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")
/__w/junifer/junifer/junifer/utils/logging.py:155: 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))
2025-09-22 15:48:47,012 - JUNIFER - INFO - ===== Lib Versions =====
2025-09-22 15:48:47,012 - JUNIFER - INFO - click: 8.1.8
2025-09-22 15:48:47,012 - JUNIFER - INFO - numpy: 1.26.4
2025-09-22 15:48:47,012 - JUNIFER - INFO - scipy: 1.15.0
2025-09-22 15:48:47,012 - JUNIFER - INFO - datalad: 1.1.6
2025-09-22 15:48:47,012 - JUNIFER - INFO - pandas: 2.1.4
2025-09-22 15:48:47,012 - JUNIFER - INFO - nibabel: 5.3.2
2025-09-22 15:48:47,012 - JUNIFER - INFO - nilearn: 0.10.4
2025-09-22 15:48:47,012 - JUNIFER - INFO - sqlalchemy: 2.0.43
2025-09-22 15:48:47,012 - JUNIFER - INFO - ruamel.yaml: 0.18.15
2025-09-22 15:48:47,012 - JUNIFER - INFO - tqdm: 4.66.6
2025-09-22 15:48:47,012 - JUNIFER - INFO - templateflow: 24.2.2
2025-09-22 15:48:47,012 - JUNIFER - INFO - junifer_data: None
2025-09-22 15:48:47,012 - JUNIFER - INFO - junifer: 0.0.7.dev206
2025-09-22 15:48:47,012 - 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:
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
2025-09-22 15:48:47,030 - JUNIFER - INFO - Validating Marker Collection
2025-09-22 15:48:47,031 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2025-09-22 15:48:47,031 - JUNIFER - INFO - Validating Data Reader:
2025-09-22 15:48:47,031 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2025-09-22 15:48:47,031 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2025-09-22 15:48:47,031 - JUNIFER - INFO - Marker output type: ['vector']
2025-09-22 15:48:47,031 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2025-09-22 15:48:47,031 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2025-09-22 15:48:47,031 - JUNIFER - INFO - Marker output type: ['vector']
2025-09-22 15:48:47,031 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2025-09-22 15:48:47,036 - JUNIFER - INFO - Getting element sub-01
2025-09-22 15:48:47,036 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:48:47,036 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:48:47,036 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:48:47,037 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:48:47,037 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:48:47,037 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:48:47,037 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:48:47,037 - JUNIFER - INFO - resolution: None
2025-09-22 15:48:47,037 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:48:47,037 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:48:47,037 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:48:47,111 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:48:49,406 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:48:49,909 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp2efmz2pq/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a063fede-97cb-11f0-a4c0-5ace1b2a80e5am53qvrz/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp2efmz2pq/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a063fede-97cb-11f0-a4c0-5ace1b2a80e5am53qvrz/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp2efmz2pq/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a063fede-97cb-11f0-a4c0-5ace1b2a80e5am53qvrz/parcellation_warped.nii.gz
2025-09-22 15:48:56,231 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:48:57,690 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:48:57,737 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:48:57,737 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:48:57,737 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:48:57,737 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:48:57,737 - JUNIFER - INFO - resolution: None
2025-09-22 15:48:57,737 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:48:57,737 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:48:57,737 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:48:57,812 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:49:00,133 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:49:00,639 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp2efmz2pq/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a6c59c92-97cb-11f0-a4c0-5ace1b2a80e5tcpbrwyk/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp2efmz2pq/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a6c59c92-97cb-11f0-a4c0-5ace1b2a80e5tcpbrwyk/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp2efmz2pq/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a6c59c92-97cb-11f0-a4c0-5ace1b2a80e5tcpbrwyk/parcellation_warped.nii.gz
2025-09-22 15:49:12,053 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:49:13,524 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:49:13,576 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:49:13,582 - JUNIFER - INFO - Getting element sub-02
2025-09-22 15:49:13,582 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:49:13,582 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:49:13,582 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:49:13,583 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:49:13,583 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:49:13,584 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:49:13,584 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:49:13,584 - JUNIFER - INFO - resolution: None
2025-09-22 15:49:13,584 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:49:13,584 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:49:13,584 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:49:13,660 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:49:15,949 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:49:16,454 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmplldpqsn8/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b037a2c0-97cb-11f0-a4c0-5ace1b2a80e5canif7uh/prewarp_parcellation.nii.gz -r /tmp/junifer/tmplldpqsn8/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b037a2c0-97cb-11f0-a4c0-5ace1b2a80e5canif7uh/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmplldpqsn8/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b037a2c0-97cb-11f0-a4c0-5ace1b2a80e5canif7uh/parcellation_warped.nii.gz
2025-09-22 15:49:22,753 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:49:24,148 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:49:24,182 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:49:24,182 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:49:24,182 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:49:24,182 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:49:24,182 - JUNIFER - INFO - resolution: None
2025-09-22 15:49:24,182 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:49:24,182 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:49:24,182 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:49:24,256 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:49:26,539 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:49:27,045 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmplldpqsn8/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b688511a-97cb-11f0-a4c0-5ace1b2a80e5pqcgqnfu/prewarp_parcellation.nii.gz -r /tmp/junifer/tmplldpqsn8/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b688511a-97cb-11f0-a4c0-5ace1b2a80e5pqcgqnfu/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmplldpqsn8/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b688511a-97cb-11f0-a4c0-5ace1b2a80e5pqcgqnfu/parcellation_warped.nii.gz
2025-09-22 15:49:38,352 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:49:39,762 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:49:39,814 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:49:39,820 - JUNIFER - INFO - Getting element sub-03
2025-09-22 15:49:39,820 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:49:39,820 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:49:39,820 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:49:39,821 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:49:39,821 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:49:39,821 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:49:39,821 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:49:39,821 - JUNIFER - INFO - resolution: None
2025-09-22 15:49:39,821 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:49:39,821 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:49:39,821 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:49:39,896 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:49:42,180 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:49:42,684 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp86dmjyqn/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_bfda90b6-97cb-11f0-a4c0-5ace1b2a80e57tjz1d_h/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp86dmjyqn/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_bfda90b6-97cb-11f0-a4c0-5ace1b2a80e57tjz1d_h/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp86dmjyqn/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_bfda90b6-97cb-11f0-a4c0-5ace1b2a80e57tjz1d_h/parcellation_warped.nii.gz
2025-09-22 15:49:49,009 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:49:50,437 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:49:50,470 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:49:50,471 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:49:50,471 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:49:50,471 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:49:50,471 - JUNIFER - INFO - resolution: None
2025-09-22 15:49:50,471 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:49:50,471 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:49:50,471 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:49:50,546 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:49:52,841 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:49:53,347 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp86dmjyqn/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c6346806-97cb-11f0-a4c0-5ace1b2a80e5q_6bqt2x/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp86dmjyqn/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c6346806-97cb-11f0-a4c0-5ace1b2a80e5q_6bqt2x/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp86dmjyqn/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c6346806-97cb-11f0-a4c0-5ace1b2a80e5q_6bqt2x/parcellation_warped.nii.gz
2025-09-22 15:50:04,764 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:50:06,172 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:50:06,224 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:50:06,230 - JUNIFER - INFO - Getting element sub-04
2025-09-22 15:50:06,230 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:50:06,230 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:50:06,230 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:50:06,231 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:50:06,231 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:50:06,231 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:50:06,231 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:50:06,231 - JUNIFER - INFO - resolution: None
2025-09-22 15:50:06,231 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:50:06,231 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:50:06,231 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:50:06,306 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:50:08,616 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:50:09,121 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmphpsl17sq/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cf9886fc-97cb-11f0-a4c0-5ace1b2a80e50e9q45n5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmphpsl17sq/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cf9886fc-97cb-11f0-a4c0-5ace1b2a80e50e9q45n5/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmphpsl17sq/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cf9886fc-97cb-11f0-a4c0-5ace1b2a80e50e9q45n5/parcellation_warped.nii.gz
2025-09-22 15:50:15,434 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:50:16,814 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:50:16,847 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:50:16,847 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:50:16,847 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:50:16,847 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:50:16,847 - JUNIFER - INFO - resolution: None
2025-09-22 15:50:16,847 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:50:16,847 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:50:16,847 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:50:16,921 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:50:19,223 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:50:19,730 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmphpsl17sq/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d5eccacc-97cb-11f0-a4c0-5ace1b2a80e5xo_38e5m/prewarp_parcellation.nii.gz -r /tmp/junifer/tmphpsl17sq/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d5eccacc-97cb-11f0-a4c0-5ace1b2a80e5xo_38e5m/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmphpsl17sq/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d5eccacc-97cb-11f0-a4c0-5ace1b2a80e5xo_38e5m/parcellation_warped.nii.gz
2025-09-22 15:50:31,012 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:50:32,406 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:50:32,458 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:50:32,464 - JUNIFER - INFO - Getting element sub-05
2025-09-22 15:50:32,464 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:50:32,464 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:50:32,464 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:50:32,465 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:50:32,465 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:50:32,465 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:50:32,465 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:50:32,465 - JUNIFER - INFO - resolution: None
2025-09-22 15:50:32,465 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:50:32,465 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:50:32,465 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:50:32,539 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:50:34,838 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:50:35,343 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpmc4xrly1/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_df3b362c-97cb-11f0-a4c0-5ace1b2a80e5ncz6j8am/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpmc4xrly1/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_df3b362c-97cb-11f0-a4c0-5ace1b2a80e5ncz6j8am/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpmc4xrly1/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_df3b362c-97cb-11f0-a4c0-5ace1b2a80e5ncz6j8am/parcellation_warped.nii.gz
2025-09-22 15:50:41,671 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:50:43,143 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:50:43,177 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:50:43,178 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:50:43,178 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:50:43,178 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:50:43,178 - JUNIFER - INFO - resolution: None
2025-09-22 15:50:43,178 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:50:43,178 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:50:43,178 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:50:43,252 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:50:45,599 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:50:46,106 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpmc4xrly1/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e59f1b14-97cb-11f0-a4c0-5ace1b2a80e5iu41z4_f/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpmc4xrly1/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e59f1b14-97cb-11f0-a4c0-5ace1b2a80e5iu41z4_f/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpmc4xrly1/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e59f1b14-97cb-11f0-a4c0-5ace1b2a80e5iu41z4_f/parcellation_warped.nii.gz
2025-09-22 15:50:57,404 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:50:58,859 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:50:58,911 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:50:58,917 - JUNIFER - INFO - Getting element sub-06
2025-09-22 15:50:58,917 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:50:58,917 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:50:58,917 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:50:58,918 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:50:58,918 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:50:58,918 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:50:58,918 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:50:58,918 - JUNIFER - INFO - resolution: None
2025-09-22 15:50:58,918 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:50:58,918 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:50:58,918 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:50:58,992 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:51:01,291 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:51:01,795 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpizp7t84w/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_eefff5f2-97cb-11f0-a4c0-5ace1b2a80e53r4b1txy/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpizp7t84w/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_eefff5f2-97cb-11f0-a4c0-5ace1b2a80e53r4b1txy/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpizp7t84w/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_eefff5f2-97cb-11f0-a4c0-5ace1b2a80e53r4b1txy/parcellation_warped.nii.gz
2025-09-22 15:51:08,083 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:51:09,500 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:51:09,534 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:51:09,534 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:51:09,534 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:51:09,534 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:51:09,534 - JUNIFER - INFO - resolution: None
2025-09-22 15:51:09,534 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:51:09,534 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:51:09,534 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:51:09,608 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:51:11,915 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:51:12,421 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpizp7t84w/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f5540b1e-97cb-11f0-a4c0-5ace1b2a80e5oy5ykcpa/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpizp7t84w/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f5540b1e-97cb-11f0-a4c0-5ace1b2a80e5oy5ykcpa/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpizp7t84w/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f5540b1e-97cb-11f0-a4c0-5ace1b2a80e5oy5ykcpa/parcellation_warped.nii.gz
2025-09-22 15:51:23,766 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:51:25,174 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:51:25,226 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:51:25,231 - JUNIFER - INFO - Getting element sub-07
2025-09-22 15:51:25,231 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:51:25,231 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:51:25,231 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:51:25,232 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:51:25,232 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:51:25,233 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:51:25,233 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:51:25,233 - JUNIFER - INFO - resolution: None
2025-09-22 15:51:25,233 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:51:25,233 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:51:25,233 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:51:25,307 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:51:27,601 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:51:28,120 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp7yf653l2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_feaf0aba-97cb-11f0-a4c0-5ace1b2a80e50r92w8rs/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp7yf653l2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_feaf0aba-97cb-11f0-a4c0-5ace1b2a80e50r92w8rs/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp7yf653l2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_feaf0aba-97cb-11f0-a4c0-5ace1b2a80e50r92w8rs/parcellation_warped.nii.gz
2025-09-22 15:51:34,412 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:51:35,786 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:51:35,820 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:51:35,820 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:51:35,820 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:51:35,820 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:51:35,820 - JUNIFER - INFO - resolution: None
2025-09-22 15:51:35,820 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:51:35,820 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:51:35,820 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:51:35,895 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:51:38,188 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:51:38,695 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp7yf653l2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_04ff19c8-97cc-11f0-a4c0-5ace1b2a80e5yy8131kd/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp7yf653l2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_04ff19c8-97cc-11f0-a4c0-5ace1b2a80e5yy8131kd/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp7yf653l2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_04ff19c8-97cc-11f0-a4c0-5ace1b2a80e5yy8131kd/parcellation_warped.nii.gz
2025-09-22 15:51:50,004 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:51:51,394 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:51:51,445 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:51:51,451 - JUNIFER - INFO - Getting element sub-08
2025-09-22 15:51:51,451 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:51:51,451 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:51:51,451 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:51:51,452 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:51:51,452 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:51:51,452 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:51:51,452 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:51:51,452 - JUNIFER - INFO - resolution: None
2025-09-22 15:51:51,452 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:51:51,452 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:51:51,452 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:51:51,526 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:51:53,824 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:51:54,329 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpb5dpeo90/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0e4fb8ac-97cc-11f0-a4c0-5ace1b2a80e59y0uhqse/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpb5dpeo90/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0e4fb8ac-97cc-11f0-a4c0-5ace1b2a80e59y0uhqse/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpb5dpeo90/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0e4fb8ac-97cc-11f0-a4c0-5ace1b2a80e59y0uhqse/parcellation_warped.nii.gz
2025-09-22 15:52:00,657 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:52:02,050 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:52:02,084 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:52:02,084 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:52:02,084 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:52:02,084 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:52:02,084 - JUNIFER - INFO - resolution: None
2025-09-22 15:52:02,084 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:52:02,084 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:52:02,084 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:52:02,159 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:52:04,446 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:52:04,950 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpb5dpeo90/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_14a68910-97cc-11f0-a4c0-5ace1b2a80e5bspyurl4/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpb5dpeo90/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_14a68910-97cc-11f0-a4c0-5ace1b2a80e5bspyurl4/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpb5dpeo90/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_14a68910-97cc-11f0-a4c0-5ace1b2a80e5bspyurl4/parcellation_warped.nii.gz
2025-09-22 15:52:16,375 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:52:17,769 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:52:17,823 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:52:17,828 - JUNIFER - INFO - Getting element sub-09
2025-09-22 15:52:17,828 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:52:17,828 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:52:17,829 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:52:17,829 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:52:17,830 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:52:17,830 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:52:17,830 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:52:17,830 - JUNIFER - INFO - resolution: None
2025-09-22 15:52:17,830 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:52:17,830 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:52:17,830 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:52:17,904 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:52:20,195 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:52:20,699 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpwgvsere9/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_1e08b280-97cc-11f0-a4c0-5ace1b2a80e5grairilc/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpwgvsere9/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_1e08b280-97cc-11f0-a4c0-5ace1b2a80e5grairilc/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpwgvsere9/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_1e08b280-97cc-11f0-a4c0-5ace1b2a80e5grairilc/parcellation_warped.nii.gz
2025-09-22 15:52:27,054 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:52:28,521 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:52:28,554 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:52:28,554 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:52:28,554 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:52:28,554 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:52:28,554 - JUNIFER - INFO - resolution: None
2025-09-22 15:52:28,554 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:52:28,554 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:52:28,554 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:52:28,630 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:52:30,936 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:52:31,439 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpwgvsere9/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_246da694-97cc-11f0-a4c0-5ace1b2a80e5ejv4p399/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpwgvsere9/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_246da694-97cc-11f0-a4c0-5ace1b2a80e5ejv4p399/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpwgvsere9/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_246da694-97cc-11f0-a4c0-5ace1b2a80e5ejv4p399/parcellation_warped.nii.gz
2025-09-22 15:52:42,760 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:52:44,225 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:52:44,277 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:52:44,283 - JUNIFER - INFO - Getting element sub-10
2025-09-22 15:52:44,283 - JUNIFER - INFO - Fitting pipeline
2025-09-22 15:52:44,283 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-22 15:52:44,283 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-22 15:52:44,284 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-22 15:52:44,284 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:52:44,284 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:52:44,284 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:52:44,284 - JUNIFER - INFO - resolution: None
2025-09-22 15:52:44,284 - JUNIFER - INFO - n_rois: 100
2025-09-22 15:52:44,284 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:52:44,284 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:52:44,358 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:52:46,674 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:52:47,188 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmput2h1_4f/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_2dcd3fa6-97cc-11f0-a4c0-5ace1b2a80e5flx24zwn/prewarp_parcellation.nii.gz -r /tmp/junifer/tmput2h1_4f/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_2dcd3fa6-97cc-11f0-a4c0-5ace1b2a80e5flx24zwn/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmput2h1_4f/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_2dcd3fa6-97cc-11f0-a4c0-5ace1b2a80e5flx24zwn/parcellation_warped.nii.gz
2025-09-22 15:52:53,487 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:52:54,884 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:52:54,919 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-22 15:52:54,919 - JUNIFER - INFO - Computing VBM_GM
2025-09-22 15:52:54,919 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-22 15:52:54,919 - JUNIFER - INFO - Parcellation parameters:
2025-09-22 15:52:54,919 - JUNIFER - INFO - resolution: None
2025-09-22 15:52:54,919 - JUNIFER - INFO - n_rois: 200
2025-09-22 15:52:54,919 - JUNIFER - INFO - yeo_networks: 17
2025-09-22 15:52:54,919 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-22 15:52:54,993 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-22 15:52:57,308 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-22 15:52:57,813 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmput2h1_4f/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3424978c-97cc-11f0-a4c0-5ace1b2a80e541qvcaa1/prewarp_parcellation.nii.gz -r /tmp/junifer/tmput2h1_4f/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3424978c-97cc-11f0-a4c0-5ace1b2a80e541qvcaa1/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v4/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmput2h1_4f/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3424978c-97cc-11f0-a4c0-5ace1b2a80e541qvcaa1/parcellation_warped.nii.gz
2025-09-22 15:53:09,186 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-22 15:53:10,631 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1aumxghc/test.sqlite (multiple output)>
2025-09-22 15:53:10,683 - JUNIFER - INFO - Marker collection fitting done
2025-09-22 15:53:10,688 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2025-09-22 15:53:10,689 - JUNIFER - INFO - Collecting data from /tmp/tmp1aumxghc/*test.sqlite
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2025-09-22 15:53:12,422 - 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 0.145725 0.021328 ... 0 509497eb21da473048117e0c6704d3ea
1 0.148916 0.020719 ... 1 509497eb21da473048117e0c6704d3ea
2 0.145239 0.020617 ... 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: (4 minutes 26.101 seconds)