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")
2024-09-30 11:47:32,097 - JUNIFER - INFO - ===== Lib Versions =====
2024-09-30 11:47:32,097 - JUNIFER - INFO - numpy: 1.26.4
2024-09-30 11:47:32,097 - JUNIFER - INFO - scipy: 1.14.0
2024-09-30 11:47:32,097 - JUNIFER - INFO - pandas: 2.1.4
2024-09-30 11:47:32,097 - JUNIFER - INFO - nilearn: 0.10.4
2024-09-30 11:47:32,097 - JUNIFER - INFO - nibabel: 5.2.1
2024-09-30 11:47:32,097 - JUNIFER - INFO - junifer: 0.0.6.dev90
2024-09-30 11:47:32,097 - 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
2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Marker Collection
2024-09-30 11:47:32,111 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Data Reader:
2024-09-30 11:47:32,111 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-09-30 11:47:32,111 - JUNIFER - INFO - Marker output type: ['vector']
2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-09-30 11:47:32,111 - JUNIFER - INFO - Marker output type: ['vector']
2024-09-30 11:47:32,111 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2024-09-30 11:47:32,116 - JUNIFER - INFO - Getting element sub-01
2024-09-30 11:47:32,116 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:47:32,116 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:47:32,116 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:47:32,117 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:47:32,117 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:32,117 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:32,117 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:32,118 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:32,118 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:47:32,118 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:32,119 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:32,149 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:33,135 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:33,231 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations7yobja7a/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations7yobja7a/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzc62ehui/parcellations5h13d0hm/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:34,629 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:35,592 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:35,623 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:47:35,623 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:35,624 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:35,624 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:35,624 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:35,624 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:47:35,624 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:35,625 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:35,655 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:36,651 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:36,748 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations2vqismtq/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations2vqismtq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzc62ehui/parcellations5j8ftn2u/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:38,802 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:39,772 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:39,819 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:47:39,820 - JUNIFER - INFO - Getting element sub-02
2024-09-30 11:47:39,820 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:47:39,820 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:47:39,820 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:47:39,821 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:47:39,821 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:39,821 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:39,821 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:39,821 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:39,822 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:47:39,822 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:39,823 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:39,852 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:40,840 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:40,937 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsrtkhvrv6/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsrtkhvrv6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpl6otsjap/parcellationsl4ooka2v/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:42,333 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:43,298 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:43,329 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:47:43,329 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:43,330 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:43,330 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:43,330 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:43,330 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:47:43,330 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:43,331 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:43,361 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:44,354 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:44,451 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations3zeab1yk/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations3zeab1yk/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpl6otsjap/parcellations7atjxw46/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:46,508 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:47,481 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:47,528 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:47:47,528 - JUNIFER - INFO - Getting element sub-03
2024-09-30 11:47:47,528 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:47:47,528 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:47:47,528 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:47:47,529 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:47:47,529 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:47,530 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:47,530 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:47,530 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:47,530 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:47:47,530 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:47,531 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:47,561 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:48,549 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:48,645 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsihgjxp_t/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsihgjxp_t/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp1n61hxz9/parcellationsjqtajn1k/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:50,042 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:51,001 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:51,032 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:47:51,032 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:51,033 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:51,033 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:51,033 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:51,033 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:47:51,033 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:51,034 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:51,064 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:52,054 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:52,151 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsrcl0d07l/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsrcl0d07l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp1n61hxz9/parcellations28bp5cql/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:54,185 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:55,160 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:55,206 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:47:55,207 - JUNIFER - INFO - Getting element sub-04
2024-09-30 11:47:55,207 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:47:55,207 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:47:55,207 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:47:55,208 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:47:55,208 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:55,209 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:55,209 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:55,209 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:55,209 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:47:55,209 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:55,210 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:55,240 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:56,229 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:56,326 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations2ssf3v4z/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations2ssf3v4z/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpk68358mf/parcellationsh46h7qt7/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:57,716 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:47:58,679 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:47:58,712 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:47:58,712 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:47:58,713 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:58,713 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:58,713 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:47:58,713 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:47:58,713 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:47:58,714 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:58,744 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:59,726 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:59,822 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsilr2qvwb/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsilr2qvwb/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpk68358mf/parcellationskvifndro/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:01,871 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:02,839 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:02,886 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:02,886 - JUNIFER - INFO - Getting element sub-05
2024-09-30 11:48:02,887 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:48:02,887 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:48:02,887 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:48:02,888 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:48:02,888 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:02,888 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:02,888 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:02,888 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:02,888 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:48:02,888 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:02,890 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:02,919 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:03,915 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:04,012 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsroierx5v/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsroierx5v/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp39hv7ipj/parcellations3k_otbmx/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:05,403 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:06,346 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:06,377 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:48:06,378 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:06,378 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:06,378 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:06,378 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:06,378 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:48:06,378 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:06,380 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:06,409 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:07,398 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:07,495 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsj1snpmm1/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsj1snpmm1/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp39hv7ipj/parcellationsjnei0bk4/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:09,576 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:10,535 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:10,581 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:10,582 - JUNIFER - INFO - Getting element sub-06
2024-09-30 11:48:10,582 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:48:10,582 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:48:10,582 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:48:10,583 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:48:10,583 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:10,584 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:10,584 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:10,584 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:10,584 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:48:10,584 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:10,585 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:10,614 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:11,600 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:11,696 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationszohfyyt_/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationszohfyyt_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpriiyy9d2/parcellations06b6x8ce/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:13,083 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:14,031 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:14,062 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:48:14,062 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:14,063 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:14,063 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:14,063 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:14,063 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:48:14,063 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:14,064 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:14,094 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:15,085 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:15,182 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations4sovg_g2/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations4sovg_g2/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpriiyy9d2/parcellationsoqox3uxo/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:17,213 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:18,190 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:18,237 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:18,237 - JUNIFER - INFO - Getting element sub-07
2024-09-30 11:48:18,237 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:48:18,237 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:48:18,237 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:48:18,238 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:48:18,238 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:18,239 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:18,239 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:18,239 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:18,239 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:48:18,239 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:18,240 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:18,270 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:19,267 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:19,363 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations_te21wj8/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations_te21wj8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpkk6k28bg/parcellationswjgpskij/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:20,752 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:21,720 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:21,750 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:48:21,750 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:21,751 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:21,751 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:21,751 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:21,751 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:48:21,751 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:21,752 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:21,782 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:22,770 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:22,867 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsn33nktx_/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsn33nktx_/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpkk6k28bg/parcellationsgug_n1_9/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:24,906 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:25,871 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:25,919 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:25,920 - JUNIFER - INFO - Getting element sub-08
2024-09-30 11:48:25,920 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:48:25,920 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:48:25,920 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:48:25,921 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:48:25,921 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:25,921 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:25,922 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:25,922 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:25,922 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:48:25,922 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:25,923 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:25,952 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:26,946 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:27,043 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsrl2yc7oi/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsrl2yc7oi/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpmaaxbbsu/parcellationsqkwyi1wr/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:28,432 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:29,382 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:29,413 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:48:29,413 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:29,414 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:29,414 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:29,414 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:29,414 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:48:29,414 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:29,415 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:29,445 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:30,435 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:30,532 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationslatc9300/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationslatc9300/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpmaaxbbsu/parcellationsmjzo1mu4/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:32,551 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:33,529 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:33,575 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:33,576 - JUNIFER - INFO - Getting element sub-09
2024-09-30 11:48:33,576 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:48:33,576 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:48:33,576 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:48:33,577 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:48:33,577 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:33,578 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:33,578 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:33,578 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:33,578 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:48:33,578 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:33,579 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:33,609 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:34,606 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:34,703 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsctbnkpwq/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsctbnkpwq/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp3e6tjupk/parcellationsnyoa7bn8/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:36,090 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:37,091 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:37,122 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:48:37,123 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:37,123 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:37,123 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:37,123 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:37,123 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:48:37,123 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:37,124 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:37,154 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:38,149 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:38,246 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsa141u0cj/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsa141u0cj/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp3e6tjupk/parcellationscrufte29/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:40,292 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:41,276 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:41,323 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:41,323 - JUNIFER - INFO - Getting element sub-10
2024-09-30 11:48:41,323 - JUNIFER - INFO - Fitting pipeline
2024-09-30 11:48:41,323 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:48:41,323 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:48:41,324 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-09-30 11:48:41,324 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:41,325 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:41,325 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:41,325 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:41,325 - JUNIFER - INFO - n_rois: 100
2024-09-30 11:48:41,325 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:41,326 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:41,355 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:42,349 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:42,445 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationshuyx__of/Schaefer100x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellationshuyx__of/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptxbv8j1g/parcellationsalww9zwu/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:43,835 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:44,792 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:44,823 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-09-30 11:48:44,823 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:48:44,824 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:48:44,824 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:48:44,824 - JUNIFER - INFO - resolution: 2.0
2024-09-30 11:48:44,824 - JUNIFER - INFO - n_rois: 200
2024-09-30 11:48:44,824 - JUNIFER - INFO - yeo_networks: 17
2024-09-30 11:48:44,825 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:48:44,855 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:48:45,859 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:48:45,956 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations9reys9x6/Schaefer200x17.nii.gz -r /tmp/tmpn9vwo4yf/parcellations9reys9x6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmptxbv8j1g/parcellations4r06idi1/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:48:47,977 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-09-30 11:48:48,951 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpzyev4mjh/test.sqlite (multiple output)>
2024-09-30 11:48:48,998 - JUNIFER - INFO - Marker collection fitting done
2024-09-30 11:48:48,998 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-09-30 11:48:48,998 - JUNIFER - INFO - Collecting data from /tmp/tmpzyev4mjh/*test.sqlite
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2024-09-30 11:48:50,487 - 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 0.133041 0.019066 ... 0 509497eb21da473048117e0c6704d3ea
1 0.131912 0.018796 ... 1 509497eb21da473048117e0c6704d3ea
2 0.133265 0.018951 ... 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 19.009 seconds)