.. 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 2024-08-14 13:31:37,193 - JUNIFER - INFO - ===== Lib Versions ===== 2024-08-14 13:31:37,193 - JUNIFER - INFO - numpy: 1.26.4 2024-08-14 13:31:37,193 - JUNIFER - INFO - scipy: 1.14.0 2024-08-14 13:31:37,193 - JUNIFER - INFO - pandas: 2.1.4 2024-08-14 13:31:37,193 - JUNIFER - INFO - nilearn: 0.10.4 2024-08-14 13:31:37,193 - JUNIFER - INFO - nibabel: 5.2.1 2024-08-14 13:31:37,193 - JUNIFER - INFO - junifer: 0.0.6.dev23 2024-08-14 13:31:37,193 - 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 2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Marker Collection 2024-08-14 13:31:37,207 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM'] 2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Data Reader: 2024-08-14 13:31:37,207 - JUNIFER - INFO - Data Reader output type: ['VBM_GM'] 2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80 2024-08-14 13:31:37,207 - JUNIFER - INFO - Marker output type: ['vector'] 2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80 2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean 2024-08-14 13:31:37,208 - JUNIFER - INFO - Marker output type: ['vector'] 2024-08-14 13:31:37,208 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean 2024-08-14 13:31:37,212 - JUNIFER - INFO - Getting element sub-01 2024-08-14 13:31:37,212 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:31:37,212 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:31:37,212 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:31:37,213 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:31:37,213 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:31:37,213 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:31:37,214 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:31:37,214 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:31:37,214 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:31:37,214 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:31:37,215 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:31:37,245 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:31:38,273 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:31:38,370 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsk_7rlurr/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsk_7rlurr/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpyf0mk8g3/parcellations01lh7bnf/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:31:39,758 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:31:40,778 - JUNIFER - INFO - Storing in 2024-08-14 13:31:40,811 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:31:40,811 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:31:40,812 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:31:40,812 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:31:40,812 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:31:40,812 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:31:40,812 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:31:40,813 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:31:40,844 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:31:41,894 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:31:41,991 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsn1cbu0s3/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsn1cbu0s3/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpyf0mk8g3/parcellations76xt8d63/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:31:44,030 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:31:45,057 - JUNIFER - INFO - Storing in 2024-08-14 13:31:45,103 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:31:45,104 - JUNIFER - INFO - Getting element sub-02 2024-08-14 13:31:45,104 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:31:45,104 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:31:45,104 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:31:45,105 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:31:45,105 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:31:45,105 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:31:45,105 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:31:45,105 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:31:45,105 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:31:45,106 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:31:45,107 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:31:45,136 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:31:46,172 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:31:46,268 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsze7on4ow/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsze7on4ow/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpehxlabxz/parcellationslsci3gpa/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:31:47,672 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:31:48,693 - JUNIFER - INFO - Storing in 2024-08-14 13:31:48,728 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:31:48,728 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:31:48,729 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:31:48,729 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:31:48,729 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:31:48,729 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:31:48,729 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:31:48,730 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:31:48,761 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:31:49,798 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:31:49,895 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations_n837ejg/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations_n837ejg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpehxlabxz/parcellationsea2v8nng/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:31:51,924 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:31:52,911 - JUNIFER - INFO - Storing in 2024-08-14 13:31:52,958 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:31:52,959 - JUNIFER - INFO - Getting element sub-03 2024-08-14 13:31:52,959 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:31:52,959 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:31:52,959 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:31:52,960 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:31:52,960 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:31:52,960 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:31:52,960 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:31:52,961 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:31:52,961 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:31:52,961 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:31:52,962 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:31:52,991 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:31:54,002 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:31:54,099 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationskhx67939/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationskhx67939/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmplbrzzzt_/parcellationscn0krced/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:31:55,485 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:31:56,487 - JUNIFER - INFO - Storing in 2024-08-14 13:31:56,518 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:31:56,518 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:31:56,518 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:31:56,519 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:31:56,519 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:31:56,519 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:31:56,519 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:31:56,520 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:31:56,550 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:31:57,578 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:31:57,675 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsp7_2emuc/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsp7_2emuc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmplbrzzzt_/parcellations2u0_jtr1/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:31:59,706 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:00,771 - JUNIFER - INFO - Storing in 2024-08-14 13:32:00,818 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:00,818 - JUNIFER - INFO - Getting element sub-04 2024-08-14 13:32:00,819 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:00,819 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:00,819 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:00,820 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:00,820 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:00,820 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:00,820 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:00,820 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:00,820 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:00,821 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:00,822 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:00,852 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:01,909 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:02,006 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationstp4y7ax8/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationstp4y7ax8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa8btuy0o/parcellations_s2i5892/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:03,400 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:04,506 - JUNIFER - INFO - Storing in 2024-08-14 13:32:04,539 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:04,539 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:04,540 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:04,540 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:04,540 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:04,540 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:04,540 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:04,541 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:04,572 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:05,634 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:05,731 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsf56ght22/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsf56ght22/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa8btuy0o/parcellationseukriiwm/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:07,759 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:08,763 - JUNIFER - INFO - Storing in 2024-08-14 13:32:08,809 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:08,809 - JUNIFER - INFO - Getting element sub-05 2024-08-14 13:32:08,810 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:08,810 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:08,810 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:08,811 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:08,811 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:08,811 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:08,811 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:08,811 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:08,811 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:08,812 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:08,813 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:08,842 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:09,911 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:10,008 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations3aydknh0/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations3aydknh0/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpqtg8ujtl/parcellationsotc7h1wh/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:11,393 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:12,392 - JUNIFER - INFO - Storing in 2024-08-14 13:32:12,422 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:12,423 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:12,423 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:12,423 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:12,423 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:12,423 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:12,423 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:12,425 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:12,455 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:13,479 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:13,576 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations756e923l/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations756e923l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpqtg8ujtl/parcellationsp7jnsh3z/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:15,608 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:16,593 - JUNIFER - INFO - Storing in 2024-08-14 13:32:16,638 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:16,639 - JUNIFER - INFO - Getting element sub-06 2024-08-14 13:32:16,639 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:16,639 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:16,639 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:16,640 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:16,640 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:16,641 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:16,641 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:16,641 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:16,641 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:16,641 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:16,642 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:16,672 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:17,691 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:17,787 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations__0x6lgs/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations__0x6lgs/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpy93ai3yc/parcellationsg0ee7xqy/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:19,179 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:20,177 - JUNIFER - INFO - Storing in 2024-08-14 13:32:20,210 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:20,210 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:20,210 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:20,210 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:20,210 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:20,211 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:20,211 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:20,212 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:20,242 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:21,271 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:21,369 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationssj1c90m3/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationssj1c90m3/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpy93ai3yc/parcellations3jcgmobs/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:23,407 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:24,402 - JUNIFER - INFO - Storing in 2024-08-14 13:32:24,449 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:24,449 - JUNIFER - INFO - Getting element sub-07 2024-08-14 13:32:24,449 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:24,449 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:24,449 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:24,450 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:24,450 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:24,451 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:24,451 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:24,451 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:24,451 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:24,451 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:24,452 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:24,482 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:25,519 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:25,616 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations7h6rfx6r/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations7h6rfx6r/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5xe2_a29/parcellations0e2bl88y/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:27,005 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:28,019 - JUNIFER - INFO - Storing in 2024-08-14 13:32:28,049 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:28,049 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:28,049 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:28,050 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:28,050 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:28,050 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:28,050 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:28,051 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:28,082 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:29,122 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:29,220 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsfngfzmv9/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsfngfzmv9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5xe2_a29/parcellationsgmzoforx/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:31,240 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:32,291 - JUNIFER - INFO - Storing in 2024-08-14 13:32:32,338 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:32,339 - JUNIFER - INFO - Getting element sub-08 2024-08-14 13:32:32,339 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:32,339 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:32,339 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:32,340 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:32,340 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:32,341 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:32,341 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:32,341 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:32,341 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:32,341 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:32,342 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:32,372 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:33,422 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:33,521 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsaw8_w077/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsaw8_w077/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzugufs9u/parcellationst_44g44z/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:34,909 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:35,985 - JUNIFER - INFO - Storing in 2024-08-14 13:32:36,018 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:36,018 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:36,019 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:36,019 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:36,019 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:36,019 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:36,019 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:36,021 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:36,051 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:37,112 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:37,210 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations18_tv4sz/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations18_tv4sz/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzugufs9u/parcellations2dd0_ar6/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:39,254 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:40,326 - JUNIFER - INFO - Storing in 2024-08-14 13:32:40,373 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:40,373 - JUNIFER - INFO - Getting element sub-09 2024-08-14 13:32:40,373 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:40,374 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:40,374 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:40,375 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:40,375 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:40,375 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:40,375 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:40,375 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:40,375 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:40,375 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:40,377 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:40,406 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:41,454 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:41,552 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsb0n2se5k/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsb0n2se5k/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmphskxfxzs/parcellationscv61ycth/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:42,941 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:44,046 - JUNIFER - INFO - Storing in 2024-08-14 13:32:44,080 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:44,080 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:44,081 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:44,081 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:44,081 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:44,081 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:44,081 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:44,082 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:44,113 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:45,166 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:45,264 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsodev0ycx/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsodev0ycx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmphskxfxzs/parcellationsonq8_2nd/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:47,289 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:48,369 - JUNIFER - INFO - Storing in 2024-08-14 13:32:48,420 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:48,420 - JUNIFER - INFO - Getting element sub-10 2024-08-14 13:32:48,421 - JUNIFER - INFO - Fitting pipeline 2024-08-14 13:32:48,421 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-08-14 13:32:48,421 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-08-14 13:32:48,422 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-08-14 13:32:48,422 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:48,422 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:48,422 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:48,422 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:48,422 - JUNIFER - INFO - n_rois: 100 2024-08-14 13:32:48,423 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:48,424 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:48,454 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:49,506 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:49,603 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsbw9yjhtk/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsbw9yjhtk/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6kuq71nf/parcellationsmf3ak3f6/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:50,983 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:52,041 - JUNIFER - INFO - Storing in 2024-08-14 13:32:52,075 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-08-14 13:32:52,075 - JUNIFER - INFO - Computing VBM_GM 2024-08-14 13:32:52,076 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-08-14 13:32:52,076 - JUNIFER - INFO - Parcellation parameters: 2024-08-14 13:32:52,076 - JUNIFER - INFO - resolution: 2.0 2024-08-14 13:32:52,076 - JUNIFER - INFO - n_rois: 200 2024-08-14 13:32:52,076 - JUNIFER - INFO - yeo_networks: 17 2024-08-14 13:32:52,078 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-08-14 13:32:52,108 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-08-14 13:32:53,166 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-08-14 13:32:53,262 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations5nwsw_yx/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations5nwsw_yx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6kuq71nf/parcellations16_zsodk/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-08-14 13:32:55,286 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-08-14 13:32:56,341 - JUNIFER - INFO - Storing in 2024-08-14 13:32:56,388 - JUNIFER - INFO - Marker collection fitting done 2024-08-14 13:32:56,389 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage 2024-08-14 13:32:56,389 - JUNIFER - INFO - Collecting data from /tmp/tmpqe457sad/*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 `_