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))
2025-05-09 12:40:32,100 - JUNIFER - INFO - ===== Lib Versions =====
2025-05-09 12:40:32,100 - JUNIFER - INFO - click: 8.1.8
2025-05-09 12:40:32,100 - JUNIFER - INFO - numpy: 1.26.4
2025-05-09 12:40:32,101 - JUNIFER - INFO - scipy: 1.15.0
2025-05-09 12:40:32,101 - JUNIFER - INFO - datalad: 1.1.5
2025-05-09 12:40:32,101 - JUNIFER - INFO - pandas: 2.1.4
2025-05-09 12:40:32,101 - JUNIFER - INFO - nibabel: 5.3.2
2025-05-09 12:40:32,101 - JUNIFER - INFO - nilearn: 0.10.4
2025-05-09 12:40:32,101 - JUNIFER - INFO - sqlalchemy: 2.0.40
2025-05-09 12:40:32,101 - JUNIFER - INFO - ruamel.yaml: 0.18.10
2025-05-09 12:40:32,101 - JUNIFER - INFO - tqdm: 4.66.6
2025-05-09 12:40:32,101 - JUNIFER - INFO - templateflow: 24.2.2
2025-05-09 12:40:32,101 - JUNIFER - INFO - junifer_data: None
2025-05-09 12:40:32,101 - JUNIFER - INFO - junifer: 0.0.7.dev83
2025-05-09 12:40:32,101 - 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
2025-05-09 12:40:32,119 - JUNIFER - INFO - Validating Marker Collection
2025-05-09 12:40:32,119 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2025-05-09 12:40:32,119 - JUNIFER - INFO - Validating Data Reader:
2025-05-09 12:40:32,119 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2025-05-09 12:40:32,119 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2025-05-09 12:40:32,119 - JUNIFER - INFO - Marker output type: ['vector']
2025-05-09 12:40:32,119 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2025-05-09 12:40:32,119 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2025-05-09 12:40:32,119 - JUNIFER - INFO - Marker output type: ['vector']
2025-05-09 12:40:32,119 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2025-05-09 12:40:32,124 - JUNIFER - INFO - Getting element sub-01
2025-05-09 12:40:32,124 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:40:32,124 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:40:32,124 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:40:32,125 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:40:32,125 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:40:32,125 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:40:32,125 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:40:32,125 - JUNIFER - INFO - resolution: None
2025-05-09 12:40:32,125 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:40:32,125 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:40:32,125 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:40:32,200 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:40:34,428 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:40:34,930 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpxughy02g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cbeb4a30-2cd2-11f0-b407-763dc8eb2af05ty0ua0y/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpxughy02g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cbeb4a30-2cd2-11f0-b407-763dc8eb2af05ty0ua0y/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpxughy02g/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cbeb4a30-2cd2-11f0-b407-763dc8eb2af05ty0ua0y/parcellation_warped.nii.gz
2025-05-09 12:40:41,183 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:40:42,550 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:40:42,585 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:40:42,585 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:40:42,585 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:40:42,585 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:40:42,585 - JUNIFER - INFO - resolution: None
2025-05-09 12:40:42,585 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:40:42,585 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:40:42,585 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:40:42,659 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:40:44,947 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:40:45,453 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpxughy02g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d22822ce-2cd2-11f0-b407-763dc8eb2af08qg3p12s/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpxughy02g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d22822ce-2cd2-11f0-b407-763dc8eb2af08qg3p12s/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpxughy02g/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d22822ce-2cd2-11f0-b407-763dc8eb2af08qg3p12s/parcellation_warped.nii.gz
2025-05-09 12:40:56,854 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:40:58,180 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:40:58,233 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:40:58,238 - JUNIFER - INFO - Getting element sub-02
2025-05-09 12:40:58,238 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:40:58,238 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:40:58,238 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:40:58,239 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:40:58,239 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:40:58,240 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:40:58,240 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:40:58,240 - JUNIFER - INFO - resolution: None
2025-05-09 12:40:58,240 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:40:58,240 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:40:58,240 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:40:58,313 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:41:00,571 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:41:01,075 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpb0yfw5rd/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_db7c0dae-2cd2-11f0-b407-763dc8eb2af0qyvsgvut/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpb0yfw5rd/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_db7c0dae-2cd2-11f0-b407-763dc8eb2af0qyvsgvut/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpb0yfw5rd/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_db7c0dae-2cd2-11f0-b407-763dc8eb2af0qyvsgvut/parcellation_warped.nii.gz
2025-05-09 12:41:07,337 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:41:08,740 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:41:08,776 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:41:08,777 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:41:08,777 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:41:08,777 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:41:08,777 - JUNIFER - INFO - resolution: None
2025-05-09 12:41:08,777 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:41:08,777 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:41:08,777 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:41:08,850 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:41:11,106 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:41:11,612 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpb0yfw5rd/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e1c432ae-2cd2-11f0-b407-763dc8eb2af0c6blc4ux/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpb0yfw5rd/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e1c432ae-2cd2-11f0-b407-763dc8eb2af0c6blc4ux/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpb0yfw5rd/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e1c432ae-2cd2-11f0-b407-763dc8eb2af0c6blc4ux/parcellation_warped.nii.gz
2025-05-09 12:41:22,928 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:41:24,326 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:41:24,379 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:41:24,384 - JUNIFER - INFO - Getting element sub-03
2025-05-09 12:41:24,384 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:41:24,384 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:41:24,384 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:41:24,385 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:41:24,385 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:41:24,385 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:41:24,385 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:41:24,385 - JUNIFER - INFO - resolution: None
2025-05-09 12:41:24,385 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:41:24,385 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:41:24,385 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:41:24,458 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:41:26,699 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:41:27,204 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp2dhfi91k/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_eb117146-2cd2-11f0-b407-763dc8eb2af008q9fqax/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp2dhfi91k/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_eb117146-2cd2-11f0-b407-763dc8eb2af008q9fqax/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp2dhfi91k/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_eb117146-2cd2-11f0-b407-763dc8eb2af008q9fqax/parcellation_warped.nii.gz
2025-05-09 12:41:33,485 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:41:34,838 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:41:34,872 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:41:34,872 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:41:34,872 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:41:34,872 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:41:34,872 - JUNIFER - INFO - resolution: None
2025-05-09 12:41:34,872 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:41:34,872 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:41:34,872 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:41:34,945 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:41:37,199 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:41:37,708 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp2dhfi91k/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f1522122-2cd2-11f0-b407-763dc8eb2af02u5divr5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp2dhfi91k/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f1522122-2cd2-11f0-b407-763dc8eb2af02u5divr5/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp2dhfi91k/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f1522122-2cd2-11f0-b407-763dc8eb2af02u5divr5/parcellation_warped.nii.gz
2025-05-09 12:41:49,076 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:41:50,448 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:41:50,502 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:41:50,507 - JUNIFER - INFO - Getting element sub-04
2025-05-09 12:41:50,507 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:41:50,507 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:41:50,507 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:41:50,508 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:41:50,508 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:41:50,508 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:41:50,508 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:41:50,509 - JUNIFER - INFO - resolution: None
2025-05-09 12:41:50,509 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:41:50,509 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:41:50,509 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:41:50,583 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:41:52,882 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:41:53,386 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpa6p_8dqa/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_faa3ff16-2cd2-11f0-b407-763dc8eb2af04tglge1n/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpa6p_8dqa/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_faa3ff16-2cd2-11f0-b407-763dc8eb2af04tglge1n/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpa6p_8dqa/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_faa3ff16-2cd2-11f0-b407-763dc8eb2af04tglge1n/parcellation_warped.nii.gz
2025-05-09 12:41:59,617 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:42:01,020 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:42:01,055 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:42:01,055 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:42:01,055 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:42:01,055 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:42:01,055 - JUNIFER - INFO - resolution: None
2025-05-09 12:42:01,055 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:42:01,055 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:42:01,055 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:42:01,128 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:42:03,427 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:42:03,946 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpa6p_8dqa/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_00ed9080-2cd3-11f0-b407-763dc8eb2af0y4x45srh/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpa6p_8dqa/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_00ed9080-2cd3-11f0-b407-763dc8eb2af0y4x45srh/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpa6p_8dqa/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_00ed9080-2cd3-11f0-b407-763dc8eb2af0y4x45srh/parcellation_warped.nii.gz
2025-05-09 12:42:15,264 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:42:16,631 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:42:16,687 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:42:16,693 - JUNIFER - INFO - Getting element sub-05
2025-05-09 12:42:16,693 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:42:16,693 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:42:16,693 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:42:16,694 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:42:16,694 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:42:16,694 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:42:16,694 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:42:16,694 - JUNIFER - INFO - resolution: None
2025-05-09 12:42:16,694 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:42:16,694 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:42:16,694 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:42:16,768 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:42:19,010 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:42:19,515 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpf87ziuue/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0a3f3e68-2cd3-11f0-b407-763dc8eb2af0hk5m27py/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpf87ziuue/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0a3f3e68-2cd3-11f0-b407-763dc8eb2af0hk5m27py/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpf87ziuue/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0a3f3e68-2cd3-11f0-b407-763dc8eb2af0hk5m27py/parcellation_warped.nii.gz
2025-05-09 12:42:25,830 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:42:27,182 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:42:27,216 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:42:27,216 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:42:27,216 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:42:27,216 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:42:27,216 - JUNIFER - INFO - resolution: None
2025-05-09 12:42:27,216 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:42:27,216 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:42:27,216 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:42:27,290 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:42:29,598 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:42:30,103 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpf87ziuue/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_1085c31e-2cd3-11f0-b407-763dc8eb2af0aeane_jy/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpf87ziuue/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_1085c31e-2cd3-11f0-b407-763dc8eb2af0aeane_jy/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpf87ziuue/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_1085c31e-2cd3-11f0-b407-763dc8eb2af0aeane_jy/parcellation_warped.nii.gz
2025-05-09 12:42:41,445 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:42:42,818 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:42:42,872 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:42:42,877 - JUNIFER - INFO - Getting element sub-06
2025-05-09 12:42:42,878 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:42:42,878 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:42:42,878 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:42:42,879 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:42:42,879 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:42:42,879 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:42:42,879 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:42:42,879 - JUNIFER - INFO - resolution: None
2025-05-09 12:42:42,879 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:42:42,879 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:42:42,879 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:42:42,952 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:42:45,202 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:42:45,707 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpabktw2c3/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_19daf1e6-2cd3-11f0-b407-763dc8eb2af0mer9td59/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpabktw2c3/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_19daf1e6-2cd3-11f0-b407-763dc8eb2af0mer9td59/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpabktw2c3/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_19daf1e6-2cd3-11f0-b407-763dc8eb2af0mer9td59/parcellation_warped.nii.gz
2025-05-09 12:42:51,984 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:42:53,313 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:42:53,347 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:42:53,347 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:42:53,348 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:42:53,348 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:42:53,348 - JUNIFER - INFO - resolution: None
2025-05-09 12:42:53,348 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:42:53,348 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:42:53,348 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:42:53,421 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:42:55,663 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:42:56,168 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpabktw2c3/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_20186d36-2cd3-11f0-b407-763dc8eb2af0ha6ax515/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpabktw2c3/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_20186d36-2cd3-11f0-b407-763dc8eb2af0ha6ax515/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpabktw2c3/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_20186d36-2cd3-11f0-b407-763dc8eb2af0ha6ax515/parcellation_warped.nii.gz
2025-05-09 12:43:07,441 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:43:08,802 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:43:08,855 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:43:08,860 - JUNIFER - INFO - Getting element sub-07
2025-05-09 12:43:08,860 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:43:08,861 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:43:08,861 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:43:08,861 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:43:08,862 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:43:08,862 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:43:08,862 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:43:08,862 - JUNIFER - INFO - resolution: None
2025-05-09 12:43:08,862 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:43:08,862 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:43:08,862 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:43:08,934 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:43:11,183 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:43:11,687 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmppyqvtqh4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_29576636-2cd3-11f0-b407-763dc8eb2af0mdcayv9v/prewarp_parcellation.nii.gz -r /tmp/junifer/tmppyqvtqh4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_29576636-2cd3-11f0-b407-763dc8eb2af0mdcayv9v/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmppyqvtqh4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_29576636-2cd3-11f0-b407-763dc8eb2af0mdcayv9v/parcellation_warped.nii.gz
2025-05-09 12:43:17,950 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:43:19,308 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:43:19,344 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:43:19,344 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:43:19,344 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:43:19,344 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:43:19,344 - JUNIFER - INFO - resolution: None
2025-05-09 12:43:19,344 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:43:19,344 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:43:19,344 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:43:19,417 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:43:21,665 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:43:22,172 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmppyqvtqh4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_2f974a2a-2cd3-11f0-b407-763dc8eb2af02qrlzwky/prewarp_parcellation.nii.gz -r /tmp/junifer/tmppyqvtqh4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_2f974a2a-2cd3-11f0-b407-763dc8eb2af02qrlzwky/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmppyqvtqh4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_2f974a2a-2cd3-11f0-b407-763dc8eb2af02qrlzwky/parcellation_warped.nii.gz
2025-05-09 12:43:33,426 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:43:34,790 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:43:34,842 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:43:34,848 - JUNIFER - INFO - Getting element sub-08
2025-05-09 12:43:34,848 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:43:34,848 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:43:34,848 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:43:34,849 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:43:34,849 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:43:34,849 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:43:34,849 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:43:34,849 - JUNIFER - INFO - resolution: None
2025-05-09 12:43:34,849 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:43:34,849 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:43:34,849 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:43:34,923 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:43:37,201 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:43:37,706 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp4hm2j2xz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_38d5427c-2cd3-11f0-b407-763dc8eb2af0wd7ppkf4/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp4hm2j2xz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_38d5427c-2cd3-11f0-b407-763dc8eb2af0wd7ppkf4/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp4hm2j2xz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_38d5427c-2cd3-11f0-b407-763dc8eb2af0wd7ppkf4/parcellation_warped.nii.gz
2025-05-09 12:43:44,007 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:43:45,417 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:43:45,452 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:43:45,453 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:43:45,453 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:43:45,453 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:43:45,453 - JUNIFER - INFO - resolution: None
2025-05-09 12:43:45,453 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:43:45,453 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:43:45,453 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:43:45,526 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:43:47,824 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:43:48,330 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp4hm2j2xz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3f279c1a-2cd3-11f0-b407-763dc8eb2af0366yk_2n/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp4hm2j2xz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3f279c1a-2cd3-11f0-b407-763dc8eb2af0366yk_2n/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp4hm2j2xz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3f279c1a-2cd3-11f0-b407-763dc8eb2af0366yk_2n/parcellation_warped.nii.gz
2025-05-09 12:43:59,731 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:44:01,118 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:44:01,171 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:44:01,177 - JUNIFER - INFO - Getting element sub-09
2025-05-09 12:44:01,177 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:44:01,177 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:44:01,177 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:44:01,178 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:44:01,178 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:44:01,178 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:44:01,178 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:44:01,178 - JUNIFER - INFO - resolution: None
2025-05-09 12:44:01,178 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:44:01,178 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:44:01,178 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:44:01,251 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:44:03,540 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:44:04,045 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpkd8ku6h1/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_4886969e-2cd3-11f0-b407-763dc8eb2af007117o47/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpkd8ku6h1/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_4886969e-2cd3-11f0-b407-763dc8eb2af007117o47/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpkd8ku6h1/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_4886969e-2cd3-11f0-b407-763dc8eb2af007117o47/parcellation_warped.nii.gz
2025-05-09 12:44:10,304 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:44:11,753 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:44:11,789 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:44:11,789 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:44:11,790 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:44:11,790 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:44:11,790 - JUNIFER - INFO - resolution: None
2025-05-09 12:44:11,790 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:44:11,790 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:44:11,790 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:44:11,864 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:44:14,122 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:44:14,631 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpkd8ku6h1/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4eda7d26-2cd3-11f0-b407-763dc8eb2af04baodqer/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpkd8ku6h1/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4eda7d26-2cd3-11f0-b407-763dc8eb2af04baodqer/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpkd8ku6h1/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4eda7d26-2cd3-11f0-b407-763dc8eb2af04baodqer/parcellation_warped.nii.gz
2025-05-09 12:44:25,920 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:44:27,276 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:44:27,329 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:44:27,334 - JUNIFER - INFO - Getting element sub-10
2025-05-09 12:44:27,334 - JUNIFER - INFO - Fitting pipeline
2025-05-09 12:44:27,334 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:44:27,334 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:44:27,335 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-05-09 12:44:27,335 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:44:27,335 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:44:27,335 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:44:27,336 - JUNIFER - INFO - resolution: None
2025-05-09 12:44:27,336 - JUNIFER - INFO - n_rois: 100
2025-05-09 12:44:27,336 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:44:27,336 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:44:27,410 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:44:29,656 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:44:30,160 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptz8yozh8/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_581d519c-2cd3-11f0-b407-763dc8eb2af0uipyupjt/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptz8yozh8/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_581d519c-2cd3-11f0-b407-763dc8eb2af0uipyupjt/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmptz8yozh8/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_581d519c-2cd3-11f0-b407-763dc8eb2af0uipyupjt/parcellation_warped.nii.gz
2025-05-09 12:44:36,407 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:44:37,750 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:44:37,788 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-05-09 12:44:37,788 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:44:37,788 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:44:37,788 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:44:37,788 - JUNIFER - INFO - resolution: None
2025-05-09 12:44:37,788 - JUNIFER - INFO - n_rois: 200
2025-05-09 12:44:37,788 - JUNIFER - INFO - yeo_networks: 17
2025-05-09 12:44:37,788 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:44:37,861 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:44:40,137 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:44:40,643 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptz8yozh8/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_5e58a296-2cd3-11f0-b407-763dc8eb2af05p0ksgrr/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptz8yozh8/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_5e58a296-2cd3-11f0-b407-763dc8eb2af05p0ksgrr/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmptz8yozh8/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_5e58a296-2cd3-11f0-b407-763dc8eb2af05p0ksgrr/parcellation_warped.nii.gz
2025-05-09 12:44:51,953 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-05-09 12:44:53,338 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpll5vcf_n/test.sqlite (multiple output)>
2025-05-09 12:44:53,392 - JUNIFER - INFO - Marker collection fitting done
2025-05-09 12:44:53,397 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2025-05-09 12:44:53,397 - JUNIFER - INFO - Collecting data from /tmp/tmpll5vcf_n/*test.sqlite
file: 0it [00:00, ?it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 13.33it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 13.31it/s]
file: 1it [00:00, 6.13it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.05it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.02it/s]
file: 2it [00:00, 6.54it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.23it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.20it/s]
file: 3it [00:00, 6.73it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.97it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.94it/s]
file: 4it [00:00, 6.78it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 7.58it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 7.57it/s]
file: 5it [00:00, 5.16it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.17it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.13it/s]
file: 6it [00:01, 5.64it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.88it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.85it/s]
file: 7it [00:01, 5.98it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.17it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.14it/s]
file: 8it [00:01, 6.26it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.73it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 14.70it/s]
file: 9it [00:01, 6.41it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 7.67it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 7.66it/s]
file: 10it [00:01, 5.20it/s]
file: 10it [00:01, 5.78it/s]
2025-05-09 12:44:55,128 - 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 0.145709 0.020355 ... 0 509497eb21da473048117e0c6704d3ea
1 0.143907 0.020940 ... 1 509497eb21da473048117e0c6704d3ea
2 0.144006 0.020337 ... 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 23.713 seconds)