34,936 - JUNIFER - INFO - n_rois: 100 2024-07-22 09:35:34,936 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:34,937 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:34,967 - 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 09:35:36,023 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:36,120 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsqpe_3pfx/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsqpe_3pfx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6rrxadz8/parcellations7afzj14g/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:37,513 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:38,526 - JUNIFER - INFO - Storing in 2024-07-22 09:35:38,556 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-07-22 09:35:38,556 - JUNIFER - INFO - Computing VBM_GM 2024-07-22 09:35:38,556 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-07-22 09:35:38,556 - JUNIFER - INFO - Parcellation parameters: 2024-07-22 09:35:38,556 - JUNIFER - INFO - resolution: 2.0 2024-07-22 09:35:38,556 - JUNIFER - INFO - n_rois: 200 2024-07-22 09:35:38,556 - JUNIFER - INFO - yeo_networks: 17 2024-07-22 09:35:38,557 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-07-22 09:35:38,588 - 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 09:35:39,641 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-07-22 09:35:39,738 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations6cinw0go/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations6cinw0go/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6rrxadz8/parcellations0xbpfe2h/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-07-22 09:35:41,765 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: b'' 2024-07-22 09:35:42,777 - JUNIFER - INFO - Storing in 2024-07-22 09:35:42,823 - JUNIFER - INFO - Marker collection fitting done 2024-07-22 09:35:42,823 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage 2024-07-22 09:35:42,823 - JUNIFER - INFO - Collecting data from /tmp/tmp__qxy8ry/*test.sqlite file: 0it [00:00, ?it/s] feature: 0%| | 0/2 [00:00` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: run_junifer_julearn.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_