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))
2025-01-29 11:01:59,928 - JUNIFER - INFO - ===== Lib Versions =====
2025-01-29 11:01:59,928 - JUNIFER - INFO - numpy: 1.26.4
2025-01-29 11:01:59,928 - JUNIFER - INFO - scipy: 1.15.0
2025-01-29 11:01:59,928 - JUNIFER - INFO - pandas: 2.1.4
2025-01-29 11:01:59,928 - JUNIFER - INFO - nilearn: 0.10.4
2025-01-29 11:01:59,928 - JUNIFER - INFO - nibabel: 5.3.2
2025-01-29 11:01:59,928 - JUNIFER - INFO - junifer: 0.0.6.dev429
2025-01-29 11:01:59,929 - 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
2025-01-29 11:01:59,946 - JUNIFER - INFO - Validating Marker Collection
2025-01-29 11:01:59,946 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2025-01-29 11:01:59,946 - JUNIFER - INFO - Validating Data Reader:
2025-01-29 11:01:59,946 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2025-01-29 11:01:59,946 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2025-01-29 11:01:59,946 - JUNIFER - INFO - Marker output type: ['vector']
2025-01-29 11:01:59,946 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2025-01-29 11:01:59,946 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2025-01-29 11:01:59,946 - JUNIFER - INFO - Marker output type: ['vector']
2025-01-29 11:01:59,946 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2025-01-29 11:01:59,951 - JUNIFER - INFO - Getting element sub-01
2025-01-29 11:01:59,951 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:01:59,951 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:01:59,951 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:01:59,952 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:01:59,952 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:01:59,952 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:01:59,952 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:01:59,953 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:01:59,953 - JUNIFER - INFO - resolution: None
2025-01-29 11:01:59,953 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:01:59,953 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:01:59,953 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:01:59,954 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:02:00,222 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:02:01,300 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:02:01,802 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpf3pmyu85/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_76a2dcdc-de30-11ef-acef-0242ac120002crjjb_ku/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpf3pmyu85/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_76a2dcdc-de30-11ef-acef-0242ac120002crjjb_ku/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpf3pmyu85/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_76a2dcdc-de30-11ef-acef-0242ac120002crjjb_ku/parcellation_warped.nii.gz
2025-01-29 11:02:08,058 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:02:09,422 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:02:09,457 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:02:09,457 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:02:09,457 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:02:09,458 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:02:09,458 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:02:09,458 - JUNIFER - INFO - resolution: None
2025-01-29 11:02:09,458 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:02:09,458 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:02:09,458 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:02:09,459 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:02:09,733 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:02:10,825 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:02:11,329 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpf3pmyu85/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_7c4e26d2-de30-11ef-acef-0242ac120002hy72bfmp/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpf3pmyu85/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_7c4e26d2-de30-11ef-acef-0242ac120002hy72bfmp/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpf3pmyu85/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_7c4e26d2-de30-11ef-acef-0242ac120002hy72bfmp/parcellation_warped.nii.gz
2025-01-29 11:02:22,534 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:02:23,862 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:02:23,914 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:02:23,919 - JUNIFER - INFO - Getting element sub-02
2025-01-29 11:02:23,919 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:02:23,919 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:02:23,920 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:02:23,920 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:02:23,921 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:02:23,921 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:02:23,921 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:02:23,921 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:02:23,921 - JUNIFER - INFO - resolution: None
2025-01-29 11:02:23,921 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:02:23,921 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:02:23,921 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:02:23,922 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:02:24,190 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:02:25,263 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:02:25,764 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpe_1q5jgy/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_84ec3982-de30-11ef-acef-0242ac120002cotniqtc/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpe_1q5jgy/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_84ec3982-de30-11ef-acef-0242ac120002cotniqtc/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpe_1q5jgy/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_84ec3982-de30-11ef-acef-0242ac120002cotniqtc/parcellation_warped.nii.gz
2025-01-29 11:02:31,886 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:02:33,196 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:02:33,230 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:02:33,231 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:02:33,231 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:02:33,231 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:02:33,231 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:02:33,231 - JUNIFER - INFO - resolution: None
2025-01-29 11:02:33,231 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:02:33,231 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:02:33,231 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:02:33,232 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:02:33,501 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:02:34,597 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:02:35,100 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpe_1q5jgy/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8a78f8d6-de30-11ef-acef-0242ac1200026wtosamo/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpe_1q5jgy/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8a78f8d6-de30-11ef-acef-0242ac1200026wtosamo/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpe_1q5jgy/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_8a78f8d6-de30-11ef-acef-0242ac1200026wtosamo/parcellation_warped.nii.gz
2025-01-29 11:02:46,351 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:02:47,665 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:02:47,717 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:02:47,721 - JUNIFER - INFO - Getting element sub-03
2025-01-29 11:02:47,721 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:02:47,721 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:02:47,721 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:02:47,722 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:02:47,722 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:02:47,722 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:02:47,722 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:02:47,722 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:02:47,722 - JUNIFER - INFO - resolution: None
2025-01-29 11:02:47,722 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:02:47,723 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:02:47,723 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:02:47,724 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:02:47,991 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:02:49,072 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:02:49,578 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpeyns53rx/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_931be39a-de30-11ef-acef-0242ac120002dhb6ewdj/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpeyns53rx/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_931be39a-de30-11ef-acef-0242ac120002dhb6ewdj/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpeyns53rx/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_931be39a-de30-11ef-acef-0242ac120002dhb6ewdj/parcellation_warped.nii.gz
2025-01-29 11:02:55,727 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:02:57,128 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:02:57,164 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:02:57,164 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:02:57,165 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:02:57,165 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:02:57,165 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:02:57,165 - JUNIFER - INFO - resolution: None
2025-01-29 11:02:57,165 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:02:57,165 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:02:57,165 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:02:57,166 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:02:57,435 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:02:58,526 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:02:59,031 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpeyns53rx/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_98bcf956-de30-11ef-acef-0242ac120002i74u3o07/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpeyns53rx/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_98bcf956-de30-11ef-acef-0242ac120002i74u3o07/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpeyns53rx/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_98bcf956-de30-11ef-acef-0242ac120002i74u3o07/parcellation_warped.nii.gz
2025-01-29 11:03:10,151 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:03:11,489 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:03:11,541 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:03:11,546 - JUNIFER - INFO - Getting element sub-04
2025-01-29 11:03:11,546 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:03:11,546 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:03:11,546 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:03:11,547 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:03:11,547 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:03:11,547 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:03:11,547 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:03:11,547 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:03:11,547 - JUNIFER - INFO - resolution: None
2025-01-29 11:03:11,547 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:03:11,547 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:03:11,547 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:03:11,548 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:03:11,817 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:03:12,901 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:03:13,404 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpmdlh023m/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a14f5a8c-de30-11ef-acef-0242ac120002_nb8owl2/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpmdlh023m/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a14f5a8c-de30-11ef-acef-0242ac120002_nb8owl2/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpmdlh023m/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_a14f5a8c-de30-11ef-acef-0242ac120002_nb8owl2/parcellation_warped.nii.gz
2025-01-29 11:03:19,590 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:03:20,935 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:03:20,969 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:03:20,969 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:03:20,969 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:03:20,969 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:03:20,969 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:03:20,969 - JUNIFER - INFO - resolution: None
2025-01-29 11:03:20,969 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:03:20,969 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:03:20,969 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:03:20,971 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:03:21,241 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:03:22,325 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:03:22,831 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpmdlh023m/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a6ed6236-de30-11ef-acef-0242ac120002v4i80b7u/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpmdlh023m/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a6ed6236-de30-11ef-acef-0242ac120002v4i80b7u/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpmdlh023m/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_a6ed6236-de30-11ef-acef-0242ac120002v4i80b7u/parcellation_warped.nii.gz
2025-01-29 11:03:33,986 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:03:35,298 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:03:35,421 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:03:35,426 - JUNIFER - INFO - Getting element sub-05
2025-01-29 11:03:35,426 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:03:35,426 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:03:35,426 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:03:35,427 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:03:35,427 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:03:35,427 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:03:35,427 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:03:35,427 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:03:35,427 - JUNIFER - INFO - resolution: None
2025-01-29 11:03:35,427 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:03:35,427 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:03:35,428 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:03:35,429 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:03:35,700 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:03:36,798 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:03:37,301 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpa5ivxizz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_af8bb942-de30-11ef-acef-0242ac1200020agf9lt4/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpa5ivxizz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_af8bb942-de30-11ef-acef-0242ac1200020agf9lt4/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpa5ivxizz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_af8bb942-de30-11ef-acef-0242ac1200020agf9lt4/parcellation_warped.nii.gz
2025-01-29 11:03:43,466 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:03:44,814 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:03:44,850 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:03:44,850 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:03:44,850 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:03:44,850 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:03:44,850 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:03:44,850 - JUNIFER - INFO - resolution: None
2025-01-29 11:03:44,850 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:03:44,850 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:03:44,850 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:03:44,852 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:03:45,122 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:03:46,211 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:03:46,715 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpa5ivxizz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b5294874-de30-11ef-acef-0242ac120002fwmt5ofu/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpa5ivxizz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b5294874-de30-11ef-acef-0242ac120002fwmt5ofu/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpa5ivxizz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_b5294874-de30-11ef-acef-0242ac120002fwmt5ofu/parcellation_warped.nii.gz
2025-01-29 11:03:57,879 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:03:59,326 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:03:59,380 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:03:59,385 - JUNIFER - INFO - Getting element sub-06
2025-01-29 11:03:59,385 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:03:59,385 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:03:59,385 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:03:59,386 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:03:59,386 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:03:59,386 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:03:59,386 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:03:59,387 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:03:59,387 - JUNIFER - INFO - resolution: None
2025-01-29 11:03:59,387 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:03:59,387 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:03:59,387 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:03:59,388 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:03:59,658 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:04:00,776 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:04:01,280 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp77pv9v3d/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_bdd34cea-de30-11ef-acef-0242ac120002je3p5mc_/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp77pv9v3d/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_bdd34cea-de30-11ef-acef-0242ac120002je3p5mc_/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp77pv9v3d/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_bdd34cea-de30-11ef-acef-0242ac120002je3p5mc_/parcellation_warped.nii.gz
2025-01-29 11:04:07,501 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:04:08,911 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:04:08,945 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:04:08,945 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:04:08,945 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:04:08,945 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:04:08,945 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:04:08,946 - JUNIFER - INFO - resolution: None
2025-01-29 11:04:08,946 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:04:08,946 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:04:08,946 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:04:08,947 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:04:09,219 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:04:10,316 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:04:10,818 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp77pv9v3d/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c3864002-de30-11ef-acef-0242ac12000266bd8fy0/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp77pv9v3d/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c3864002-de30-11ef-acef-0242ac12000266bd8fy0/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp77pv9v3d/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_c3864002-de30-11ef-acef-0242ac12000266bd8fy0/parcellation_warped.nii.gz
2025-01-29 11:04:21,924 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:04:23,287 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:04:23,339 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:04:23,343 - JUNIFER - INFO - Getting element sub-07
2025-01-29 11:04:23,344 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:04:23,344 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:04:23,344 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:04:23,345 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:04:23,345 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:04:23,345 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:04:23,345 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:04:23,345 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:04:23,345 - JUNIFER - INFO - resolution: None
2025-01-29 11:04:23,345 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:04:23,345 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:04:23,345 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:04:23,346 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:04:23,614 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:04:24,685 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:04:25,186 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmphotgmqco/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cc1ae2f4-de30-11ef-acef-0242ac120002qyg59bqc/prewarp_parcellation.nii.gz -r /tmp/junifer/tmphotgmqco/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cc1ae2f4-de30-11ef-acef-0242ac120002qyg59bqc/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmphotgmqco/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_cc1ae2f4-de30-11ef-acef-0242ac120002qyg59bqc/parcellation_warped.nii.gz
2025-01-29 11:04:31,400 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:04:32,730 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:04:32,765 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:04:32,765 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:04:32,765 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:04:32,765 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:04:32,765 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:04:32,766 - JUNIFER - INFO - resolution: None
2025-01-29 11:04:32,766 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:04:32,766 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:04:32,766 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:04:32,767 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:04:33,037 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:04:34,126 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:04:34,646 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmphotgmqco/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d1b87d34-de30-11ef-acef-0242ac120002o88xcezy/prewarp_parcellation.nii.gz -r /tmp/junifer/tmphotgmqco/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d1b87d34-de30-11ef-acef-0242ac120002o88xcezy/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmphotgmqco/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_d1b87d34-de30-11ef-acef-0242ac120002o88xcezy/parcellation_warped.nii.gz
2025-01-29 11:04:45,851 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:04:47,193 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:04:47,245 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:04:47,250 - JUNIFER - INFO - Getting element sub-08
2025-01-29 11:04:47,250 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:04:47,250 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:04:47,250 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:04:47,251 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:04:47,251 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:04:47,251 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:04:47,251 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:04:47,251 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:04:47,251 - JUNIFER - INFO - resolution: None
2025-01-29 11:04:47,251 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:04:47,251 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:04:47,251 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:04:47,253 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:04:47,520 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:04:48,592 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:04:49,094 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptn1kfiep/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_da5a91de-de30-11ef-acef-0242ac120002k_xj8va3/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptn1kfiep/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_da5a91de-de30-11ef-acef-0242ac120002k_xj8va3/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmptn1kfiep/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_da5a91de-de30-11ef-acef-0242ac120002k_xj8va3/parcellation_warped.nii.gz
2025-01-29 11:04:55,255 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:04:56,626 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:04:56,660 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:04:56,660 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:04:56,660 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:04:56,660 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:04:56,660 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:04:56,660 - JUNIFER - INFO - resolution: None
2025-01-29 11:04:56,660 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:04:56,660 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:04:56,660 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:04:56,662 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:04:56,932 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:04:58,010 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:04:58,513 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptn1kfiep/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_dff6c216-de30-11ef-acef-0242ac120002sm9apwwu/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptn1kfiep/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_dff6c216-de30-11ef-acef-0242ac120002sm9apwwu/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmptn1kfiep/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_dff6c216-de30-11ef-acef-0242ac120002sm9apwwu/parcellation_warped.nii.gz
2025-01-29 11:05:09,623 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:05:10,987 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:05:11,040 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:05:11,045 - JUNIFER - INFO - Getting element sub-09
2025-01-29 11:05:11,045 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:05:11,045 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:05:11,045 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:05:11,046 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:05:11,046 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:05:11,046 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:05:11,046 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:05:11,046 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:05:11,046 - JUNIFER - INFO - resolution: None
2025-01-29 11:05:11,046 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:05:11,046 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:05:11,046 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:05:11,048 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:05:11,317 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:05:12,408 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:05:12,919 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpkpwll_ih/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e8899f34-de30-11ef-acef-0242ac120002ercqaqda/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpkpwll_ih/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e8899f34-de30-11ef-acef-0242ac120002ercqaqda/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpkpwll_ih/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e8899f34-de30-11ef-acef-0242ac120002ercqaqda/parcellation_warped.nii.gz
2025-01-29 11:05:19,149 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:05:20,556 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:05:20,590 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:05:20,591 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:05:20,591 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:05:20,591 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:05:20,591 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:05:20,591 - JUNIFER - INFO - resolution: None
2025-01-29 11:05:20,591 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:05:20,591 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:05:20,591 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:05:20,592 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:05:20,863 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:05:21,948 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:05:22,452 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpkpwll_ih/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_ee3a5996-de30-11ef-acef-0242ac120002v3lvvyph/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpkpwll_ih/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_ee3a5996-de30-11ef-acef-0242ac120002v3lvvyph/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpkpwll_ih/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_ee3a5996-de30-11ef-acef-0242ac120002v3lvvyph/parcellation_warped.nii.gz
2025-01-29 11:05:33,682 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:05:35,063 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:05:35,117 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:05:35,121 - JUNIFER - INFO - Getting element sub-10
2025-01-29 11:05:35,121 - JUNIFER - INFO - Fitting pipeline
2025-01-29 11:05:35,122 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-29 11:05:35,122 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-29 11:05:35,123 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2025-01-29 11:05:35,123 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:05:35,123 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:05:35,123 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:05:35,123 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:05:35,123 - JUNIFER - INFO - resolution: None
2025-01-29 11:05:35,123 - JUNIFER - INFO - n_rois: 100
2025-01-29 11:05:35,123 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:05:35,123 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:05:35,124 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:05:35,393 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:05:36,481 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:05:36,983 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp7dl0mq33/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f6e3611e-de30-11ef-acef-0242ac120002465k3ca_/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp7dl0mq33/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f6e3611e-de30-11ef-acef-0242ac120002465k3ca_/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp7dl0mq33/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_f6e3611e-de30-11ef-acef-0242ac120002465k3ca_/parcellation_warped.nii.gz
2025-01-29 11:05:43,224 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:05:44,583 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:05:44,618 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2025-01-29 11:05:44,618 - JUNIFER - INFO - Computing VBM_GM
2025-01-29 11:05:44,618 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-29 11:05:44,618 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2025-01-29 11:05:44,619 - JUNIFER - INFO - Parcellation parameters:
2025-01-29 11:05:44,619 - JUNIFER - INFO - resolution: None
2025-01-29 11:05:44,619 - JUNIFER - INFO - n_rois: 200
2025-01-29 11:05:44,619 - JUNIFER - INFO - yeo_networks: 17
2025-01-29 11:05:44,619 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-29 11:05:44,620 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2025-01-29 11:05:44,891 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5
2025-01-29 11:05:45,997 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1
2025-01-29 11:05:46,499 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp7dl0mq33/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_fc8cbe8a-de30-11ef-acef-0242ac120002eq7wyr_6/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp7dl0mq33/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_fc8cbe8a-de30-11ef-acef-0242ac120002eq7wyr_6/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmp7dl0mq33/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_fc8cbe8a-de30-11ef-acef-0242ac120002eq7wyr_6/parcellation_warped.nii.gz
2025-01-29 11:05:57,594 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2025-01-29 11:05:58,977 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp083ed45k/test.sqlite (multiple output)>
2025-01-29 11:05:59,028 - JUNIFER - INFO - Marker collection fitting done
2025-01-29 11:05:59,033 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2025-01-29 11:05:59,034 - JUNIFER - INFO - Collecting data from /tmp/tmp083ed45k/*test.sqlite
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2025-01-29 11:06:00,589 - 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 0.142608 0.020489 ... 0 509497eb21da473048117e0c6704d3ea
1 0.142186 0.020590 ... 1 509497eb21da473048117e0c6704d3ea
2 0.140137 0.020490 ... 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 1.465 seconds)