.. 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 2024-09-30 11:47:32,097 - JUNIFER - INFO - ===== Lib Versions ===== 2024-09-30 11:47:32,097 - JUNIFER - INFO - numpy: 1.26.4 2024-09-30 11:47:32,097 - JUNIFER - INFO - scipy: 1.14.0 2024-09-30 11:47:32,097 - JUNIFER - INFO - pandas: 2.1.4 2024-09-30 11:47:32,097 - JUNIFER - INFO - nilearn: 0.10.4 2024-09-30 11:47:32,097 - JUNIFER - INFO - nibabel: 5.2.1 2024-09-30 11:47:32,097 - JUNIFER - INFO - junifer: 0.0.6.dev90 2024-09-30 11:47:32,097 - 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 2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Marker Collection 2024-09-30 11:47:32,111 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM'] 2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Data Reader: 2024-09-30 11:47:32,111 - JUNIFER - INFO - Data Reader output type: ['VBM_GM'] 2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80 2024-09-30 11:47:32,111 - JUNIFER - INFO - Marker output type: ['vector'] 2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80 2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean 2024-09-30 11:47:32,111 - JUNIFER - INFO - Marker output type: ['vector'] 2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean 2024-09-30 11:47:32,116 - JUNIFER - INFO - Getting element sub-01 2024-09-30 11:47:32,116 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:47:32,116 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:47:32,116 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:47:32,117 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:47:32,117 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:32,117 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:32,117 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:32,118 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:32,118 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:47:32,118 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:32,119 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:32,149 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:33,135 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:33,231 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations7yobja7a/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations7yobja7a/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzc62ehui/parcellations5h13d0hm/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:34,629 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:35,592 - JUNIFER - INFO - Storing in 2024-09-30 11:47:35,623 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:47:35,623 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:35,624 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:35,624 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:35,624 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:35,624 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:47:35,624 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:35,625 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:35,655 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:36,651 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:36,748 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations2vqismtq/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations2vqismtq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzc62ehui/parcellations5j8ftn2u/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:38,802 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:39,772 - JUNIFER - INFO - Storing in 2024-09-30 11:47:39,819 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:47:39,820 - JUNIFER - INFO - Getting element sub-02 2024-09-30 11:47:39,820 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:47:39,820 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:47:39,820 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:47:39,821 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:47:39,821 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:39,821 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:39,821 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:39,821 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:39,822 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:47:39,822 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:39,823 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:39,852 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:40,840 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:40,937 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsrtkhvrv6/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsrtkhvrv6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpl6otsjap/parcellationsl4ooka2v/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:42,333 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:43,298 - JUNIFER - INFO - Storing in 2024-09-30 11:47:43,329 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:47:43,329 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:43,330 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:43,330 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:43,330 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:43,330 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:47:43,330 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:43,331 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:43,361 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:44,354 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:44,451 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations3zeab1yk/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations3zeab1yk/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpl6otsjap/parcellations7atjxw46/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:46,508 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:47,481 - JUNIFER - INFO - Storing in 2024-09-30 11:47:47,528 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:47:47,528 - JUNIFER - INFO - Getting element sub-03 2024-09-30 11:47:47,528 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:47:47,528 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:47:47,528 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:47:47,529 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:47:47,529 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:47,530 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:47,530 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:47,530 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:47,530 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:47:47,530 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:47,531 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:47,561 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:48,549 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:48,645 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsihgjxp_t/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsihgjxp_t/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp1n61hxz9/parcellationsjqtajn1k/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:50,042 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:51,001 - JUNIFER - INFO - Storing in 2024-09-30 11:47:51,032 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:47:51,032 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:51,033 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:51,033 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:51,033 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:51,033 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:47:51,033 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:51,034 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:51,064 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:52,054 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:52,151 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsrcl0d07l/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsrcl0d07l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp1n61hxz9/parcellations28bp5cql/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:54,185 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:55,160 - JUNIFER - INFO - Storing in 2024-09-30 11:47:55,206 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:47:55,207 - JUNIFER - INFO - Getting element sub-04 2024-09-30 11:47:55,207 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:47:55,207 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:47:55,207 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:47:55,208 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:47:55,208 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:55,209 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:55,209 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:55,209 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:55,209 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:47:55,209 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:55,210 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:55,240 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:56,229 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:56,326 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations2ssf3v4z/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations2ssf3v4z/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpk68358mf/parcellationsh46h7qt7/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:47:57,716 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:47:58,679 - JUNIFER - INFO - Storing in 2024-09-30 11:47:58,712 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:47:58,712 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:47:58,713 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:47:58,713 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:47:58,713 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:47:58,713 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:47:58,713 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:47:58,714 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:47:58,744 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:47:59,726 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:47:59,822 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsilr2qvwb/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsilr2qvwb/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpk68358mf/parcellationskvifndro/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:01,871 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:02,839 - JUNIFER - INFO - Storing in 2024-09-30 11:48:02,886 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:02,886 - JUNIFER - INFO - Getting element sub-05 2024-09-30 11:48:02,887 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:48:02,887 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:48:02,887 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:48:02,888 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:48:02,888 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:02,888 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:02,888 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:02,888 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:02,888 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:48:02,888 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:02,890 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:02,919 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:03,915 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:04,012 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsroierx5v/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsroierx5v/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp39hv7ipj/parcellations3k_otbmx/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:05,403 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:06,346 - JUNIFER - INFO - Storing in 2024-09-30 11:48:06,377 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:48:06,378 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:06,378 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:06,378 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:06,378 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:06,378 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:48:06,378 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:06,380 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:06,409 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:07,398 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:07,495 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsj1snpmm1/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsj1snpmm1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp39hv7ipj/parcellationsjnei0bk4/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:09,576 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:10,535 - JUNIFER - INFO - Storing in 2024-09-30 11:48:10,581 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:10,582 - JUNIFER - INFO - Getting element sub-06 2024-09-30 11:48:10,582 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:48:10,582 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:48:10,582 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:48:10,583 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:48:10,583 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:10,584 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:10,584 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:10,584 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:10,584 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:48:10,584 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:10,585 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:10,614 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:11,600 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:11,696 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationszohfyyt_/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationszohfyyt_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpriiyy9d2/parcellations06b6x8ce/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:13,083 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:14,031 - JUNIFER - INFO - Storing in 2024-09-30 11:48:14,062 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:48:14,062 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:14,063 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:14,063 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:14,063 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:14,063 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:48:14,063 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:14,064 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:14,094 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:15,085 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:15,182 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations4sovg_g2/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations4sovg_g2/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpriiyy9d2/parcellationsoqox3uxo/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:17,213 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:18,190 - JUNIFER - INFO - Storing in 2024-09-30 11:48:18,237 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:18,237 - JUNIFER - INFO - Getting element sub-07 2024-09-30 11:48:18,237 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:48:18,237 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:48:18,237 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:48:18,238 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:48:18,238 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:18,239 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:18,239 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:18,239 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:18,239 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:48:18,239 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:18,240 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:18,270 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:19,267 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:19,363 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations_te21wj8/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations_te21wj8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpkk6k28bg/parcellationswjgpskij/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:20,752 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:21,720 - JUNIFER - INFO - Storing in 2024-09-30 11:48:21,750 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:48:21,750 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:21,751 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:21,751 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:21,751 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:21,751 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:48:21,751 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:21,752 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:21,782 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:22,770 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:22,867 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsn33nktx_/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsn33nktx_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpkk6k28bg/parcellationsgug_n1_9/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:24,906 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:25,871 - JUNIFER - INFO - Storing in 2024-09-30 11:48:25,919 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:25,920 - JUNIFER - INFO - Getting element sub-08 2024-09-30 11:48:25,920 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:48:25,920 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:48:25,920 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:48:25,921 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:48:25,921 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:25,921 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:25,922 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:25,922 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:25,922 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:48:25,922 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:25,923 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:25,952 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:26,946 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:27,043 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsrl2yc7oi/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsrl2yc7oi/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpmaaxbbsu/parcellationsqkwyi1wr/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:28,432 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:29,382 - JUNIFER - INFO - Storing in 2024-09-30 11:48:29,413 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:48:29,413 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:29,414 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:29,414 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:29,414 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:29,414 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:48:29,414 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:29,415 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:29,445 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:30,435 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:30,532 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationslatc9300/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationslatc9300/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpmaaxbbsu/parcellationsmjzo1mu4/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:32,551 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:33,529 - JUNIFER - INFO - Storing in 2024-09-30 11:48:33,575 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:33,576 - JUNIFER - INFO - Getting element sub-09 2024-09-30 11:48:33,576 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:48:33,576 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:48:33,576 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:48:33,577 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:48:33,577 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:33,578 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:33,578 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:33,578 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:33,578 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:48:33,578 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:33,579 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:33,609 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:34,606 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:34,703 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsctbnkpwq/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsctbnkpwq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp3e6tjupk/parcellationsnyoa7bn8/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:36,090 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:37,091 - JUNIFER - INFO - Storing in 2024-09-30 11:48:37,122 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:48:37,123 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:37,123 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:37,123 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:37,123 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:37,123 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:48:37,123 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:37,124 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:37,154 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:38,149 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:38,246 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsa141u0cj/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsa141u0cj/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp3e6tjupk/parcellationscrufte29/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:40,292 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:41,276 - JUNIFER - INFO - Storing in 2024-09-30 11:48:41,323 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:41,323 - JUNIFER - INFO - Getting element sub-10 2024-09-30 11:48:41,323 - JUNIFER - INFO - Fitting pipeline 2024-09-30 11:48:41,323 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-09-30 11:48:41,323 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-09-30 11:48:41,324 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-09-30 11:48:41,324 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:41,325 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:41,325 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:41,325 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:41,325 - JUNIFER - INFO - n_rois: 100 2024-09-30 11:48:41,325 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:41,326 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:41,355 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:42,349 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:42,445 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationshuyx__of/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationshuyx__of/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptxbv8j1g/parcellationsalww9zwu/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:43,835 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:44,792 - JUNIFER - INFO - Storing in 2024-09-30 11:48:44,823 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-09-30 11:48:44,823 - JUNIFER - INFO - Computing VBM_GM 2024-09-30 11:48:44,824 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-09-30 11:48:44,824 - JUNIFER - INFO - Parcellation parameters: 2024-09-30 11:48:44,824 - JUNIFER - INFO - resolution: 2.0 2024-09-30 11:48:44,824 - JUNIFER - INFO - n_rois: 200 2024-09-30 11:48:44,824 - JUNIFER - INFO - yeo_networks: 17 2024-09-30 11:48:44,825 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-09-30 11:48:44,855 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-09-30 11:48:45,859 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-09-30 11:48:45,956 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations9reys9x6/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations9reys9x6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptxbv8j1g/parcellations4r06idi1/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-09-30 11:48:47,977 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-09-30 11:48:48,951 - JUNIFER - INFO - Storing in 2024-09-30 11:48:48,998 - JUNIFER - INFO - Marker collection fitting done 2024-09-30 11:48:48,998 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage 2024-09-30 11:48:48,998 - JUNIFER - INFO - Collecting data from /tmp/tmpzyev4mjh/*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 `_