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))
2024-12-06 13:55:51,448 - JUNIFER - INFO - ===== Lib Versions =====
2024-12-06 13:55:51,448 - JUNIFER - INFO - numpy: 1.26.4
2024-12-06 13:55:51,448 - JUNIFER - INFO - scipy: 1.14.1
2024-12-06 13:55:51,448 - JUNIFER - INFO - pandas: 2.1.4
2024-12-06 13:55:51,449 - JUNIFER - INFO - nilearn: 0.10.4
2024-12-06 13:55:51,449 - JUNIFER - INFO - nibabel: 5.3.2
2024-12-06 13:55:51,449 - JUNIFER - INFO - junifer: 0.0.6.dev358
2024-12-06 13:55:51,449 - 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
2024-12-06 13:55:51,467 - JUNIFER - INFO - Validating Marker Collection
2024-12-06 13:55:51,467 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-12-06 13:55:51,467 - JUNIFER - INFO - Validating Data Reader:
2024-12-06 13:55:51,467 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-12-06 13:55:51,467 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-12-06 13:55:51,468 - JUNIFER - INFO - Marker output type: ['vector']
2024-12-06 13:55:51,468 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-12-06 13:55:51,468 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-12-06 13:55:51,468 - JUNIFER - INFO - Marker output type: ['vector']
2024-12-06 13:55:51,468 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2024-12-06 13:55:51,473 - JUNIFER - INFO - Getting element sub-01
2024-12-06 13:55:51,473 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:55:51,473 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:55:51,473 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:55:51,474 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:55:51,474 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:55:51,474 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:55:51,474 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:55:51,474 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:55:51,474 - JUNIFER - INFO - resolution: None
2024-12-06 13:55:51,474 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:55:51,474 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:55:51,474 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:55:51,475 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:55:51,745 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:55:52,894 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:55:53,397 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpv7a_mbrc/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_ce00597c-b3d9-11ef-9645-0242ac120002_z5e5oag/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpv7a_mbrc/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_ce00597c-b3d9-11ef-9645-0242ac120002_z5e5oag/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpv7a_mbrc/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_ce00597c-b3d9-11ef-9645-0242ac120002_z5e5oag/parcellation_warped.nii.gz
2024-12-06 13:56:02,420 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:56:03,846 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:56:03,881 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:56:03,881 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:56:03,881 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:56:03,881 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:56:03,881 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:56:03,881 - JUNIFER - INFO - resolution: None
2024-12-06 13:56:03,881 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:56:03,881 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:56:03,881 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:56:03,883 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:56:04,156 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:56:05,301 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:56:05,805 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpv7a_mbrc/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d56635ce-b3d9-11ef-9645-0242ac120002tc3a192z/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpv7a_mbrc/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d56635ce-b3d9-11ef-9645-0242ac120002tc3a192z/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpv7a_mbrc/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d56635ce-b3d9-11ef-9645-0242ac120002tc3a192z/parcellation_warped.nii.gz
2024-12-06 13:56:22,732 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:56:24,156 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:56:24,210 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:56:24,214 - JUNIFER - INFO - Getting element sub-02
2024-12-06 13:56:24,214 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:56:24,214 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:56:24,214 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:56:24,215 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:56:24,215 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:56:24,216 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:56:24,216 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:56:24,216 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:56:24,216 - JUNIFER - INFO - resolution: None
2024-12-06 13:56:24,216 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:56:24,216 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:56:24,216 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:56:24,217 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:56:24,487 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:56:25,627 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:56:26,130 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpetbimmax/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e1847b90-b3d9-11ef-9645-0242ac120002acq9d33e/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpetbimmax/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e1847b90-b3d9-11ef-9645-0242ac120002acq9d33e/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpetbimmax/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e1847b90-b3d9-11ef-9645-0242ac120002acq9d33e/parcellation_warped.nii.gz
2024-12-06 13:56:35,162 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:56:36,580 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:56:36,615 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:56:36,616 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:56:36,616 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:56:36,616 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:56:36,616 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:56:36,616 - JUNIFER - INFO - resolution: None
2024-12-06 13:56:36,616 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:56:36,616 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:56:36,616 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:56:36,618 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:56:36,890 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:56:38,007 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:56:38,511 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpetbimmax/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e8e91a30-b3d9-11ef-9645-0242ac120002qu4qu26y/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpetbimmax/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e8e91a30-b3d9-11ef-9645-0242ac120002qu4qu26y/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpetbimmax/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_e8e91a30-b3d9-11ef-9645-0242ac120002qu4qu26y/parcellation_warped.nii.gz
2024-12-06 13:56:55,320 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:56:56,710 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:56:56,764 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:56:56,768 - JUNIFER - INFO - Getting element sub-03
2024-12-06 13:56:56,768 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:56:56,769 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:56:56,769 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:56:56,770 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:56:56,770 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:56:56,770 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:56:56,770 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:56:56,770 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:56:56,770 - JUNIFER - INFO - resolution: None
2024-12-06 13:56:56,770 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:56:56,770 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:56:56,770 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:56:56,771 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:56:57,040 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:56:58,172 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:56:58,674 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpfkzpa49u/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f4eba80c-b3d9-11ef-9645-0242ac120002h_zq86c2/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpfkzpa49u/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f4eba80c-b3d9-11ef-9645-0242ac120002h_zq86c2/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpfkzpa49u/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f4eba80c-b3d9-11ef-9645-0242ac120002h_zq86c2/parcellation_warped.nii.gz
2024-12-06 13:57:07,662 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:57:09,014 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:57:09,048 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:57:09,048 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:57:09,048 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:57:09,048 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:57:09,048 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:57:09,048 - JUNIFER - INFO - resolution: None
2024-12-06 13:57:09,048 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:57:09,048 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:57:09,048 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:57:09,050 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:57:09,321 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:57:10,489 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:57:10,994 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpfkzpa49u/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_fc3db712-b3d9-11ef-9645-0242ac120002054n1on1/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpfkzpa49u/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_fc3db712-b3d9-11ef-9645-0242ac120002054n1on1/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpfkzpa49u/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_fc3db712-b3d9-11ef-9645-0242ac120002054n1on1/parcellation_warped.nii.gz
2024-12-06 13:57:27,903 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:57:29,312 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:57:29,365 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:57:29,369 - JUNIFER - INFO - Getting element sub-04
2024-12-06 13:57:29,370 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:57:29,370 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:57:29,370 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:57:29,371 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:57:29,371 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:57:29,371 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:57:29,371 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:57:29,371 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:57:29,371 - JUNIFER - INFO - resolution: None
2024-12-06 13:57:29,371 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:57:29,371 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:57:29,371 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:57:29,373 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:57:29,642 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:57:30,782 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:57:31,286 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpw1sl6aey/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_085a72b0-b3da-11ef-9645-0242ac12000258nyzdfd/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpw1sl6aey/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_085a72b0-b3da-11ef-9645-0242ac12000258nyzdfd/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpw1sl6aey/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_085a72b0-b3da-11ef-9645-0242ac12000258nyzdfd/parcellation_warped.nii.gz
2024-12-06 13:57:40,289 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:57:41,695 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:57:41,729 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:57:41,729 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:57:41,730 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:57:41,730 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:57:41,730 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:57:41,730 - JUNIFER - INFO - resolution: None
2024-12-06 13:57:41,730 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:57:41,730 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:57:41,730 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:57:41,731 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:57:42,005 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:57:43,154 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:57:43,658 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpw1sl6aey/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_0fb8d06a-b3da-11ef-9645-0242ac120002w3s891g0/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpw1sl6aey/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_0fb8d06a-b3da-11ef-9645-0242ac120002w3s891g0/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpw1sl6aey/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_0fb8d06a-b3da-11ef-9645-0242ac120002w3s891g0/parcellation_warped.nii.gz
2024-12-06 13:58:00,436 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:58:01,856 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:58:01,909 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:58:01,914 - JUNIFER - INFO - Getting element sub-05
2024-12-06 13:58:01,914 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:58:01,914 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:58:01,914 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:58:01,915 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:58:01,915 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:58:01,915 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:58:01,915 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:58:01,915 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:58:01,915 - JUNIFER - INFO - resolution: None
2024-12-06 13:58:01,915 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:58:01,916 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:58:01,916 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:58:01,917 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:58:02,187 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:58:03,333 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:58:03,838 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpq95405mr/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_1bc048f2-b3da-11ef-9645-0242ac1200026mq22dis/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpq95405mr/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_1bc048f2-b3da-11ef-9645-0242ac1200026mq22dis/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpq95405mr/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_1bc048f2-b3da-11ef-9645-0242ac1200026mq22dis/parcellation_warped.nii.gz
2024-12-06 13:58:12,815 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:58:14,177 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:58:14,211 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:58:14,211 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:58:14,211 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:58:14,211 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:58:14,211 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:58:14,211 - JUNIFER - INFO - resolution: None
2024-12-06 13:58:14,211 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:58:14,211 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:58:14,211 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:58:14,213 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:58:14,485 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:58:15,631 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:58:16,134 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpq95405mr/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_2314ce84-b3da-11ef-9645-0242ac120002jpuexe53/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpq95405mr/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_2314ce84-b3da-11ef-9645-0242ac120002jpuexe53/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpq95405mr/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_2314ce84-b3da-11ef-9645-0242ac120002jpuexe53/parcellation_warped.nii.gz
2024-12-06 13:58:32,992 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:58:34,429 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:58:34,484 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:58:34,489 - JUNIFER - INFO - Getting element sub-06
2024-12-06 13:58:34,489 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:58:34,489 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:58:34,489 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:58:34,490 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:58:34,490 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:58:34,490 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:58:34,490 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:58:34,490 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:58:34,490 - JUNIFER - INFO - resolution: None
2024-12-06 13:58:34,490 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:58:34,490 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:58:34,490 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:58:34,492 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:58:34,762 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:58:35,908 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:58:36,412 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpjt_vl4nt/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_2f2aeaf0-b3da-11ef-9645-0242ac120002zd2l16pn/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpjt_vl4nt/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_2f2aeaf0-b3da-11ef-9645-0242ac120002zd2l16pn/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpjt_vl4nt/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_2f2aeaf0-b3da-11ef-9645-0242ac120002zd2l16pn/parcellation_warped.nii.gz
2024-12-06 13:58:45,418 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:58:46,884 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:58:46,918 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:58:46,918 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:58:46,918 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:58:46,919 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:58:46,919 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:58:46,919 - JUNIFER - INFO - resolution: None
2024-12-06 13:58:46,919 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:58:46,919 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:58:46,919 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:58:46,920 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:58:47,195 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:58:48,363 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:58:48,872 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpjt_vl4nt/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_36940aba-b3da-11ef-9645-0242ac1200029jbpr5vg/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpjt_vl4nt/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_36940aba-b3da-11ef-9645-0242ac1200029jbpr5vg/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpjt_vl4nt/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_36940aba-b3da-11ef-9645-0242ac1200029jbpr5vg/parcellation_warped.nii.gz
2024-12-06 13:59:05,692 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:59:07,190 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:59:07,243 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:59:07,248 - JUNIFER - INFO - Getting element sub-07
2024-12-06 13:59:07,248 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:59:07,248 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:59:07,248 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:59:07,249 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:59:07,249 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:59:07,249 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:59:07,249 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:59:07,249 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:59:07,249 - JUNIFER - INFO - resolution: None
2024-12-06 13:59:07,249 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:59:07,249 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:59:07,249 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:59:07,251 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:59:07,520 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:59:08,670 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:59:09,175 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpeq_3bcvo/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_42b15c3a-b3da-11ef-9645-0242ac120002s46iuyz8/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpeq_3bcvo/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_42b15c3a-b3da-11ef-9645-0242ac120002s46iuyz8/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpeq_3bcvo/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_42b15c3a-b3da-11ef-9645-0242ac120002s46iuyz8/parcellation_warped.nii.gz
2024-12-06 13:59:18,219 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:59:19,644 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:59:19,678 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:59:19,678 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:59:19,679 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:59:19,679 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:59:19,679 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:59:19,679 - JUNIFER - INFO - resolution: None
2024-12-06 13:59:19,679 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:59:19,679 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:59:19,679 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:59:19,680 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:59:19,956 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:59:21,112 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:59:21,616 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpeq_3bcvo/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4a1aee0a-b3da-11ef-9645-0242ac120002e7kf9_p5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpeq_3bcvo/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4a1aee0a-b3da-11ef-9645-0242ac120002e7kf9_p5/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpeq_3bcvo/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4a1aee0a-b3da-11ef-9645-0242ac120002e7kf9_p5/parcellation_warped.nii.gz
2024-12-06 13:59:38,390 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:59:39,797 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:59:39,851 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 13:59:39,856 - JUNIFER - INFO - Getting element sub-08
2024-12-06 13:59:39,856 - JUNIFER - INFO - Fitting pipeline
2024-12-06 13:59:39,856 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:59:39,856 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:59:39,857 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 13:59:39,857 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:59:39,857 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:59:39,857 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:59:39,858 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:59:39,858 - JUNIFER - INFO - resolution: None
2024-12-06 13:59:39,858 - JUNIFER - INFO - n_rois: 100
2024-12-06 13:59:39,858 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:59:39,858 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:59:39,859 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:59:40,130 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:59:41,278 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:59:41,782 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpj7vcnoxp/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_56214294-b3da-11ef-9645-0242ac120002yvcrf21r/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpj7vcnoxp/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_56214294-b3da-11ef-9645-0242ac120002yvcrf21r/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpj7vcnoxp/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_56214294-b3da-11ef-9645-0242ac120002yvcrf21r/parcellation_warped.nii.gz
2024-12-06 13:59:50,746 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 13:59:52,218 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 13:59:52,253 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 13:59:52,253 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:59:52,253 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:59:52,253 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:59:52,253 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:59:52,253 - JUNIFER - INFO - resolution: None
2024-12-06 13:59:52,253 - JUNIFER - INFO - n_rois: 200
2024-12-06 13:59:52,254 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 13:59:52,254 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:59:52,255 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:59:52,529 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:59:53,693 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:59:54,198 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpj7vcnoxp/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_5d8535e0-b3da-11ef-9645-0242ac120002wm2px9hs/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpj7vcnoxp/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_5d8535e0-b3da-11ef-9645-0242ac120002wm2px9hs/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpj7vcnoxp/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_5d8535e0-b3da-11ef-9645-0242ac120002wm2px9hs/parcellation_warped.nii.gz
2024-12-06 14:00:10,952 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 14:00:12,415 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 14:00:12,468 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 14:00:12,472 - JUNIFER - INFO - Getting element sub-09
2024-12-06 14:00:12,473 - JUNIFER - INFO - Fitting pipeline
2024-12-06 14:00:12,473 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 14:00:12,473 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 14:00:12,474 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 14:00:12,474 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 14:00:12,474 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 14:00:12,474 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 14:00:12,474 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 14:00:12,474 - JUNIFER - INFO - resolution: None
2024-12-06 14:00:12,474 - JUNIFER - INFO - n_rois: 100
2024-12-06 14:00:12,474 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 14:00:12,474 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 14:00:12,476 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 14:00:12,748 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 14:00:13,902 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 14:00:14,405 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpi3nt6qpz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_699233e2-b3da-11ef-9645-0242ac1200025t3fgojo/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpi3nt6qpz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_699233e2-b3da-11ef-9645-0242ac1200025t3fgojo/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpi3nt6qpz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_699233e2-b3da-11ef-9645-0242ac1200025t3fgojo/parcellation_warped.nii.gz
2024-12-06 14:00:23,385 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 14:00:24,832 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 14:00:24,867 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 14:00:24,867 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 14:00:24,867 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 14:00:24,867 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 14:00:24,867 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 14:00:24,867 - JUNIFER - INFO - resolution: None
2024-12-06 14:00:24,867 - JUNIFER - INFO - n_rois: 200
2024-12-06 14:00:24,867 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 14:00:24,867 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 14:00:24,869 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 14:00:25,138 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 14:00:26,297 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 14:00:26,802 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpi3nt6qpz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_70f502cc-b3da-11ef-9645-0242ac120002hehk7yl_/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpi3nt6qpz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_70f502cc-b3da-11ef-9645-0242ac120002hehk7yl_/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpi3nt6qpz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_70f502cc-b3da-11ef-9645-0242ac120002hehk7yl_/parcellation_warped.nii.gz
2024-12-06 14:00:43,533 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 14:00:44,974 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 14:00:45,028 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 14:00:45,033 - JUNIFER - INFO - Getting element sub-10
2024-12-06 14:00:45,033 - JUNIFER - INFO - Fitting pipeline
2024-12-06 14:00:45,033 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 14:00:45,033 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 14:00:45,034 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-06 14:00:45,034 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 14:00:45,034 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 14:00:45,034 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 14:00:45,034 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 14:00:45,034 - JUNIFER - INFO - resolution: None
2024-12-06 14:00:45,034 - JUNIFER - INFO - n_rois: 100
2024-12-06 14:00:45,034 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 14:00:45,034 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 14:00:45,036 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 14:00:45,303 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 14:00:46,443 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 14:00:46,948 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpwcd5qjwb/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_7cf9c724-b3da-11ef-9645-0242ac120002b0jah5p0/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpwcd5qjwb/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_7cf9c724-b3da-11ef-9645-0242ac120002b0jah5p0/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpwcd5qjwb/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_7cf9c724-b3da-11ef-9645-0242ac120002b0jah5p0/parcellation_warped.nii.gz
2024-12-06 14:00:55,910 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 14:00:57,269 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 14:00:57,303 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-06 14:00:57,303 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 14:00:57,303 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 14:00:57,303 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 14:00:57,303 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 14:00:57,303 - JUNIFER - INFO - resolution: None
2024-12-06 14:00:57,303 - JUNIFER - INFO - n_rois: 200
2024-12-06 14:00:57,303 - JUNIFER - INFO - yeo_networks: 17
2024-12-06 14:00:57,303 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 14:00:57,305 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 14:00:57,577 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 14:00:58,704 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 14:00:59,212 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpwcd5qjwb/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_844ac2bc-b3da-11ef-9645-0242ac1200028sfwvr7j/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpwcd5qjwb/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_844ac2bc-b3da-11ef-9645-0242ac1200028sfwvr7j/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmpwcd5qjwb/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_844ac2bc-b3da-11ef-9645-0242ac1200028sfwvr7j/parcellation_warped.nii.gz
2024-12-06 14:01:15,951 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-06 14:01:17,376 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpck_vrlrg/test.sqlite (multiple output)>
2024-12-06 14:01:17,431 - JUNIFER - INFO - Marker collection fitting done
2024-12-06 14:01:17,435 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-12-06 14:01:17,436 - JUNIFER - INFO - Collecting data from /tmp/tmpck_vrlrg/*test.sqlite
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2024-12-06 14:01:19,192 - 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 0.143536 0.020405 ... 0 509497eb21da473048117e0c6704d3ea
1 0.140624 0.020330 ... 1 509497eb21da473048117e0c6704d3ea
2 0.141432 0.020372 ... 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: (5 minutes 28.422 seconds)