Note
Click here 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
import junifer.testing.registry # noqa
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")
2023-05-16 14:03:02,387 - JUNIFER - INFO - ===== Lib Versions =====
2023-05-16 14:03:02,387 - JUNIFER - INFO - numpy: 1.23.5
2023-05-16 14:03:02,387 - JUNIFER - INFO - scipy: 1.10.1
2023-05-16 14:03:02,387 - JUNIFER - INFO - pandas: 1.5.3
2023-05-16 14:03:02,387 - JUNIFER - INFO - nilearn: 0.10.0
2023-05-16 14:03:02,388 - JUNIFER - INFO - nibabel: 4.0.2
2023-05-16 14:03:02,388 - JUNIFER - INFO - junifer: 0.0.3.dev104
2023-05-16 14:03:02,388 - 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/3.10.11/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:733: 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
/opt/hostedtoolcache/Python/3.10.11/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:733: 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)
2023-05-16 14:03:02,412 - JUNIFER - INFO - Getting element sub-01
2023-05-16 14:03:02,412 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:02,413 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:02,413 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:02,414 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:02,414 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:02,414 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:02,414 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:02,414 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:02,414 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:02,414 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:02,416 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:03,027 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:03,071 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:03,071 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:03,072 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:03,072 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:03,072 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:03,072 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:03,072 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:03,074 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:03,713 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:03,791 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:03,791 - JUNIFER - INFO - Getting element sub-02
2023-05-16 14:03:03,791 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:03,791 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:03,791 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:03,792 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:03,792 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:03,792 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:03,792 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:03,793 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:03,793 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:03,793 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:03,795 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:04,406 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:04,450 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:04,451 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:04,451 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:04,451 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:04,451 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:04,451 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:04,451 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:04,453 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:05,092 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:05,169 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:05,169 - JUNIFER - INFO - Getting element sub-03
2023-05-16 14:03:05,169 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:05,169 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:05,169 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:05,170 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:05,170 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:05,170 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:05,171 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:05,171 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:05,171 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:05,171 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:05,173 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:05,774 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:05,819 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:05,820 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:05,820 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:05,820 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:05,820 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:05,820 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:05,820 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:05,822 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:06,448 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:06,530 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:06,530 - JUNIFER - INFO - Getting element sub-04
2023-05-16 14:03:06,530 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:06,530 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:06,530 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:06,531 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:06,531 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:06,532 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:06,532 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:06,532 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:06,532 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:06,532 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:06,534 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:07,139 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:07,185 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:07,185 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:07,185 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:07,185 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:07,185 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:07,186 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:07,186 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:07,188 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:07,821 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:07,899 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:07,899 - JUNIFER - INFO - Getting element sub-05
2023-05-16 14:03:07,899 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:07,899 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:07,900 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:07,900 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:07,901 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:07,901 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:07,901 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:07,901 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:07,901 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:07,901 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:07,903 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:08,519 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:08,565 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:08,565 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:08,566 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:08,566 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:08,566 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:08,566 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:08,566 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:08,568 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:09,213 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:09,292 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:09,292 - JUNIFER - INFO - Getting element sub-06
2023-05-16 14:03:09,292 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:09,293 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:09,293 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:09,294 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:09,294 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:09,294 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:09,294 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:09,294 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:09,294 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:09,294 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:09,296 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:09,921 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:09,966 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:09,966 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:09,966 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:09,966 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:09,966 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:09,966 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:09,966 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:09,968 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:10,613 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:10,693 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:10,693 - JUNIFER - INFO - Getting element sub-07
2023-05-16 14:03:10,693 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:10,693 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:10,693 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:10,694 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:10,694 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:10,694 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:10,695 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:10,695 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:10,695 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:10,695 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:10,697 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:11,332 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:11,376 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:11,376 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:11,376 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:11,376 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:11,376 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:11,376 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:11,376 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:11,379 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:12,045 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:12,122 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:12,123 - JUNIFER - INFO - Getting element sub-08
2023-05-16 14:03:12,123 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:12,123 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:12,123 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:12,124 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:12,124 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:12,124 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:12,124 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:12,124 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:12,124 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:12,124 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:12,127 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:12,771 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:12,816 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:12,816 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:12,817 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:12,817 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:12,817 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:12,817 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:12,817 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:12,819 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:13,476 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:13,554 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:13,554 - JUNIFER - INFO - Getting element sub-09
2023-05-16 14:03:13,555 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:13,555 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:13,555 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:13,556 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:13,556 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:13,556 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:13,556 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:13,556 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:13,556 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:13,556 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:13,558 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:14,198 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:14,244 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:14,244 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:14,244 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:14,244 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:14,245 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:14,245 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:14,245 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:14,247 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:14,924 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:15,002 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:15,002 - JUNIFER - INFO - Getting element sub-10
2023-05-16 14:03:15,002 - JUNIFER - INFO - Fitting pipeline
2023-05-16 14:03:15,002 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-05-16 14:03:15,002 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-05-16 14:03:15,003 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-05-16 14:03:15,003 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:15,003 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:15,003 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:15,003 - JUNIFER - INFO - n_rois: 100
2023-05-16 14:03:15,003 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:15,003 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:15,005 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:15,649 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:15,695 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-05-16 14:03:15,695 - JUNIFER - INFO - Computing VBM_GM
2023-05-16 14:03:15,695 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-05-16 14:03:15,695 - JUNIFER - INFO - Parcellation parameters:
2023-05-16 14:03:15,695 - JUNIFER - INFO - n_rois: 200
2023-05-16 14:03:15,695 - JUNIFER - INFO - yeo_networks: 17
2023-05-16 14:03:15,696 - JUNIFER - INFO - resolution: 2.0
2023-05-16 14:03:15,698 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-05-16 14:03:16,351 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpchzgbi4q/test.sqlite (multiple output)>
2023-05-16 14:03:16,429 - JUNIFER - INFO - Marker collection fitting done
2023-05-16 14:03:16,429 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2023-05-16 14:03:16,430 - JUNIFER - INFO - Collecting data from /tmp/tmpchzgbi4q/*test.sqlite
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2023-05-16 14:03:18,598 - JUNIFER - INFO - Collect done
Using julearn for machine learning: We predict the age given our vbm features and sex as a confound.
fit_time score_time test_score repeat fold
0 0.162777 0.023476 -0.779885 0 0
1 0.157673 0.023720 -140.026073 0 1
2 0.156715 0.023214 -0.559247 0 2
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: ( 0 minutes 16.968 seconds)