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))
2024-12-09 11:22:40,160 - JUNIFER - INFO - ===== Lib Versions =====
2024-12-09 11:22:40,160 - JUNIFER - INFO - numpy: 1.26.4
2024-12-09 11:22:40,160 - JUNIFER - INFO - scipy: 1.14.1
2024-12-09 11:22:40,160 - JUNIFER - INFO - pandas: 2.1.4
2024-12-09 11:22:40,160 - JUNIFER - INFO - nilearn: 0.10.4
2024-12-09 11:22:40,160 - JUNIFER - INFO - nibabel: 5.3.2
2024-12-09 11:22:40,160 - JUNIFER - INFO - junifer: 0.0.6.dev366
2024-12-09 11:22:40,160 - 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
2024-12-09 11:22:40,178 - JUNIFER - INFO - Validating Marker Collection
2024-12-09 11:22:40,178 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-12-09 11:22:40,178 - JUNIFER - INFO - Validating Data Reader:
2024-12-09 11:22:40,178 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-12-09 11:22:40,178 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-12-09 11:22:40,178 - JUNIFER - INFO - Marker output type: ['vector']
2024-12-09 11:22:40,178 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-12-09 11:22:40,178 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-12-09 11:22:40,178 - JUNIFER - INFO - Marker output type: ['vector']
2024-12-09 11:22:40,178 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2024-12-09 11:22:40,183 - JUNIFER - INFO - Getting element sub-01
2024-12-09 11:22:40,183 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:22:40,183 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:22:40,183 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:22:40,184 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:22:40,184 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:22:40,184 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:22:40,184 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:22:40,184 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:22:40,184 - JUNIFER - INFO - resolution: None
2024-12-09 11:22:40,184 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:22:40,184 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:22:40,184 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:22:40,186 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:22:40,453 - 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
2024-12-09 11:22:41,548 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:22:42,050 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptrzf6355/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e6cde6e8-b61f-11ef-88f6-0242ac120002o4bdgu9f/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptrzf6355/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e6cde6e8-b61f-11ef-88f6-0242ac120002o4bdgu9f/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/tmptrzf6355/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_e6cde6e8-b61f-11ef-88f6-0242ac120002o4bdgu9f/parcellation_warped.nii.gz
2024-12-09 11:22:51,016 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:22:52,337 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:22:52,376 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:22:52,376 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:22:52,376 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:22:52,377 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:22:52,377 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:22:52,377 - JUNIFER - INFO - resolution: None
2024-12-09 11:22:52,377 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:22:52,377 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:22:52,377 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:22:52,378 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:22:52,649 - 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
2024-12-09 11:22:53,741 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:22:54,245 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmptrzf6355/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_ee12ee6c-b61f-11ef-88f6-0242ac120002155ajtw4/prewarp_parcellation.nii.gz -r /tmp/junifer/tmptrzf6355/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_ee12ee6c-b61f-11ef-88f6-0242ac120002155ajtw4/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/tmptrzf6355/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_ee12ee6c-b61f-11ef-88f6-0242ac120002155ajtw4/parcellation_warped.nii.gz
2024-12-09 11:23:11,073 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:23:12,424 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:23:12,481 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:23:12,485 - JUNIFER - INFO - Getting element sub-02
2024-12-09 11:23:12,485 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:23:12,485 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:23:12,485 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:23:12,486 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:23:12,486 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:23:12,486 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:23:12,486 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:23:12,487 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:23:12,487 - JUNIFER - INFO - resolution: None
2024-12-09 11:23:12,487 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:23:12,487 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:23:12,487 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:23:12,488 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:23:12,757 - 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
2024-12-09 11:23:13,841 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:23:14,343 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp913enx2v/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_fa0f1114-b61f-11ef-88f6-0242ac120002okhpfna5/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp913enx2v/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_fa0f1114-b61f-11ef-88f6-0242ac120002okhpfna5/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/tmp913enx2v/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_fa0f1114-b61f-11ef-88f6-0242ac120002okhpfna5/parcellation_warped.nii.gz
2024-12-09 11:23:23,323 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:23:24,842 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:23:24,879 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:23:24,879 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:23:24,879 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:23:24,879 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:23:24,879 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:23:24,879 - JUNIFER - INFO - resolution: None
2024-12-09 11:23:24,879 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:23:24,879 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:23:24,879 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:23:24,881 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:23:25,153 - 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
2024-12-09 11:23:26,287 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:23:26,791 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp913enx2v/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_017294da-b620-11ef-88f6-0242ac120002c2i2dgr2/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp913enx2v/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_017294da-b620-11ef-88f6-0242ac120002c2i2dgr2/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/tmp913enx2v/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_017294da-b620-11ef-88f6-0242ac120002c2i2dgr2/parcellation_warped.nii.gz
2024-12-09 11:23:43,520 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:23:44,948 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:23:45,005 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:23:45,011 - JUNIFER - INFO - Getting element sub-03
2024-12-09 11:23:45,011 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:23:45,011 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:23:45,011 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:23:45,012 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:23:45,012 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:23:45,012 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:23:45,012 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:23:45,012 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:23:45,012 - JUNIFER - INFO - resolution: None
2024-12-09 11:23:45,012 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:23:45,013 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:23:45,013 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:23:45,014 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:23:45,284 - 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
2024-12-09 11:23:46,390 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:23:46,891 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpanolnzk4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0d7252de-b620-11ef-88f6-0242ac120002l_4v982_/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpanolnzk4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0d7252de-b620-11ef-88f6-0242ac120002l_4v982_/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/tmpanolnzk4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_0d7252de-b620-11ef-88f6-0242ac120002l_4v982_/parcellation_warped.nii.gz
2024-12-09 11:23:55,782 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:23:57,203 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:23:57,238 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:23:57,238 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:23:57,238 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:23:57,238 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:23:57,239 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:23:57,239 - JUNIFER - INFO - resolution: None
2024-12-09 11:23:57,239 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:23:57,239 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:23:57,239 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:23:57,240 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:23:57,512 - 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
2024-12-09 11:23:58,637 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:23:59,142 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpanolnzk4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_14bc149e-b620-11ef-88f6-0242ac1200023tp41rzg/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpanolnzk4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_14bc149e-b620-11ef-88f6-0242ac1200023tp41rzg/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/tmpanolnzk4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_14bc149e-b620-11ef-88f6-0242ac1200023tp41rzg/parcellation_warped.nii.gz
2024-12-09 11:24:16,156 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:24:17,640 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:24:17,695 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:24:17,700 - JUNIFER - INFO - Getting element sub-04
2024-12-09 11:24:17,700 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:24:17,700 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:24:17,700 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:24:17,701 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:24:17,701 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:24:17,701 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:24:17,701 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:24:17,701 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:24:17,701 - JUNIFER - INFO - resolution: None
2024-12-09 11:24:17,701 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:24:17,701 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:24:17,701 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:24:17,703 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:24:17,973 - 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
2024-12-09 11:24:19,095 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:24:19,596 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpqinjpo_4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_20ee2964-b620-11ef-88f6-0242ac120002mqsz7ye8/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpqinjpo_4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_20ee2964-b620-11ef-88f6-0242ac120002mqsz7ye8/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/tmpqinjpo_4/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_20ee2964-b620-11ef-88f6-0242ac120002mqsz7ye8/parcellation_warped.nii.gz
2024-12-09 11:24:28,582 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:24:29,927 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:24:29,962 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:24:29,962 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:24:29,962 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:24:29,962 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:24:29,962 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:24:29,963 - JUNIFER - INFO - resolution: None
2024-12-09 11:24:29,963 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:24:29,963 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:24:29,963 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:24:29,964 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:24:30,234 - 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
2024-12-09 11:24:31,332 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:24:31,836 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpqinjpo_4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_283d29e0-b620-11ef-88f6-0242ac120002v7dht4ty/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpqinjpo_4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_283d29e0-b620-11ef-88f6-0242ac120002v7dht4ty/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/tmpqinjpo_4/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_283d29e0-b620-11ef-88f6-0242ac120002v7dht4ty/parcellation_warped.nii.gz
2024-12-09 11:24:48,779 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:24:50,221 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:24:50,275 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:24:50,280 - JUNIFER - INFO - Getting element sub-05
2024-12-09 11:24:50,280 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:24:50,280 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:24:50,280 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:24:50,281 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:24:50,281 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:24:50,282 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:24:50,282 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:24:50,282 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:24:50,282 - JUNIFER - INFO - resolution: None
2024-12-09 11:24:50,282 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:24:50,282 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:24:50,282 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:24:50,283 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:24:50,554 - 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
2024-12-09 11:24:51,683 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:24:52,184 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpa55hfcjz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_3459aaaa-b620-11ef-88f6-0242ac120002h6wihm1m/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpa55hfcjz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_3459aaaa-b620-11ef-88f6-0242ac120002h6wihm1m/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/tmpa55hfcjz/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_3459aaaa-b620-11ef-88f6-0242ac120002h6wihm1m/parcellation_warped.nii.gz
2024-12-09 11:25:01,181 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:25:02,524 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:25:02,558 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:25:02,558 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:25:02,558 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:25:02,558 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:25:02,558 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:25:02,558 - JUNIFER - INFO - resolution: None
2024-12-09 11:25:02,558 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:25:02,558 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:25:02,558 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:25:02,560 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:25:02,831 - 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
2024-12-09 11:25:03,934 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:25:04,436 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpa55hfcjz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3bab13f2-b620-11ef-88f6-0242ac120002_o5qbuix/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpa55hfcjz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3bab13f2-b620-11ef-88f6-0242ac120002_o5qbuix/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/tmpa55hfcjz/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_3bab13f2-b620-11ef-88f6-0242ac120002_o5qbuix/parcellation_warped.nii.gz
2024-12-09 11:25:21,433 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:25:22,800 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:25:22,852 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:25:22,857 - JUNIFER - INFO - Getting element sub-06
2024-12-09 11:25:22,857 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:25:22,858 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:25:22,858 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:25:22,858 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:25:22,859 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:25:22,859 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:25:22,859 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:25:22,859 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:25:22,859 - JUNIFER - INFO - resolution: None
2024-12-09 11:25:22,859 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:25:22,859 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:25:22,859 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:25:22,860 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:25:23,128 - 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
2024-12-09 11:25:24,210 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:25:24,710 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpimwqxecl/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_47c42ec6-b620-11ef-88f6-0242ac120002dfb0btfk/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpimwqxecl/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_47c42ec6-b620-11ef-88f6-0242ac120002dfb0btfk/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/tmpimwqxecl/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_47c42ec6-b620-11ef-88f6-0242ac120002dfb0btfk/parcellation_warped.nii.gz
2024-12-09 11:25:33,759 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:25:35,161 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:25:35,199 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:25:35,199 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:25:35,199 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:25:35,199 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:25:35,199 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:25:35,200 - JUNIFER - INFO - resolution: None
2024-12-09 11:25:35,200 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:25:35,200 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:25:35,200 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:25:35,201 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:25:35,473 - 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
2024-12-09 11:25:36,556 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:25:37,062 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpimwqxecl/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4f1fe1ec-b620-11ef-88f6-0242ac120002aqvv9q2s/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpimwqxecl/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4f1fe1ec-b620-11ef-88f6-0242ac120002aqvv9q2s/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/tmpimwqxecl/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_4f1fe1ec-b620-11ef-88f6-0242ac120002aqvv9q2s/parcellation_warped.nii.gz
2024-12-09 11:25:53,962 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:25:55,344 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:25:55,398 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:25:55,403 - JUNIFER - INFO - Getting element sub-07
2024-12-09 11:25:55,403 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:25:55,403 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:25:55,403 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:25:55,404 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:25:55,404 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:25:55,404 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:25:55,404 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:25:55,404 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:25:55,404 - JUNIFER - INFO - resolution: None
2024-12-09 11:25:55,404 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:25:55,404 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:25:55,404 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:25:55,406 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:25:55,675 - 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
2024-12-09 11:25:56,805 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:25:57,307 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpbplhhxpf/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_5b2a60de-b620-11ef-88f6-0242ac120002ja7_tdjg/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpbplhhxpf/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_5b2a60de-b620-11ef-88f6-0242ac120002ja7_tdjg/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/tmpbplhhxpf/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_5b2a60de-b620-11ef-88f6-0242ac120002ja7_tdjg/parcellation_warped.nii.gz
2024-12-09 11:26:06,290 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:26:07,612 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:26:07,655 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:26:07,655 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:26:07,655 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:26:07,655 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:26:07,655 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:26:07,655 - JUNIFER - INFO - resolution: None
2024-12-09 11:26:07,655 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:26:07,655 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:26:07,655 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:26:07,657 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:26:07,928 - 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
2024-12-09 11:26:09,026 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:26:09,529 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpbplhhxpf/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_62781c6e-b620-11ef-88f6-0242ac120002lrm3v4fv/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpbplhhxpf/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_62781c6e-b620-11ef-88f6-0242ac120002lrm3v4fv/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/tmpbplhhxpf/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_62781c6e-b620-11ef-88f6-0242ac120002lrm3v4fv/parcellation_warped.nii.gz
2024-12-09 11:26:26,408 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:26:27,742 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:26:27,793 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:26:27,798 - JUNIFER - INFO - Getting element sub-08
2024-12-09 11:26:27,798 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:26:27,798 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:26:27,798 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:26:27,799 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:26:27,799 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:26:27,799 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:26:27,799 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:26:27,799 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:26:27,799 - JUNIFER - INFO - resolution: None
2024-12-09 11:26:27,799 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:26:27,799 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:26:27,799 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:26:27,801 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:26:28,069 - 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
2024-12-09 11:26:29,158 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:26:29,660 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp684jzjos/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_6e795d3e-b620-11ef-88f6-0242ac120002ch7zr6qq/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp684jzjos/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_6e795d3e-b620-11ef-88f6-0242ac120002ch7zr6qq/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/tmp684jzjos/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_6e795d3e-b620-11ef-88f6-0242ac120002ch7zr6qq/parcellation_warped.nii.gz
2024-12-09 11:26:38,673 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:26:40,048 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:26:40,083 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:26:40,083 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:26:40,084 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:26:40,084 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:26:40,084 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:26:40,084 - JUNIFER - INFO - resolution: None
2024-12-09 11:26:40,084 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:26:40,084 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:26:40,084 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:26:40,085 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:26:40,360 - 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
2024-12-09 11:26:41,455 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:26:41,959 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp684jzjos/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_75ccb7de-b620-11ef-88f6-0242ac120002kolvnzx9/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp684jzjos/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_75ccb7de-b620-11ef-88f6-0242ac120002kolvnzx9/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/tmp684jzjos/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_75ccb7de-b620-11ef-88f6-0242ac120002kolvnzx9/parcellation_warped.nii.gz
2024-12-09 11:26:58,803 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:27:00,181 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:27:00,233 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:27:00,238 - JUNIFER - INFO - Getting element sub-09
2024-12-09 11:27:00,238 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:27:00,238 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:27:00,238 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:27:00,239 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:27:00,239 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:27:00,240 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:27:00,240 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:27:00,240 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:27:00,240 - JUNIFER - INFO - resolution: None
2024-12-09 11:27:00,240 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:27:00,240 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:27:00,240 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:27:00,241 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:27:00,511 - 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
2024-12-09 11:27:01,608 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:27:02,109 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpttqsp5a6/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_81cf9a74-b620-11ef-88f6-0242ac120002jj1s_rw2/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpttqsp5a6/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_81cf9a74-b620-11ef-88f6-0242ac120002jj1s_rw2/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/tmpttqsp5a6/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_81cf9a74-b620-11ef-88f6-0242ac120002jj1s_rw2/parcellation_warped.nii.gz
2024-12-09 11:27:11,118 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:27:12,484 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:27:12,520 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:27:12,520 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:27:12,520 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:27:12,520 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:27:12,521 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:27:12,521 - JUNIFER - INFO - resolution: None
2024-12-09 11:27:12,521 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:27:12,521 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:27:12,521 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:27:12,522 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:27:12,792 - 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
2024-12-09 11:27:13,888 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:27:14,392 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpttqsp5a6/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_89217d10-b620-11ef-88f6-0242ac1200022q30sf42/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpttqsp5a6/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_89217d10-b620-11ef-88f6-0242ac1200022q30sf42/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/tmpttqsp5a6/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_89217d10-b620-11ef-88f6-0242ac1200022q30sf42/parcellation_warped.nii.gz
2024-12-09 11:27:31,151 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:27:32,558 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:27:32,610 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:27:32,614 - JUNIFER - INFO - Getting element sub-10
2024-12-09 11:27:32,614 - JUNIFER - INFO - Fitting pipeline
2024-12-09 11:27:32,614 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:27:32,614 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:27:32,615 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-12-09 11:27:32,615 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:27:32,615 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:27:32,616 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:27:32,616 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:27:32,616 - JUNIFER - INFO - resolution: None
2024-12-09 11:27:32,616 - JUNIFER - INFO - n_rois: 100
2024-12-09 11:27:32,616 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:27:32,616 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:27:32,617 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:27:32,884 - 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
2024-12-09 11:27:34,004 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:27:34,506 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpq7yu977j/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_951b4b00-b620-11ef-88f6-0242ac120002xvnw0mtb/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpq7yu977j/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_951b4b00-b620-11ef-88f6-0242ac120002xvnw0mtb/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/tmpq7yu977j/ants_parcellation_warper_Schaefer100x17_from_MNI152NLin6Asym_to_MNI152Lin_951b4b00-b620-11ef-88f6-0242ac120002xvnw0mtb/parcellation_warped.nii.gz
2024-12-09 11:27:43,478 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:27:44,807 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:27:44,845 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-12-09 11:27:44,845 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:27:44,845 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:27:44,845 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:27:44,845 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:27:44,845 - JUNIFER - INFO - resolution: None
2024-12-09 11:27:44,845 - JUNIFER - INFO - n_rois: 200
2024-12-09 11:27:44,845 - JUNIFER - INFO - yeo_networks: 17
2024-12-09 11:27:44,845 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:27:44,847 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:27:45,119 - 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
2024-12-09 11:27:46,241 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:27:46,743 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpq7yu977j/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_9c6633a2-b620-11ef-88f6-0242ac1200020_bfhccc/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpq7yu977j/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_9c6633a2-b620-11ef-88f6-0242ac1200020_bfhccc/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/tmpq7yu977j/ants_parcellation_warper_Schaefer200x17_from_MNI152NLin6Asym_to_MNI152Lin_9c6633a2-b620-11ef-88f6-0242ac1200020_bfhccc/parcellation_warped.nii.gz
2024-12-09 11:28:03,526 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-12-09 11:28:04,994 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpx7ckyojk/test.sqlite (multiple output)>
2024-12-09 11:28:05,048 - JUNIFER - INFO - Marker collection fitting done
2024-12-09 11:28:05,053 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-12-09 11:28:05,053 - JUNIFER - INFO - Collecting data from /tmp/tmpx7ckyojk/*test.sqlite
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2024-12-09 11:28:06,782 - 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 0.142955 0.020238 ... 0 509497eb21da473048117e0c6704d3ea
1 0.140785 0.020152 ... 1 509497eb21da473048117e0c6704d3ea
2 0.140755 0.020010 ... 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 27.296 seconds)