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:193: 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))
2025-01-27 11:18:54,963 - JUNIFER - INFO - ===== Lib Versions =====
2025-01-27 11:18:54,963 - JUNIFER - INFO - numpy: 1.26.4
2025-01-27 11:18:54,963 - JUNIFER - INFO - scipy: 1.15.0
2025-01-27 11:18:54,963 - JUNIFER - INFO - pandas: 2.1.4
2025-01-27 11:18:54,963 - JUNIFER - INFO - nilearn: 0.10.4
2025-01-27 11:18:54,963 - JUNIFER - INFO - nibabel: 5.3.2
2025-01-27 11:18:54,963 - JUNIFER - INFO - junifer: 0.0.6.dev450
2025-01-27 11:18:54,963 - 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
2025-01-27 11:18:54,980 - JUNIFER - INFO - Validating Marker Collection
2025-01-27 11:18:54,980 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2025-01-27 11:18:54,980 - JUNIFER - INFO - Validating Data Reader:
2025-01-27 11:18:54,980 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2025-01-27 11:18:54,981 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2025-01-27 11:18:54,981 - JUNIFER - INFO - Marker output type: ['vector']
2025-01-27 11:18:54,981 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2025-01-27 11:18:54,981 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2025-01-27 11:18:54,981 - JUNIFER - INFO - Marker output type: ['vector']
2025-01-27 11:18:54,981 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2025-01-27 11:18:54,985 - JUNIFER - INFO - Getting element sub-01
2025-01-27 11:18:54,985 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:18:54,985 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:18:54,985 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:18:54,986 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:18:54,986 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:18:54,987 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:18:54,987 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:18:54,987 - JUNIFER - INFO - resolution: None
2025-01-27 11:18:54,987 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:18:54,987 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:18:54,987 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:18:56,195 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:18:58,017 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:18:58,516 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp0y5dqtwh/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_7f89084e-dca0-11ef-bd11-0242ac120002opgx02t_/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp0y5dqtwh/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_7f89084e-dca0-11ef-bd11-0242ac120002opgx02t_/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp0y5dqtwh/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_7f89084e-dca0-11ef-bd11-0242ac120002opgx02t_/parcellation_warped.nii.gz
2025-01-27 11:19:04,711 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:19:05,939 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:19:05,976 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:19:05,976 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:19:05,976 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:19:05,976 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:19:05,976 - JUNIFER - INFO - resolution: None
2025-01-27 11:19:05,977 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:19:05,977 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:19:05,977 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:19:07,185 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:19:09,134 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:19:09,634 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp0y5dqtwh/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8616c3fe-dca0-11ef-bd11-0242ac120002u2dl0ujy/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp0y5dqtwh/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8616c3fe-dca0-11ef-bd11-0242ac120002u2dl0ujy/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp0y5dqtwh/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8616c3fe-dca0-11ef-bd11-0242ac120002u2dl0ujy/parcellation_warped.nii.gz
2025-01-27 11:19:20,939 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:19:22,153 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:19:22,206 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:19:22,211 - JUNIFER - INFO - Getting element sub-02
2025-01-27 11:19:22,211 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:19:22,211 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:19:22,211 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:19:22,212 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:19:22,212 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:19:22,212 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:19:22,212 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:19:22,212 - JUNIFER - INFO - resolution: None
2025-01-27 11:19:22,212 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:19:22,212 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:19:22,212 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:19:23,493 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:19:25,325 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:19:25,825 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp1p26kkah/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_8fcea740-dca0-11ef-bd11-0242ac120002sbushpnr/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp1p26kkah/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_8fcea740-dca0-11ef-bd11-0242ac120002sbushpnr/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp1p26kkah/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_8fcea740-dca0-11ef-bd11-0242ac120002sbushpnr/parcellation_warped.nii.gz
2025-01-27 11:19:32,081 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:19:33,298 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:19:33,337 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:19:33,337 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:19:33,337 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:19:33,337 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:19:33,337 - JUNIFER - INFO - resolution: None
2025-01-27 11:19:33,337 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:19:33,337 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:19:33,337 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:19:34,447 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:19:36,344 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:19:36,844 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp1p26kkah/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_9656b008-dca0-11ef-bd11-0242ac1200024t7n8gtr/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp1p26kkah/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_9656b008-dca0-11ef-bd11-0242ac1200024t7n8gtr/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp1p26kkah/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_9656b008-dca0-11ef-bd11-0242ac1200024t7n8gtr/parcellation_warped.nii.gz
2025-01-27 11:19:48,194 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:19:49,424 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:19:49,476 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:19:49,481 - JUNIFER - INFO - Getting element sub-03
2025-01-27 11:19:49,481 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:19:49,481 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:19:49,481 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:19:49,482 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:19:49,482 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:19:49,482 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:19:49,482 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:19:49,482 - JUNIFER - INFO - resolution: None
2025-01-27 11:19:49,482 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:19:49,482 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:19:49,482 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:19:50,581 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:19:52,409 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:19:52,909 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpk8e6za7l/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_9ff3f6d4-dca0-11ef-bd11-0242ac120002q2avmbvv/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpk8e6za7l/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_9ff3f6d4-dca0-11ef-bd11-0242ac120002q2avmbvv/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpk8e6za7l/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_9ff3f6d4-dca0-11ef-bd11-0242ac120002q2avmbvv/parcellation_warped.nii.gz
2025-01-27 11:19:59,108 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:20:00,349 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:20:00,386 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:20:00,386 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:20:00,386 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:20:00,386 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:20:00,386 - JUNIFER - INFO - resolution: None
2025-01-27 11:20:00,387 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:20:00,387 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:20:00,387 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:20:01,574 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:20:03,595 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:20:04,095 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpk8e6za7l/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a681e5a6-dca0-11ef-bd11-0242ac120002ww_l930b/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpk8e6za7l/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a681e5a6-dca0-11ef-bd11-0242ac120002ww_l930b/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpk8e6za7l/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a681e5a6-dca0-11ef-bd11-0242ac120002ww_l930b/parcellation_warped.nii.gz
2025-01-27 11:20:15,347 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:20:16,607 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:20:16,662 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:20:16,667 - JUNIFER - INFO - Getting element sub-04
2025-01-27 11:20:16,667 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:20:16,667 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:20:16,667 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:20:16,668 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:20:16,668 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:20:16,669 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:20:16,669 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:20:16,669 - JUNIFER - INFO - resolution: None
2025-01-27 11:20:16,669 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:20:16,669 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:20:16,669 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:20:17,831 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:20:19,770 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:20:20,270 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp_kf2v7qz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b0320cfc-dca0-11ef-bd11-0242ac120002s8y9z4nc/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp_kf2v7qz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b0320cfc-dca0-11ef-bd11-0242ac120002s8y9z4nc/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp_kf2v7qz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_b0320cfc-dca0-11ef-bd11-0242ac120002s8y9z4nc/parcellation_warped.nii.gz
2025-01-27 11:20:26,452 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:20:27,688 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:20:27,726 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:20:27,726 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:20:27,726 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:20:27,726 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:20:27,726 - JUNIFER - INFO - resolution: None
2025-01-27 11:20:27,726 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:20:27,726 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:20:27,726 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:20:29,196 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:20:31,028 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:20:31,531 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp_kf2v7qz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b6f88700-dca0-11ef-bd11-0242ac120002xwrd5zrw/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp_kf2v7qz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b6f88700-dca0-11ef-bd11-0242ac120002xwrd5zrw/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp_kf2v7qz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b6f88700-dca0-11ef-bd11-0242ac120002xwrd5zrw/parcellation_warped.nii.gz
2025-01-27 11:20:42,984 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:20:44,237 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:20:44,291 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:20:44,296 - JUNIFER - INFO - Getting element sub-05
2025-01-27 11:20:44,296 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:20:44,296 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:20:44,296 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:20:44,297 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:20:44,297 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:20:44,297 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:20:44,297 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:20:44,297 - JUNIFER - INFO - resolution: None
2025-01-27 11:20:44,297 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:20:44,297 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:20:44,297 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:20:46,005 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:20:48,065 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:20:48,564 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpw4eq8u_5/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_c0fd1d74-dca0-11ef-bd11-0242ac120002g0p11qdz/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpw4eq8u_5/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_c0fd1d74-dca0-11ef-bd11-0242ac120002g0p11qdz/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpw4eq8u_5/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_c0fd1d74-dca0-11ef-bd11-0242ac120002g0p11qdz/parcellation_warped.nii.gz
2025-01-27 11:20:54,759 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:20:56,022 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:20:56,058 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:20:56,058 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:20:56,058 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:20:56,058 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:20:56,058 - JUNIFER - INFO - resolution: None
2025-01-27 11:20:56,058 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:20:56,058 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:20:56,058 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:20:57,268 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:20:59,148 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:20:59,650 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpw4eq8u_5/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c7b43ecc-dca0-11ef-bd11-0242ac1200022yvxsdg2/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpw4eq8u_5/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c7b43ecc-dca0-11ef-bd11-0242ac1200022yvxsdg2/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpw4eq8u_5/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c7b43ecc-dca0-11ef-bd11-0242ac1200022yvxsdg2/parcellation_warped.nii.gz
2025-01-27 11:21:10,973 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:21:12,209 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:21:12,265 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:21:12,269 - JUNIFER - INFO - Getting element sub-06
2025-01-27 11:21:12,269 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:21:12,269 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:21:12,269 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:21:12,270 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:21:12,270 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:21:12,270 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:21:12,270 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:21:12,270 - JUNIFER - INFO - resolution: None
2025-01-27 11:21:12,270 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:21:12,270 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:21:12,270 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:21:13,993 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:21:15,928 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:21:16,428 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpywj4e0pc/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_d1abfaa0-dca0-11ef-bd11-0242ac120002n5sg6upg/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpywj4e0pc/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_d1abfaa0-dca0-11ef-bd11-0242ac120002n5sg6upg/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpywj4e0pc/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_d1abfaa0-dca0-11ef-bd11-0242ac120002n5sg6upg/parcellation_warped.nii.gz
2025-01-27 11:21:22,671 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:21:23,895 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:21:23,930 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:21:23,930 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:21:23,930 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:21:23,930 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:21:23,930 - JUNIFER - INFO - resolution: None
2025-01-27 11:21:23,930 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:21:23,930 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:21:23,930 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:21:25,067 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:21:26,912 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:21:27,413 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpywj4e0pc/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d845fc9e-dca0-11ef-bd11-0242ac120002fcvnw0l5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpywj4e0pc/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d845fc9e-dca0-11ef-bd11-0242ac120002fcvnw0l5/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpywj4e0pc/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d845fc9e-dca0-11ef-bd11-0242ac120002fcvnw0l5/parcellation_warped.nii.gz
2025-01-27 11:21:38,779 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:21:40,017 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:21:40,069 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:21:40,073 - JUNIFER - INFO - Getting element sub-07
2025-01-27 11:21:40,074 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:21:40,074 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:21:40,074 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:21:40,074 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:21:40,075 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:21:40,075 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:21:40,075 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:21:40,075 - JUNIFER - INFO - resolution: None
2025-01-27 11:21:40,075 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:21:40,075 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:21:40,075 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:21:41,299 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:21:43,135 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:21:43,635 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp3pzhzvi0/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e1f27646-dca0-11ef-bd11-0242ac120002azrs95g5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp3pzhzvi0/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e1f27646-dca0-11ef-bd11-0242ac120002azrs95g5/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp3pzhzvi0/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e1f27646-dca0-11ef-bd11-0242ac120002azrs95g5/parcellation_warped.nii.gz
2025-01-27 11:21:49,817 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:21:51,051 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:21:51,086 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:21:51,086 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:21:51,087 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:21:51,087 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:21:51,087 - JUNIFER - INFO - resolution: None
2025-01-27 11:21:51,087 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:21:51,087 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:21:51,087 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:21:52,204 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:21:54,040 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:21:54,540 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp3pzhzvi0/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e872caac-dca0-11ef-bd11-0242ac1200020_p8_9v2/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp3pzhzvi0/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e872caac-dca0-11ef-bd11-0242ac1200020_p8_9v2/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp3pzhzvi0/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e872caac-dca0-11ef-bd11-0242ac1200020_p8_9v2/parcellation_warped.nii.gz
2025-01-27 11:22:05,737 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:22:06,950 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:22:07,003 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:22:07,008 - JUNIFER - INFO - Getting element sub-08
2025-01-27 11:22:07,008 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:22:07,008 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:22:07,008 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:22:07,009 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:22:07,009 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:22:07,009 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:22:07,009 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:22:07,009 - JUNIFER - INFO - resolution: None
2025-01-27 11:22:07,009 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:22:07,009 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:22:07,009 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:22:08,290 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:22:10,127 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:22:10,627 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmps5cg7dfx/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f208ea10-dca0-11ef-bd11-0242ac12000266umtuss/prewarp_parcellation.nii.gz -r /tmp/junifer/tmps5cg7dfx/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f208ea10-dca0-11ef-bd11-0242ac12000266umtuss/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmps5cg7dfx/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f208ea10-dca0-11ef-bd11-0242ac12000266umtuss/parcellation_warped.nii.gz
2025-01-27 11:22:16,828 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:22:18,068 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:22:18,104 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:22:18,104 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:22:18,104 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:22:18,104 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:22:18,104 - JUNIFER - INFO - resolution: None
2025-01-27 11:22:18,104 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:22:18,104 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:22:18,104 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:22:19,241 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:22:21,083 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:22:21,585 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmps5cg7dfx/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f890849c-dca0-11ef-bd11-0242ac1200027f8vp8t4/prewarp_parcellation.nii.gz -r /tmp/junifer/tmps5cg7dfx/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f890849c-dca0-11ef-bd11-0242ac1200027f8vp8t4/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmps5cg7dfx/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_f890849c-dca0-11ef-bd11-0242ac1200027f8vp8t4/parcellation_warped.nii.gz
2025-01-27 11:22:32,824 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:22:34,061 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:22:34,116 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:22:34,121 - JUNIFER - INFO - Getting element sub-09
2025-01-27 11:22:34,121 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:22:34,121 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:22:34,121 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:22:34,122 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:22:34,122 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:22:34,122 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:22:34,122 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:22:34,122 - JUNIFER - INFO - resolution: None
2025-01-27 11:22:34,122 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:22:34,123 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:22:34,123 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:22:35,322 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:22:37,253 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:22:37,761 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpbk1al_0k/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_02258a5c-dca1-11ef-bd11-0242ac120002g8x6s9is/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpbk1al_0k/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_02258a5c-dca1-11ef-bd11-0242ac120002g8x6s9is/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpbk1al_0k/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_02258a5c-dca1-11ef-bd11-0242ac120002g8x6s9is/parcellation_warped.nii.gz
2025-01-27 11:22:43,908 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:22:45,191 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:22:45,227 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:22:45,227 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:22:45,227 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:22:45,227 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:22:45,228 - JUNIFER - INFO - resolution: None
2025-01-27 11:22:45,228 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:22:45,228 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:22:45,228 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:22:46,317 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:22:48,586 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:22:49,087 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpbk1al_0k/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_08b37e2e-dca1-11ef-bd11-0242ac1200020njywvy9/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpbk1al_0k/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_08b37e2e-dca1-11ef-bd11-0242ac1200020njywvy9/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpbk1al_0k/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_08b37e2e-dca1-11ef-bd11-0242ac1200020njywvy9/parcellation_warped.nii.gz
2025-01-27 11:23:00,599 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:23:01,879 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:23:01,931 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:23:01,936 - JUNIFER - INFO - Getting element sub-10
2025-01-27 11:23:01,936 - JUNIFER - INFO - Fitting pipeline
2025-01-27 11:23:01,936 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:23:01,936 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:23:01,937 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-27 11:23:01,937 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:23:01,937 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:23:01,937 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:23:01,937 - JUNIFER - INFO - resolution: None
2025-01-27 11:23:01,937 - JUNIFER - INFO - n_rois: 100
2025-01-27 11:23:01,937 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:23:01,937 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:23:03,028 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:23:04,943 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:23:05,443 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpy26fe_5m/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_12a8cd8a-dca1-11ef-bd11-0242ac1200021vuar_xf/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpy26fe_5m/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_12a8cd8a-dca1-11ef-bd11-0242ac1200021vuar_xf/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpy26fe_5m/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_12a8cd8a-dca1-11ef-bd11-0242ac1200021vuar_xf/parcellation_warped.nii.gz
2025-01-27 11:23:12,017 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:23:13,224 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:23:13,262 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-27 11:23:13,262 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:23:13,262 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:23:13,262 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:23:13,262 - JUNIFER - INFO - resolution: None
2025-01-27 11:23:13,262 - JUNIFER - INFO - n_rois: 200
2025-01-27 11:23:13,262 - JUNIFER - INFO - yeo_networks: 17
2025-01-27 11:23:13,262 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:23:14,368 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:23:16,199 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:23:16,700 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpy26fe_5m/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_196bef08-dca1-11ef-bd11-0242ac1200022zd3mtez/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpy26fe_5m/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_196bef08-dca1-11ef-bd11-0242ac1200022zd3mtez/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpy26fe_5m/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_196bef08-dca1-11ef-bd11-0242ac1200022zd3mtez/parcellation_warped.nii.gz
2025-01-27 11:23:27,940 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-27 11:23:29,204 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpm7pt5951/test.sqlite (multiple output)>
2025-01-27 11:23:29,256 - JUNIFER - INFO - Marker collection fitting done
2025-01-27 11:23:29,260 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2025-01-27 11:23:29,260 - JUNIFER - INFO - Collecting data from /tmp/tmpm7pt5951/*test.sqlite
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2025-01-27 11:23:30,908 - 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 0.139983 0.019614 ... 0 509497eb21da473048117e0c6704d3ea
1 0.138052 0.019706 ... 1 509497eb21da473048117e0c6704d3ea
2 0.138338 0.019738 ... 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 36.604 seconds)