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")
2024-04-05 15:57:08,175 - JUNIFER - INFO - ===== Lib Versions =====
2024-04-05 15:57:08,175 - JUNIFER - INFO - numpy: 1.26.4
2024-04-05 15:57:08,175 - JUNIFER - INFO - scipy: 1.11.4
2024-04-05 15:57:08,175 - JUNIFER - INFO - pandas: 2.1.4
2024-04-05 15:57:08,175 - JUNIFER - INFO - nilearn: 0.10.2
2024-04-05 15:57:08,175 - JUNIFER - INFO - nibabel: 5.2.1
2024-04-05 15:57:08,175 - JUNIFER - INFO - junifer: 0.0.4
2024-04-05 15:57:08,175 - 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
)
/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nilearn/datasets/struct.py:852: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
warnings.warn(_LEGACY_FORMAT_MSG)
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")
oasis_subjects = [x[0] for x in df_vbm.index]
df_vbm.index = oasis_subjects
2024-04-05 15:57:08,189 - JUNIFER - INFO - Validating Marker Collection
2024-04-05 15:57:08,189 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-04-05 15:57:08,189 - JUNIFER - INFO - Validating Data Reader:
2024-04-05 15:57:08,189 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-04-05 15:57:08,189 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-04-05 15:57:08,189 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-05 15:57:08,189 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-04-05 15:57:08,189 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-04-05 15:57:08,189 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-05 15:57:08,189 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nilearn/datasets/struct.py:852: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
warnings.warn(_LEGACY_FORMAT_MSG)
2024-04-05 15:57:08,193 - JUNIFER - INFO - Getting element sub-01
2024-04-05 15:57:08,193 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:08,194 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:08,194 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:08,194 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:08,194 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:08,195 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:08,195 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:08,195 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:08,195 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:08,195 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:08,196 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:08,226 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:09,291 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:09,388 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations_piezgmh/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations_piezgmh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpclpv_8_x/parcellationsnwiw3y3z/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:10,788 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:11,949 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:11,980 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:57:11,980 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:11,981 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:11,981 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:11,981 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:11,981 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:57:11,981 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:11,982 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:12,012 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:13,101 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:13,199 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsk6g6g2ok/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsk6g6g2ok/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpclpv_8_x/parcellations9q8udsxg/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:15,230 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:16,465 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:16,512 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:57:16,512 - JUNIFER - INFO - Getting element sub-02
2024-04-05 15:57:16,512 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:16,512 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:16,512 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:16,513 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:16,513 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:16,513 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:16,514 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:16,514 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:16,514 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:16,514 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:16,515 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:16,544 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:17,659 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:17,757 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsxiruwz2c/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsxiruwz2c/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpuo8dfy57/parcellationswdv_xdx3/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:19,173 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:20,415 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:20,446 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:57:20,446 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:20,446 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:20,446 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:20,446 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:20,446 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:57:20,446 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:20,448 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:20,478 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:21,593 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:21,691 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsbopc1hp9/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsbopc1hp9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpuo8dfy57/parcellationszing8xhi/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:23,716 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:24,930 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:24,978 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:57:24,978 - JUNIFER - INFO - Getting element sub-03
2024-04-05 15:57:24,978 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:24,978 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:24,978 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:24,979 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:24,979 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:24,979 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:24,979 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:24,980 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:24,980 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:24,980 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:24,981 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:25,012 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:26,126 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:26,223 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations4sgre8n8/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations4sgre8n8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpnosdvq2e/parcellationsoijypfp5/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:27,613 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:28,734 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:28,765 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:57:28,765 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:28,765 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:28,765 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:28,765 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:28,765 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:57:28,765 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:28,767 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:28,798 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:29,906 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:30,005 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations0mh7s7td/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellations0mh7s7td/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpnosdvq2e/parcellations28m51iw0/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:32,040 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:33,280 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:33,327 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:57:33,327 - JUNIFER - INFO - Getting element sub-04
2024-04-05 15:57:33,328 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:33,328 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:33,328 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:33,328 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:33,329 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:33,329 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:33,329 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:33,329 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:33,329 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:33,329 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:33,330 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:33,360 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:34,422 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:34,519 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations21sjr0aw/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations21sjr0aw/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6jy39y55/parcellationsvoojz_i6/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:35,920 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:36,991 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:37,021 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:57:37,021 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:37,021 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:37,021 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:37,021 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:37,021 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:57:37,022 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:37,023 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:37,053 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:38,109 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:38,206 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations2oww45__/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellations2oww45__/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6jy39y55/parcellationsx0ar8f_b/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:40,247 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:41,280 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:41,326 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:57:41,326 - JUNIFER - INFO - Getting element sub-05
2024-04-05 15:57:41,326 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:41,326 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:41,326 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:41,327 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:41,327 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:41,327 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:41,327 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:41,327 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:41,327 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:41,327 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:41,329 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:41,358 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:42,416 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:42,513 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations8lxga56v/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations8lxga56v/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpc0ig0b0u/parcellationspjk0zd7g/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:43,906 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:44,978 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:45,009 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:57:45,009 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:45,010 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:45,010 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:45,010 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:45,010 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:57:45,010 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:45,011 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:45,041 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:46,088 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:46,185 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationszs47p_bh/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationszs47p_bh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpc0ig0b0u/parcellations7nutcr82/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:48,195 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:49,221 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:49,267 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:57:49,268 - JUNIFER - INFO - Getting element sub-06
2024-04-05 15:57:49,268 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:49,268 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:49,268 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:49,269 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:49,269 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:49,269 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:49,269 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:49,269 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:49,269 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:49,269 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:49,271 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:49,300 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:50,342 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:50,438 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations_s7lfb4r/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations_s7lfb4r/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp3pd8nfmt/parcellationsrdz62zar/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:51,829 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:52,843 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:52,874 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:57:52,874 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:52,874 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:52,874 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:52,874 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:52,874 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:57:52,874 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:52,875 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:52,905 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:53,976 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:54,074 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsc0l034s1/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsc0l034s1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp3pd8nfmt/parcellationsak9ps4cz/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:56,111 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:57:57,256 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:57:57,303 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:57:57,304 - JUNIFER - INFO - Getting element sub-07
2024-04-05 15:57:57,304 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:57:57,304 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:57:57,304 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:57:57,305 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:57:57,305 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:57:57,305 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:57:57,305 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:57:57,305 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:57:57,305 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:57:57,305 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:57:57,307 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:57:57,336 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:57:58,408 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:57:58,505 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsmruoevlw/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsmruoevlw/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpp5tm9duh/parcellationshudceju7/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:57:59,898 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:00,904 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:00,934 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:58:00,934 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:00,935 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:00,935 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:00,935 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:00,935 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:58:00,935 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:00,936 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:00,966 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:02,015 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:02,112 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationst336ydqj/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationst336ydqj/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpp5tm9duh/parcellationsk5_c6zp9/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:04,128 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:05,130 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:05,177 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:58:05,177 - JUNIFER - INFO - Getting element sub-08
2024-04-05 15:58:05,177 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:58:05,177 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:58:05,177 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:58:05,178 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:58:05,178 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:05,178 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:05,179 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:05,179 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:05,179 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:58:05,179 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:05,180 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:05,209 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:06,286 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:06,383 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations6mnjt395/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations6mnjt395/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7fcov96c/parcellationskf2uj187/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:07,778 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:08,791 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:08,821 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:58:08,821 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:08,822 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:08,822 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:08,822 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:08,822 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:58:08,822 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:08,823 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:08,853 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:09,912 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:10,010 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationse1iopp73/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationse1iopp73/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp7fcov96c/parcellations783p4a4_/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:12,044 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:13,114 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:13,160 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:58:13,161 - JUNIFER - INFO - Getting element sub-09
2024-04-05 15:58:13,161 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:58:13,161 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:58:13,161 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:58:13,162 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:58:13,162 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:13,162 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:13,162 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:13,162 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:13,162 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:58:13,162 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:13,164 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:13,193 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:14,256 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:14,353 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellations2ipn_m3g/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellations2ipn_m3g/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpbp2y0v9n/parcellationsyvw25knx/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:15,742 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:16,864 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:16,894 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:58:16,894 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:16,895 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:16,895 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:16,895 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:16,895 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:58:16,895 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:16,896 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:16,927 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:18,041 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:18,140 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsfs2noigh/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsfs2noigh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpbp2y0v9n/parcellationsqknspvle/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:20,169 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:21,279 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:21,327 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:58:21,327 - JUNIFER - INFO - Getting element sub-10
2024-04-05 15:58:21,327 - JUNIFER - INFO - Fitting pipeline
2024-04-05 15:58:21,327 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-05 15:58:21,327 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-05 15:58:21,328 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-05 15:58:21,328 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:21,329 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:21,329 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:21,329 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:21,329 - JUNIFER - INFO - n_rois: 100
2024-04-05 15:58:21,329 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:21,330 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:21,360 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:22,419 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:22,516 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsgtgsmoir/Schaefer100x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsgtgsmoir/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp06_ojamj/parcellationsz8hp2n9v/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:23,925 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:25,048 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:25,079 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-05 15:58:25,079 - JUNIFER - INFO - Computing VBM_GM
2024-04-05 15:58:25,079 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-05 15:58:25,079 - JUNIFER - INFO - Parcellation parameters:
2024-04-05 15:58:25,079 - JUNIFER - INFO - resolution: 2.0
2024-04-05 15:58:25,079 - JUNIFER - INFO - n_rois: 200
2024-04-05 15:58:25,079 - JUNIFER - INFO - yeo_networks: 17
2024-04-05 15:58:25,081 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-05 15:58:25,111 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-05 15:58:26,187 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-05 15:58:26,285 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp56odh8d/parcellationsjzktk_x6/Schaefer200x17.nii.gz -r /tmp/tmpp56odh8d/parcellationsjzktk_x6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp06_ojamj/parcellationsmslioyc8/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-05 15:58:28,320 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-05 15:58:29,419 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpq0x8o1k_/test.sqlite (multiple output)>
2024-04-05 15:58:29,465 - JUNIFER - INFO - Marker collection fitting done
2024-04-05 15:58:29,466 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-04-05 15:58:29,466 - JUNIFER - INFO - Collecting data from /tmp/tmpq0x8o1k_/*test.sqlite
file: 0it [00:00, ?it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.67it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 15.64it/s]
file: 1it [00:00, 7.22it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.18it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.16it/s]
file: 2it [00:00, 7.60it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.16it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.13it/s]
file: 3it [00:00, 7.72it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 16.97it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 16.94it/s]
file: 4it [00:00, 7.75it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 8.31it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 8.31it/s]
file: 5it [00:00, 5.78it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.19it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.16it/s]
file: 6it [00:00, 6.35it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.13it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.10it/s]
file: 7it [00:01, 6.78it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.05it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.02it/s]
file: 8it [00:01, 7.08it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 17.02it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 16.99it/s]
file: 9it [00:01, 7.30it/s]
feature: 0%| | 0/2 [00:00<?, ?it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 8.17it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 8.16it/s]
file: 10it [00:01, 5.76it/s]
file: 10it [00:01, 6.51it/s]
2024-04-05 15:58:31,003 - 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 0.132328 0.018532 ... 0 509497eb21da473048117e0c6704d3ea
1 0.129493 0.018325 ... 1 509497eb21da473048117e0c6704d3ea
2 0.129998 0.018230 ... 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: (1 minutes 23.434 seconds)