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")

2024-07-22 09:34:23,163 - JUNIFER - INFO - ===== Lib Versions =====
2024-07-22 09:34:23,164 - JUNIFER - INFO - numpy: 1.26.4
2024-07-22 09:34:23,164 - JUNIFER - INFO - scipy: 1.14.0
2024-07-22 09:34:23,164 - JUNIFER - INFO - pandas: 2.1.4
2024-07-22 09:34:23,164 - JUNIFER - INFO - nilearn: 0.10.4
2024-07-22 09:34:23,164 - JUNIFER - INFO - nibabel: 5.2.1
2024-07-22 09:34:23,164 - JUNIFER - INFO - junifer: 0.0.5
2024-07-22 09:34:23,164 - JUNIFER - INFO - ========================

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

2024-07-22 09:34:23,177 - JUNIFER - INFO - Validating Marker Collection
2024-07-22 09:34:23,177 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating Data Reader:
2024-07-22 09:34:23,178 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-07-22 09:34:23,178 - JUNIFER - INFO - Marker output type: ['vector']
2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-07-22 09:34:23,178 - JUNIFER - INFO - Marker output type: ['vector']
2024-07-22 09:34:23,178 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2024-07-22 09:34:23,182 - JUNIFER - INFO - Getting element sub-01
2024-07-22 09:34:23,182 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:34:23,182 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:34:23,182 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:34:23,183 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:34:23,183 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:23,183 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:23,183 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:23,183 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:23,183 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:34:23,183 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:23,184 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:23,214 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:24,282 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:24,379 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationst3i99eyp/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationst3i99eyp/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprihz_ri0/parcellationsioo3p7fp/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:25,773 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:26,795 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:26,825 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:34:26,826 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:26,826 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:26,826 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:26,826 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:26,826 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:34:26,826 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:26,827 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:26,857 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:27,940 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:28,037 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsa0qxppoa/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsa0qxppoa/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprihz_ri0/parcellationsauqfh99k/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:30,095 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:31,146 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:31,192 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:34:31,193 - JUNIFER - INFO - Getting element sub-02
2024-07-22 09:34:31,193 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:34:31,193 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:34:31,193 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:34:31,194 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:34:31,194 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:31,194 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:31,194 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:31,194 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:31,194 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:34:31,194 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:31,196 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:31,225 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:32,293 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:32,390 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations38z3e0vc/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations38z3e0vc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvh0jl4rb/parcellations2eh9zimq/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:33,781 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:34,800 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:34,829 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:34:34,830 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:34,830 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:34,830 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:34,830 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:34,830 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:34:34,830 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:34,831 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:34,861 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:35,933 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:36,030 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsu8e4_09l/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsu8e4_09l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpvh0jl4rb/parcellationsmfkw14ca/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:38,066 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:39,090 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:39,136 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:34:39,137 - JUNIFER - INFO - Getting element sub-03
2024-07-22 09:34:39,137 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:34:39,137 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:34:39,137 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:34:39,138 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:34:39,138 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:39,138 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:39,138 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:39,138 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:39,138 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:34:39,138 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:39,140 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:39,169 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:40,250 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:40,347 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations_abyizpw/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations_abyizpw/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprfbrs_rk/parcellations8vtf54p8/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:41,737 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:42,768 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:42,798 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:34:42,798 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:42,798 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:42,798 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:42,798 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:42,798 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:34:42,798 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:42,800 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:42,830 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:43,910 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:44,007 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsd9nbha6y/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsd9nbha6y/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprfbrs_rk/parcellationsxudy6a8i/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:46,039 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:47,090 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:47,137 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:34:47,137 - JUNIFER - INFO - Getting element sub-04
2024-07-22 09:34:47,137 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:34:47,137 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:34:47,137 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:34:47,138 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:34:47,138 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:47,139 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:47,139 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:47,139 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:47,139 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:34:47,139 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:47,140 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:47,169 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:48,263 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:48,360 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations2osr48o9/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations2osr48o9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7bcbf8ui/parcellationskvyurlow/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:49,757 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:50,793 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:50,822 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:34:50,822 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:50,823 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:50,823 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:50,823 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:50,823 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:34:50,823 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:50,824 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:50,854 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:51,929 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:52,026 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations0f77c4c5/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations0f77c4c5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7bcbf8ui/parcellationserodyis8/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:54,067 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:55,095 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:55,141 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:34:55,141 - JUNIFER - INFO - Getting element sub-05
2024-07-22 09:34:55,142 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:34:55,142 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:34:55,142 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:34:55,142 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:34:55,143 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:55,143 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:55,143 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:55,143 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:55,143 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:34:55,143 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:55,144 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:55,174 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:56,244 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:56,341 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsnr_vaiv1/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsnr_vaiv1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprq8u3ecq/parcellationszdj1gr5a/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:34:57,736 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:34:58,744 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:34:58,774 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:34:58,774 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:34:58,774 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:34:58,775 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:34:58,775 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:34:58,775 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:34:58,775 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:34:58,776 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:34:58,806 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:34:59,863 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:34:59,960 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsj8n2ncv8/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsj8n2ncv8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmprq8u3ecq/parcellationsaxn99s4z/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:01,990 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:03,016 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:03,062 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:35:03,063 - JUNIFER - INFO - Getting element sub-06
2024-07-22 09:35:03,063 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:35:03,063 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:35:03,063 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:35:03,064 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:35:03,064 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:03,064 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:03,064 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:03,064 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:03,064 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:35:03,064 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:03,065 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:03,095 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:04,154 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:04,251 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations43z30hom/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations43z30hom/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgocnkhqz/parcellationsf6mfaxmv/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:05,646 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:06,698 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:06,727 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:35:06,727 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:06,728 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:06,728 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:06,728 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:06,728 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:35:06,728 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:06,729 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:06,759 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:07,842 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:07,940 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationswj36usot/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationswj36usot/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgocnkhqz/parcellations3lepy87z/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:09,966 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:11,001 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:11,047 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:35:11,048 - JUNIFER - INFO - Getting element sub-07
2024-07-22 09:35:11,048 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:35:11,048 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:35:11,048 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:35:11,049 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:35:11,049 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:11,049 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:11,049 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:11,049 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:11,049 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:35:11,049 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:11,050 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:11,080 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:12,140 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:12,237 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationszolq70hr/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationszolq70hr/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpsqs6vci8/parcellationsebiml_5n/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:13,628 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:14,653 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:14,683 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:35:14,683 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:14,684 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:14,684 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:14,684 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:14,684 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:35:14,684 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:14,685 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:14,715 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:15,772 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:15,869 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations6ikeall8/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations6ikeall8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpsqs6vci8/parcellationsqj5dhrm4/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:17,906 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:18,924 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:18,970 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:35:18,970 - JUNIFER - INFO - Getting element sub-08
2024-07-22 09:35:18,971 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:35:18,971 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:35:18,971 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:35:18,971 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:35:18,971 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:18,972 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:18,972 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:18,972 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:18,972 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:35:18,972 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:18,973 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:19,003 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:20,065 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:20,162 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationspivijrv_/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationspivijrv_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpwgohhjqg/parcellations0wtjix8i/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:21,561 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:22,583 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:22,612 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:35:22,612 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:22,613 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:22,613 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:22,613 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:22,613 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:35:22,613 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:22,614 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:22,644 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:23,707 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:23,804 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsr0p5c7qg/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsr0p5c7qg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpwgohhjqg/parcellationsy6sxnsni/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:25,844 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:26,873 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:26,919 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:35:26,919 - JUNIFER - INFO - Getting element sub-09
2024-07-22 09:35:26,920 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:35:26,920 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:35:26,920 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:35:26,920 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:35:26,921 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:26,921 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:26,921 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:26,921 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:26,921 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:35:26,921 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:26,922 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:26,952 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:28,010 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:28,107 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations49yg_375/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations49yg_375/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi3c49glk/parcellationszbdb6u6q/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:29,501 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:30,603 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:30,633 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:35:30,633 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:30,633 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:30,633 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:30,633 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:30,633 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:35:30,633 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:30,635 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:30,665 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:31,722 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:31,820 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsviu1_u5d/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsviu1_u5d/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpi3c49glk/parcellations6ah_6w9b/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:33,857 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:34,888 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:34,934 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:35:34,935 - JUNIFER - INFO - Getting element sub-10
2024-07-22 09:35:34,935 - JUNIFER - INFO - Fitting pipeline
2024-07-22 09:35:34,935 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-07-22 09:35:34,935 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-07-22 09:35:34,936 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-07-22 09:35:34,936 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:34,936 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:34,936 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:34,936 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:34,936 - JUNIFER - INFO -      n_rois: 100
2024-07-22 09:35:34,936 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:34,937 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:34,967 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:36,023 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:36,120 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellationsqpe_3pfx/Schaefer100x17.nii.gz -r /tmp/tmpcysmnw4q/parcellationsqpe_3pfx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6rrxadz8/parcellations7afzj14g/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:37,513 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:38,526 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:38,556 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-07-22 09:35:38,556 - JUNIFER - INFO - Computing VBM_GM
2024-07-22 09:35:38,556 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-07-22 09:35:38,556 - JUNIFER - INFO - Parcellation parameters:
2024-07-22 09:35:38,556 - JUNIFER - INFO -      resolution: 2.0
2024-07-22 09:35:38,556 - JUNIFER - INFO -      n_rois: 200
2024-07-22 09:35:38,556 - JUNIFER - INFO -      yeo_networks: 17
2024-07-22 09:35:38,557 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-07-22 09:35:38,588 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-07-22 09:35:39,641 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-07-22 09:35:39,738 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpcysmnw4q/parcellations6cinw0go/Schaefer200x17.nii.gz -r /tmp/tmpcysmnw4q/parcellations6cinw0go/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6rrxadz8/parcellations0xbpfe2h/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-07-22 09:35:41,765 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-07-22 09:35:42,777 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp__qxy8ry/test.sqlite (multiple output)>
2024-07-22 09:35:42,823 - JUNIFER - INFO - Marker collection fitting done
2024-07-22 09:35:42,823 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-07-22 09:35:42,823 - JUNIFER - INFO - Collecting data from /tmp/tmp__qxy8ry/*test.sqlite

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2024-07-22 09:35:44,228 - 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  0.134273    0.019355  ...     0  509497eb21da473048117e0c6704d3ea
1  0.131651    0.019262  ...     1  509497eb21da473048117e0c6704d3ea
2  0.132441    0.019196  ...     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 21.812 seconds)

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