Note

Go to the end to download the full example code.

8.7. 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

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

Set the logging level to info to see extra information:

configure_logging(level="INFO")

/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 - ========================

Define the markers you want:

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",
    },
]

Define target and confounds for julearn machine learning:

y = "age"
confound = "sex"

Load the VBM phenotype data for machine learning data: - Fetch the Oasis dataset

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
)

Create a temporary directory for junifer feature extraction:

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

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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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 <SQLiteFeatureStorage @ /tmp/tmptlbl6y84/test.sqlite (multiple output)>
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<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 14.07it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.04it/s]

file: 1it [00:00,  6.48it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.51it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.47it/s]

file: 2it [00:00,  6.84it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.65it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.62it/s]

file: 3it [00:00,  6.99it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.78it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.75it/s]

file: 4it [00:00,  7.09it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00,  7.90it/s]
feature: 100%|██████████| 2/2 [00:00<00:00,  7.89it/s]

file: 5it [00:00,  5.39it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.63it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.61it/s]

file: 6it [00:00,  5.89it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.68it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.65it/s]

file: 7it [00:01,  6.26it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.39it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.36it/s]

file: 8it [00:01,  6.50it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00, 15.48it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.45it/s]

file: 9it [00:01,  6.68it/s]

feature:   0%|          | 0/2 [00:00<?, ?it/s]

feature: 100%|██████████| 2/2 [00:00<00:00,  7.89it/s]
feature: 100%|██████████| 2/2 [00:00<00:00,  7.88it/s]

file: 10it [00:01,  5.40it/s]
file: 10it [00:01,  6.02it/s]
2024-10-10 16:07:32,112 - JUNIFER - INFO - Collect done

Using julearn for machine learning: We predict the age given our vbm features and sex as a confound.

X = list(df_vbm.columns)
df_vbm[y] = age
df_vbm[confound] = sex

X_types = {
    "features": X,
    "confound": confound,
}

creator = PipelineCreator(problem_type="regression", apply_to="features")
creator.add("zscore", apply_to=["features", "confound"])
creator.add("confound_removal", apply_to="features", confounds="confound")
creator.add("ridge")

scores = run_cross_validation(
    X=X + [confound],
    y=y,
    X_types=X_types,
    data=df_vbm,
    model=creator,
    cv=3,
)
print(scores)

   fit_time  score_time  ...  fold                          cv_mdsum
0  0.142803    0.020362  ...     0  509497eb21da473048117e0c6704d3ea
1  0.141779    0.020375  ...     1  509497eb21da473048117e0c6704d3ea
2  0.142537    0.020359  ...     2  509497eb21da473048117e0c6704d3ea

[3 rows x 8 columns]

Interpretation of results: Doing machine learning with only 10 datapoints is not meaningful. This explains the big variation in scores for different cross-validation folds.

Total running time of the script: (1 minutes 23.006 seconds)

Gallery generated by Sphinx-Gallery