.. 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 /home/runner/work/junifer/junifer/junifer/utils/logging.py:139: UserWarning: The '__version__' attribute is deprecated and will be removed in MarkupSafe 3.1. Use feature detection, or `importlib.metadata.version("markupsafe")`, instead. vstring = str(getattr(module, "__version__", None)) 2024-10-10 16:06:09,779 - JUNIFER - INFO - ===== Lib Versions ===== 2024-10-10 16:06:09,779 - JUNIFER - INFO - numpy: 1.26.4 2024-10-10 16:06:09,779 - JUNIFER - INFO - scipy: 1.14.1 2024-10-10 16:06:09,779 - JUNIFER - INFO - pandas: 2.1.4 2024-10-10 16:06:09,779 - JUNIFER - INFO - nilearn: 0.10.4 2024-10-10 16:06:09,780 - JUNIFER - INFO - nibabel: 5.3.0 2024-10-10 16:06:09,780 - JUNIFER - INFO - junifer: 0.0.6.dev116 2024-10-10 16:06:09,780 - 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 2024-10-10 16:06:09,794 - JUNIFER - INFO - Validating Marker Collection 2024-10-10 16:06:09,794 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM'] 2024-10-10 16:06:09,795 - JUNIFER - INFO - Validating Data Reader: 2024-10-10 16:06:09,795 - JUNIFER - INFO - Data Reader output type: ['VBM_GM'] 2024-10-10 16:06:09,795 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80 2024-10-10 16:06:09,795 - JUNIFER - INFO - Marker output type: ['vector'] 2024-10-10 16:06:09,795 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80 2024-10-10 16:06:09,795 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean 2024-10-10 16:06:09,795 - JUNIFER - INFO - Marker output type: ['vector'] 2024-10-10 16:06:09,795 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean 2024-10-10 16:06:09,800 - JUNIFER - INFO - Getting element sub-01 2024-10-10 16:06:09,800 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:09,800 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:09,800 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:09,801 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:09,802 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:09,802 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:09,802 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:09,802 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:09,802 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:09,802 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:09,804 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:09,833 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:10,917 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:11,013 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellations0v90h_9j/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellations0v90h_9j/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpk9quyy_4/parcellationsqfzvod78/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:12,408 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:13,439 - JUNIFER - INFO - Storing in 2024-10-10 16:06:13,474 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:06:13,475 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:13,475 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:13,475 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:13,475 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:13,475 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:06:13,475 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:13,477 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:13,507 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:14,594 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:14,690 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsm5b8pgtz/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsm5b8pgtz/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpk9quyy_4/parcellationspb77lr9e/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:16,739 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:17,778 - JUNIFER - INFO - Storing in 2024-10-10 16:06:17,832 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:06:17,833 - JUNIFER - INFO - Getting element sub-02 2024-10-10 16:06:17,833 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:17,833 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:17,833 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:17,834 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:17,834 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:17,835 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:17,835 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:17,835 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:17,835 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:17,835 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:17,836 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:17,865 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:18,962 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:19,057 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationssvx2xfij/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationssvx2xfij/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpome72401/parcellationso6ayg65d/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:20,453 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:21,480 - JUNIFER - INFO - Storing in 2024-10-10 16:06:21,513 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:06:21,514 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:21,514 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:21,514 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:21,514 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:21,514 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:06:21,515 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:21,516 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:21,546 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:22,637 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:22,733 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsaejl464k/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsaejl464k/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpome72401/parcellationsuomwg_ge/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:24,768 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:25,819 - JUNIFER - INFO - Storing in 2024-10-10 16:06:25,872 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:06:25,873 - JUNIFER - INFO - Getting element sub-03 2024-10-10 16:06:25,873 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:25,873 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:25,873 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:25,874 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:25,874 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:25,875 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:25,875 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:25,875 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:25,875 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:25,875 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:25,876 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:25,905 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:26,996 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:27,092 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsmqpnddtu/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsmqpnddtu/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2holn7i7/parcellationsvu_fpso1/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:28,482 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:29,538 - JUNIFER - INFO - Storing in 2024-10-10 16:06:29,574 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:06:29,574 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:29,574 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:29,575 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:29,575 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:29,575 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:06:29,575 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:29,576 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:29,606 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:30,700 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:30,796 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsdkz2fwb2/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsdkz2fwb2/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp2holn7i7/parcellationsflave26d/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:32,828 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:33,892 - JUNIFER - INFO - Storing in 2024-10-10 16:06:33,945 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:06:33,945 - JUNIFER - INFO - Getting element sub-04 2024-10-10 16:06:33,946 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:33,946 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:33,946 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:33,947 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:33,947 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:33,947 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:33,947 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:33,948 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:33,948 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:33,948 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:33,949 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:33,978 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:35,064 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:35,168 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationss75vp76i/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationss75vp76i/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpp0lhvp47/parcellations7nade7au/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:36,566 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:37,613 - JUNIFER - INFO - Storing in 2024-10-10 16:06:37,648 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:06:37,648 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:37,649 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:37,649 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:37,649 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:37,649 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:06:37,649 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:37,651 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:37,680 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:38,762 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:38,859 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellations7wsdpn6q/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellations7wsdpn6q/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpp0lhvp47/parcellationsifzut6qa/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:40,905 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:41,945 - JUNIFER - INFO - Storing in 2024-10-10 16:06:41,998 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:06:41,998 - JUNIFER - INFO - Getting element sub-05 2024-10-10 16:06:41,998 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:41,999 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:41,999 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:42,000 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:42,000 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:42,000 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:42,000 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:42,000 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:42,000 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:42,001 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:42,002 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:42,031 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:43,114 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:43,210 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellations3cihg6o4/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellations3cihg6o4/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7vuchkce/parcellationsxnar983j/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:44,602 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:45,658 - JUNIFER - INFO - Storing in 2024-10-10 16:06:45,692 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:06:45,692 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:45,693 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:45,693 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:45,693 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:45,693 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:06:45,693 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:45,694 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:45,724 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:46,826 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:46,922 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsxb8cbw4l/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsxb8cbw4l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7vuchkce/parcellations1c3jqywl/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:48,963 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:50,013 - JUNIFER - INFO - Storing in 2024-10-10 16:06:50,065 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:06:50,066 - JUNIFER - INFO - Getting element sub-06 2024-10-10 16:06:50,066 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:50,066 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:50,066 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:50,067 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:50,067 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:50,068 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:50,068 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:50,068 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:50,068 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:50,068 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:50,069 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:50,099 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:51,182 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:51,277 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellations7p28ksml/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellations7p28ksml/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvzggvnii/parcellations0m7vjzdv/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:52,668 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:53,713 - JUNIFER - INFO - Storing in 2024-10-10 16:06:53,747 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:06:53,747 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:53,748 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:53,748 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:53,748 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:53,748 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:06:53,748 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:53,749 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:53,779 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:54,879 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:54,976 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsk821t_ai/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsk821t_ai/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvzggvnii/parcellations56rupnit/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:06:57,013 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:06:58,067 - JUNIFER - INFO - Storing in 2024-10-10 16:06:58,119 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:06:58,120 - JUNIFER - INFO - Getting element sub-07 2024-10-10 16:06:58,120 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:06:58,120 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:06:58,120 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:06:58,121 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:06:58,121 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:06:58,121 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:06:58,122 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:06:58,122 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:06:58,122 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:06:58,122 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:06:58,123 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:06:58,152 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:06:59,243 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:06:59,339 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsfwv1iqlc/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsfwv1iqlc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpc20f_kvh/parcellations1lnomwwa/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:00,730 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:01,755 - JUNIFER - INFO - Storing in 2024-10-10 16:07:01,790 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:07:01,790 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:01,790 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:01,791 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:01,791 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:01,791 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:07:01,791 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:01,792 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:01,822 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:02,920 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:03,016 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsqunbr2qt/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsqunbr2qt/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpc20f_kvh/parcellationsoj84sp51/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:05,063 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:06,116 - JUNIFER - INFO - Storing in 2024-10-10 16:07:06,168 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:07:06,168 - JUNIFER - INFO - Getting element sub-08 2024-10-10 16:07:06,168 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:07:06,168 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:07:06,168 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:07:06,169 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:07:06,170 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:06,170 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:06,170 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:06,170 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:06,170 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:07:06,170 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:06,172 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:06,201 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:07,297 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:07,393 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsuu3_6y_b/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsuu3_6y_b/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp0da9v60v/parcellationsrvmucsba/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:08,787 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:09,823 - JUNIFER - INFO - Storing in 2024-10-10 16:07:09,857 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:07:09,857 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:09,858 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:09,858 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:09,858 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:09,858 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:07:09,858 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:09,860 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:09,889 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:10,990 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:11,087 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationsbafwk1bv/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationsbafwk1bv/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp0da9v60v/parcellations93aql61l/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:13,120 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:14,194 - JUNIFER - INFO - Storing in 2024-10-10 16:07:14,248 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:07:14,248 - JUNIFER - INFO - Getting element sub-09 2024-10-10 16:07:14,248 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:07:14,248 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:07:14,249 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:07:14,250 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:07:14,250 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:14,250 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:14,250 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:14,250 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:14,251 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:07:14,251 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:14,252 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:14,281 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:15,368 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:15,465 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationstmictrmf/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationstmictrmf/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp9n_dmkew/parcellationszooba69q/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:16,868 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:17,934 - JUNIFER - INFO - Storing in 2024-10-10 16:07:17,970 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:07:17,970 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:17,971 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:17,971 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:17,971 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:17,971 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:07:17,971 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:17,972 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:18,002 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:19,100 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:19,196 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationstun728cg/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationstun728cg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp9n_dmkew/parcellationsn819eeb8/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:21,228 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:22,325 - JUNIFER - INFO - Storing in 2024-10-10 16:07:22,380 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:07:22,381 - JUNIFER - INFO - Getting element sub-10 2024-10-10 16:07:22,381 - JUNIFER - INFO - Fitting pipeline 2024-10-10 16:07:22,381 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz 2024-10-10 16:07:22,381 - JUNIFER - INFO - VBM_GM is of type NIFTI 2024-10-10 16:07:22,382 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80 2024-10-10 16:07:22,382 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:22,383 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:22,383 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:22,383 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:22,383 - JUNIFER - INFO - n_rois: 100 2024-10-10 16:07:22,383 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:22,384 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:22,414 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:23,500 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:23,596 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellationss9ia_9ld/Schaefer100x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellationss9ia_9ld/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpo1cckg7t/parcellationseubezxy7/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:24,986 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:26,034 - JUNIFER - INFO - Storing in 2024-10-10 16:07:26,069 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean 2024-10-10 16:07:26,069 - JUNIFER - INFO - Computing VBM_GM 2024-10-10 16:07:26,070 - JUNIFER - INFO - Fetching one of Schaefer parcellations. 2024-10-10 16:07:26,070 - JUNIFER - INFO - Parcellation parameters: 2024-10-10 16:07:26,070 - JUNIFER - INFO - resolution: 2.0 2024-10-10 16:07:26,070 - JUNIFER - INFO - n_rois: 200 2024-10-10 16:07:26,070 - JUNIFER - INFO - yeo_networks: 17 2024-10-10 16:07:26,072 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz 2024-10-10 16:07:26,101 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 2024-10-10 16:07:27,200 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2 2024-10-10 16:07:27,296 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpxfnbpk9d/parcellations5vh224y6/Schaefer200x17.nii.gz -r /tmp/tmpxfnbpk9d/parcellations5vh224y6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpo1cckg7t/parcellationskgy3gi4e/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz 2024-10-10 16:07:29,330 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: 2024-10-10 16:07:30,395 - JUNIFER - INFO - Storing in 2024-10-10 16:07:30,449 - JUNIFER - INFO - Marker collection fitting done 2024-10-10 16:07:30,449 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage 2024-10-10 16:07:30,449 - JUNIFER - INFO - Collecting data from /tmp/tmptlbl6y84/*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 ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: run_junifer_julearn.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_