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))
2025-09-24 13:49:11,279 - JUNIFER - INFO - ===== Lib Versions =====
2025-09-24 13:49:11,279 - JUNIFER - INFO - click: 8.1.8
2025-09-24 13:49:11,279 - JUNIFER - INFO - numpy: 1.26.4
2025-09-24 13:49:11,279 - JUNIFER - INFO - scipy: 1.15.0
2025-09-24 13:49:11,279 - JUNIFER - INFO - datalad: 1.1.6
2025-09-24 13:49:11,279 - JUNIFER - INFO - pandas: 2.1.4
2025-09-24 13:49:11,279 - JUNIFER - INFO - nibabel: 5.3.2
2025-09-24 13:49:11,279 - JUNIFER - INFO - nilearn: 0.10.4
2025-09-24 13:49:11,279 - JUNIFER - INFO - sqlalchemy: 2.0.43
2025-09-24 13:49:11,279 - JUNIFER - INFO - ruamel.yaml: 0.18.15
2025-09-24 13:49:11,279 - JUNIFER - INFO - tqdm: 4.66.6
2025-09-24 13:49:11,279 - JUNIFER - INFO - templateflow: 24.2.2
2025-09-24 13:49:11,279 - JUNIFER - INFO - junifer_data: None
2025-09-24 13:49:11,279 - JUNIFER - INFO - junifer: 0.0.7.dev217
2025-09-24 13:49:11,279 - 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
2025-09-24 13:49:11,298 - JUNIFER - INFO - Validating Marker Collection
2025-09-24 13:49:11,298 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2025-09-24 13:49:11,298 - JUNIFER - INFO - Validating Data Reader:
2025-09-24 13:49:11,298 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2025-09-24 13:49:11,298 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2025-09-24 13:49:11,299 - JUNIFER - INFO - Marker output type: ['vector']
2025-09-24 13:49:11,299 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2025-09-24 13:49:11,299 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2025-09-24 13:49:11,299 - JUNIFER - INFO - Marker output type: ['vector']
2025-09-24 13:49:11,299 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2025-09-24 13:49:11,304 - JUNIFER - INFO - Getting element sub-01
2025-09-24 13:49:11,304 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:49:11,304 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:49:11,304 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:49:11,305 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:49:11,305 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:49:11,305 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:49:11,305 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:49:11,305 - JUNIFER - INFO - resolution: None
2025-09-24 13:49:11,305 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:49:11,305 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:49:11,305 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:49:11,382 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:49:13,759 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:49:14,268 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpwc9l8wt2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_4026ab6a-994d-11f0-83de-7258d444b196sppwhsgp/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpwc9l8wt2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_4026ab6a-994d-11f0-83de-7258d444b196sppwhsgp/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/tmpwc9l8wt2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_4026ab6a-994d-11f0-83de-7258d444b196sppwhsgp/parcellation_warped.nii.gz
2025-09-24 13:49:20,663 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:49:22,189 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:49:22,223 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:49:22,223 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:49:22,223 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:49:22,223 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:49:22,223 - JUNIFER - INFO - resolution: None
2025-09-24 13:49:22,223 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:49:22,223 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:49:22,223 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:49:22,299 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:49:24,665 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:49:25,174 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpwc9l8wt2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_46a95546-994d-11f0-83de-7258d444b196zzlqbxpu/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpwc9l8wt2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_46a95546-994d-11f0-83de-7258d444b196zzlqbxpu/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/tmpwc9l8wt2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_46a95546-994d-11f0-83de-7258d444b196zzlqbxpu/parcellation_warped.nii.gz
2025-09-24 13:49:36,560 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:49:38,106 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:49:38,160 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:49:38,166 - JUNIFER - INFO - Getting element sub-02
2025-09-24 13:49:38,166 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:49:38,166 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:49:38,166 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:49:38,167 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:49:38,167 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:49:38,167 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:49:38,167 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:49:38,167 - JUNIFER - INFO - resolution: None
2025-09-24 13:49:38,167 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:49:38,167 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:49:38,167 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:49:38,245 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:49:40,621 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:49:41,127 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp1bdsr03g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_50299bc6-994d-11f0-83de-7258d444b196jgzh0yuu/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp1bdsr03g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_50299bc6-994d-11f0-83de-7258d444b196jgzh0yuu/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/tmp1bdsr03g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_50299bc6-994d-11f0-83de-7258d444b196jgzh0yuu/parcellation_warped.nii.gz
2025-09-24 13:49:47,515 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:49:49,146 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:49:49,182 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:49:49,182 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:49:49,182 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:49:49,182 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:49:49,182 - JUNIFER - INFO - resolution: None
2025-09-24 13:49:49,182 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:49:49,182 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:49:49,182 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:49:49,262 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:49:51,662 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:49:52,172 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp1bdsr03g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_56bbba1e-994d-11f0-83de-7258d444b196lypb3kcs/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp1bdsr03g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_56bbba1e-994d-11f0-83de-7258d444b196lypb3kcs/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/tmp1bdsr03g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_56bbba1e-994d-11f0-83de-7258d444b196lypb3kcs/parcellation_warped.nii.gz
2025-09-24 13:50:03,525 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:50:05,179 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:50:05,234 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:50:05,239 - JUNIFER - INFO - Getting element sub-03
2025-09-24 13:50:05,239 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:50:05,240 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:50:05,240 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:50:05,241 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:50:05,241 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:50:05,241 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:50:05,241 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:50:05,241 - JUNIFER - INFO - resolution: None
2025-09-24 13:50:05,241 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:50:05,241 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:50:05,241 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:50:05,330 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:50:07,727 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:50:08,236 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpjphh0_o3/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_604eb608-994d-11f0-83de-7258d444b196sscqs6s5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpjphh0_o3/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_604eb608-994d-11f0-83de-7258d444b196sscqs6s5/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/tmpjphh0_o3/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_604eb608-994d-11f0-83de-7258d444b196sscqs6s5/parcellation_warped.nii.gz
2025-09-24 13:50:14,586 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:50:16,132 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:50:16,170 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:50:16,170 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:50:16,170 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:50:16,170 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:50:16,170 - JUNIFER - INFO - resolution: None
2025-09-24 13:50:16,170 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:50:16,170 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:50:16,170 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:50:16,250 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:50:18,631 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:50:19,139 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpjphh0_o3/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_66d11200-994d-11f0-83de-7258d444b196qmrv05o_/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpjphh0_o3/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_66d11200-994d-11f0-83de-7258d444b196qmrv05o_/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/tmpjphh0_o3/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_66d11200-994d-11f0-83de-7258d444b196qmrv05o_/parcellation_warped.nii.gz
2025-09-24 13:50:30,399 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:50:32,022 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:50:32,078 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:50:32,084 - JUNIFER - INFO - Getting element sub-04
2025-09-24 13:50:32,084 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:50:32,084 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:50:32,084 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:50:32,086 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:50:32,086 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:50:32,086 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:50:32,086 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:50:32,086 - JUNIFER - INFO - resolution: None
2025-09-24 13:50:32,086 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:50:32,086 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:50:32,086 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:50:32,163 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:50:34,547 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:50:35,056 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp61g9k09g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_704d3ba6-994d-11f0-83de-7258d444b196e7t_dyls/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp61g9k09g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_704d3ba6-994d-11f0-83de-7258d444b196e7t_dyls/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/tmp61g9k09g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_704d3ba6-994d-11f0-83de-7258d444b196e7t_dyls/parcellation_warped.nii.gz
2025-09-24 13:50:41,398 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:50:43,080 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:50:43,116 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:50:43,116 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:50:43,116 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:50:43,116 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:50:43,116 - JUNIFER - INFO - resolution: None
2025-09-24 13:50:43,116 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:50:43,116 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:50:43,116 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:50:43,197 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:50:45,615 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:50:46,125 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp61g9k09g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_76e1950c-994d-11f0-83de-7258d444b196b422xyg0/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp61g9k09g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_76e1950c-994d-11f0-83de-7258d444b196b422xyg0/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/tmp61g9k09g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_76e1950c-994d-11f0-83de-7258d444b196b422xyg0/parcellation_warped.nii.gz
2025-09-24 13:50:57,551 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:50:59,150 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:50:59,207 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:50:59,212 - JUNIFER - INFO - Getting element sub-05
2025-09-24 13:50:59,212 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:50:59,212 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:50:59,212 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:50:59,213 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:50:59,214 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:50:59,214 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:50:59,214 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:50:59,214 - JUNIFER - INFO - resolution: None
2025-09-24 13:50:59,214 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:50:59,214 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:50:59,214 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:50:59,291 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:51:01,706 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:51:02,215 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpbm6hdu9p/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_8078d0d0-994d-11f0-83de-7258d444b1963juk6e1o/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpbm6hdu9p/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_8078d0d0-994d-11f0-83de-7258d444b1963juk6e1o/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/tmpbm6hdu9p/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_8078d0d0-994d-11f0-83de-7258d444b1963juk6e1o/parcellation_warped.nii.gz
2025-09-24 13:51:08,554 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:51:10,125 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:51:10,160 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:51:10,160 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:51:10,160 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:51:10,161 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:51:10,161 - JUNIFER - INFO - resolution: None
2025-09-24 13:51:10,161 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:51:10,161 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:51:10,161 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:51:10,248 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:51:12,655 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:51:13,168 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpbm6hdu9p/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8700c00c-994d-11f0-83de-7258d444b196kv4wh5rl/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpbm6hdu9p/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8700c00c-994d-11f0-83de-7258d444b196kv4wh5rl/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/tmpbm6hdu9p/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8700c00c-994d-11f0-83de-7258d444b196kv4wh5rl/parcellation_warped.nii.gz
2025-09-24 13:51:24,603 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:51:26,147 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:51:26,204 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:51:26,209 - JUNIFER - INFO - Getting element sub-06
2025-09-24 13:51:26,209 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:51:26,210 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:51:26,210 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:51:26,211 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:51:26,211 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:51:26,211 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:51:26,211 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:51:26,211 - JUNIFER - INFO - resolution: None
2025-09-24 13:51:26,211 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:51:26,211 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:51:26,211 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:51:26,293 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:51:28,692 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:51:29,203 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp9m8emwkz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_9090d198-994d-11f0-83de-7258d444b196sco7jf3a/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp9m8emwkz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_9090d198-994d-11f0-83de-7258d444b196sco7jf3a/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/tmp9m8emwkz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_9090d198-994d-11f0-83de-7258d444b196sco7jf3a/parcellation_warped.nii.gz
2025-09-24 13:51:35,530 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:51:37,166 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:51:37,202 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:51:37,202 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:51:37,202 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:51:37,202 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:51:37,202 - JUNIFER - INFO - resolution: None
2025-09-24 13:51:37,202 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:51:37,202 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:51:37,202 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:51:37,291 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:51:39,684 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:51:40,191 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp9m8emwkz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_971f19c0-994d-11f0-83de-7258d444b196fmbew5za/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp9m8emwkz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_971f19c0-994d-11f0-83de-7258d444b196fmbew5za/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/tmp9m8emwkz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_971f19c0-994d-11f0-83de-7258d444b196fmbew5za/parcellation_warped.nii.gz
2025-09-24 13:51:51,496 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:51:53,095 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:51:53,151 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:51:53,156 - JUNIFER - INFO - Getting element sub-07
2025-09-24 13:51:53,156 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:51:53,156 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:51:53,156 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:51:53,158 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:51:53,158 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:51:53,158 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:51:53,158 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:51:53,158 - JUNIFER - INFO - resolution: None
2025-09-24 13:51:53,158 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:51:53,158 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:51:53,158 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:51:53,236 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:51:55,657 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:51:56,168 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptb3f4zml/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a09fb72a-994d-11f0-83de-7258d444b1969dx2mkdg/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptb3f4zml/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a09fb72a-994d-11f0-83de-7258d444b1969dx2mkdg/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/tmptb3f4zml/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a09fb72a-994d-11f0-83de-7258d444b1969dx2mkdg/parcellation_warped.nii.gz
2025-09-24 13:52:02,523 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:52:04,192 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:52:04,228 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:52:04,228 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:52:04,228 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:52:04,228 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:52:04,228 - JUNIFER - INFO - resolution: None
2025-09-24 13:52:04,228 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:52:04,228 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:52:04,228 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:52:04,310 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:52:06,724 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:52:07,233 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptb3f4zml/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a739dbb0-994d-11f0-83de-7258d444b1962ffxc1qe/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptb3f4zml/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a739dbb0-994d-11f0-83de-7258d444b1962ffxc1qe/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/tmptb3f4zml/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a739dbb0-994d-11f0-83de-7258d444b1962ffxc1qe/parcellation_warped.nii.gz
2025-09-24 13:52:18,593 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:52:20,189 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:52:20,243 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:52:20,249 - JUNIFER - INFO - Getting element sub-08
2025-09-24 13:52:20,249 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:52:20,249 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:52:20,249 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:52:20,250 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:52:20,250 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:52:20,251 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:52:20,251 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:52:20,251 - JUNIFER - INFO - resolution: None
2025-09-24 13:52:20,251 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:52:20,251 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:52:20,251 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:52:20,328 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:52:22,751 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:52:23,259 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpad91hwtd/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b0c55a2e-994d-11f0-83de-7258d444b196fgiyqh22/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpad91hwtd/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b0c55a2e-994d-11f0-83de-7258d444b196fgiyqh22/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/tmpad91hwtd/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b0c55a2e-994d-11f0-83de-7258d444b196fgiyqh22/parcellation_warped.nii.gz
2025-09-24 13:52:29,627 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:52:31,189 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:52:31,223 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:52:31,223 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:52:31,223 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:52:31,224 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:52:31,224 - JUNIFER - INFO - resolution: None
2025-09-24 13:52:31,224 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:52:31,224 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:52:31,224 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:52:31,304 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:52:33,697 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:52:34,207 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpad91hwtd/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b7507a0e-994d-11f0-83de-7258d444b196aqx844mj/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpad91hwtd/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b7507a0e-994d-11f0-83de-7258d444b196aqx844mj/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/tmpad91hwtd/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b7507a0e-994d-11f0-83de-7258d444b196aqx844mj/parcellation_warped.nii.gz
2025-09-24 13:52:45,544 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:52:47,176 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:52:47,232 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:52:47,238 - JUNIFER - INFO - Getting element sub-09
2025-09-24 13:52:47,238 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:52:47,238 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:52:47,238 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:52:47,239 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:52:47,240 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:52:47,240 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:52:47,240 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:52:47,240 - JUNIFER - INFO - resolution: None
2025-09-24 13:52:47,240 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:52:47,240 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:52:47,240 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:52:47,318 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:52:49,724 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:52:50,232 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpk192z7_2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_c0dc543a-994d-11f0-83de-7258d444b196zqtm6nc7/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpk192z7_2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_c0dc543a-994d-11f0-83de-7258d444b196zqtm6nc7/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/tmpk192z7_2/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_c0dc543a-994d-11f0-83de-7258d444b196zqtm6nc7/parcellation_warped.nii.gz
2025-09-24 13:52:56,583 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:52:58,178 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:52:58,212 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:52:58,212 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:52:58,213 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:52:58,213 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:52:58,213 - JUNIFER - INFO - resolution: None
2025-09-24 13:52:58,213 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:52:58,213 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:52:58,213 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:52:58,289 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:53:00,693 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:53:01,205 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpk192z7_2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c766a01c-994d-11f0-83de-7258d444b196o8b5h_et/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpk192z7_2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c766a01c-994d-11f0-83de-7258d444b196o8b5h_et/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/tmpk192z7_2/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c766a01c-994d-11f0-83de-7258d444b196o8b5h_et/parcellation_warped.nii.gz
2025-09-24 13:53:12,591 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:53:14,232 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:53:14,288 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:53:14,293 - JUNIFER - INFO - Getting element sub-10
2025-09-24 13:53:14,293 - JUNIFER - INFO - Fitting pipeline
2025-09-24 13:53:14,293 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-09-24 13:53:14,293 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-09-24 13:53:14,294 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-09-24 13:53:14,294 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:53:14,294 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:53:14,294 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:53:14,294 - JUNIFER - INFO - resolution: None
2025-09-24 13:53:14,295 - JUNIFER - INFO - n_rois: 100
2025-09-24 13:53:14,295 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:53:14,295 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:53:14,372 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:53:16,792 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:53:17,302 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpqec3tv3s/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_d0fbff6e-994d-11f0-83de-7258d444b196taptx_kj/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpqec3tv3s/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_d0fbff6e-994d-11f0-83de-7258d444b196taptx_kj/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/tmpqec3tv3s/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_d0fbff6e-994d-11f0-83de-7258d444b196taptx_kj/parcellation_warped.nii.gz
2025-09-24 13:53:23,688 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:53:25,268 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:53:25,306 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-09-24 13:53:25,306 - JUNIFER - INFO - Computing VBM_GM
2025-09-24 13:53:25,306 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-09-24 13:53:25,306 - JUNIFER - INFO - Parcellation parameters:
2025-09-24 13:53:25,306 - JUNIFER - INFO - resolution: None
2025-09-24 13:53:25,306 - JUNIFER - INFO - n_rois: 200
2025-09-24 13:53:25,306 - JUNIFER - INFO - yeo_networks: 17
2025-09-24 13:53:25,306 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-09-24 13:53:25,395 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v4/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-09-24 13:53:27,804 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-09-24 13:53:28,315 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpqec3tv3s/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d78e959e-994d-11f0-83de-7258d444b196rvg4q9tj/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpqec3tv3s/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d78e959e-994d-11f0-83de-7258d444b196rvg4q9tj/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/tmpqec3tv3s/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d78e959e-994d-11f0-83de-7258d444b196rvg4q9tj/parcellation_warped.nii.gz
2025-09-24 13:53:39,691 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-09-24 13:53:41,282 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp77jvms2w/test.sqlite (multiple output)>
2025-09-24 13:53:41,337 - JUNIFER - INFO - Marker collection fitting done
2025-09-24 13:53:41,343 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2025-09-24 13:53:41,343 - JUNIFER - INFO - Collecting data from /tmp/tmp77jvms2w/*test.sqlite
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2025-09-24 13:53:43,220 - 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 0.150773 0.021627 ... 0 509497eb21da473048117e0c6704d3ea
1 0.148206 0.022070 ... 1 509497eb21da473048117e0c6704d3ea
2 0.149865 0.021968 ... 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 32.657 seconds)