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")
2024-02-09 10:12:12,744 - JUNIFER - INFO - ===== Lib Versions =====
2024-02-09 10:12:12,744 - JUNIFER - INFO - numpy: 1.26.4
2024-02-09 10:12:12,744 - JUNIFER - INFO - scipy: 1.11.4
2024-02-09 10:12:12,744 - JUNIFER - INFO - pandas: 2.1.4
2024-02-09 10:12:12,744 - JUNIFER - INFO - nilearn: 0.10.2
2024-02-09 10:12:12,745 - JUNIFER - INFO - nibabel: 5.2.0
2024-02-09 10:12:12,745 - JUNIFER - INFO - junifer: 0.0.4.dev563
2024-02-09 10:12:12,745 - 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/3.10.13/x64/lib/python3.10/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
/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/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)
2024-02-09 10:12:12,765 - JUNIFER - INFO - Getting element sub-01
2024-02-09 10:12:12,765 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:12,765 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:12,765 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:12,766 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:12,766 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:12,766 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:12,767 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:12,767 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:12,767 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:12,767 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:12,768 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:13,442 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:13,478 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:13,478 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:13,478 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:13,479 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:13,479 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:13,479 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:13,479 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:13,480 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:14,168 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:14,223 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:14,223 - JUNIFER - INFO - Getting element sub-02
2024-02-09 10:12:14,224 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:14,224 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:14,224 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:14,225 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:14,225 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:14,225 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:14,225 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:14,225 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:14,225 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:14,225 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:14,226 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:14,891 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:14,929 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:14,929 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:14,929 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:14,929 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:14,929 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:14,929 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:14,929 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:14,931 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:15,599 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:15,656 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:15,656 - JUNIFER - INFO - Getting element sub-03
2024-02-09 10:12:15,656 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:15,656 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:15,656 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:15,657 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:15,657 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:15,658 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:15,658 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:15,658 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:15,658 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:15,658 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:15,659 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:16,340 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:16,377 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:16,377 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:16,377 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:16,377 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:16,377 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:16,378 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:16,378 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:16,379 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:17,051 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:17,107 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:17,107 - JUNIFER - INFO - Getting element sub-04
2024-02-09 10:12:17,107 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:17,107 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:17,107 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:17,108 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:17,108 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:17,109 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:17,109 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:17,109 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:17,109 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:17,109 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:17,110 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:17,784 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:17,820 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:17,820 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:17,820 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:17,820 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:17,820 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:17,820 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:17,820 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:17,821 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:18,522 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:18,578 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:18,578 - JUNIFER - INFO - Getting element sub-05
2024-02-09 10:12:18,578 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:18,579 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:18,579 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:18,580 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:18,580 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:18,580 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:18,580 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:18,580 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:18,580 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:18,580 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:18,581 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:19,249 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:19,285 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:19,285 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:19,285 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:19,285 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:19,285 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:19,285 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:19,285 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:19,287 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:19,961 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:20,017 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:20,017 - JUNIFER - INFO - Getting element sub-06
2024-02-09 10:12:20,017 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:20,017 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:20,017 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:20,018 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:20,018 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:20,018 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:20,018 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:20,019 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:20,019 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:20,019 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:20,020 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:20,703 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:20,739 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:20,739 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:20,739 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:20,739 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:20,739 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:20,739 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:20,739 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:20,741 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:21,404 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:21,460 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:21,460 - JUNIFER - INFO - Getting element sub-07
2024-02-09 10:12:21,461 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:21,461 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:21,461 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:21,462 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:21,462 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:21,462 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:21,462 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:21,462 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:21,462 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:21,462 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:21,463 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:22,113 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:22,149 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:22,150 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:22,150 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:22,150 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:22,150 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:22,150 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:22,150 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:22,151 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:22,817 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:22,873 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:22,873 - JUNIFER - INFO - Getting element sub-08
2024-02-09 10:12:22,874 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:22,874 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:22,874 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:22,875 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:22,875 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:22,875 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:22,875 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:22,875 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:22,875 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:22,875 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:22,876 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:23,521 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:23,557 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:23,557 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:23,557 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:23,557 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:23,557 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:23,557 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:23,557 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:23,559 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:24,215 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:24,271 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:24,271 - JUNIFER - INFO - Getting element sub-09
2024-02-09 10:12:24,271 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:24,271 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:24,271 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:24,272 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:24,272 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:24,272 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:24,272 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:24,272 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:24,272 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:24,272 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:24,274 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:24,974 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:25,011 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:25,011 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:25,011 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:25,011 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:25,011 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:25,012 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:25,012 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:25,013 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:25,704 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:25,760 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:25,760 - JUNIFER - INFO - Getting element sub-10
2024-02-09 10:12:25,760 - JUNIFER - INFO - Fitting pipeline
2024-02-09 10:12:25,760 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-02-09 10:12:25,760 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-02-09 10:12:25,762 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-02-09 10:12:25,762 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:25,762 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:25,762 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:25,762 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:25,762 - JUNIFER - INFO - n_rois: 100
2024-02-09 10:12:25,762 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:25,764 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:26,420 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:26,455 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-02-09 10:12:26,455 - JUNIFER - INFO - Computing VBM_GM
2024-02-09 10:12:26,455 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-02-09 10:12:26,456 - JUNIFER - INFO - Parcellation parameters:
2024-02-09 10:12:26,456 - JUNIFER - INFO - resolution: 2.0
2024-02-09 10:12:26,456 - JUNIFER - INFO - n_rois: 200
2024-02-09 10:12:26,456 - JUNIFER - INFO - yeo_networks: 17
2024-02-09 10:12:26,457 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-02-09 10:12:27,130 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpy1zu7qf6/test.sqlite (multiple output)>
2024-02-09 10:12:27,187 - JUNIFER - INFO - Marker collection fitting done
2024-02-09 10:12:27,187 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-02-09 10:12:27,187 - JUNIFER - INFO - Collecting data from /tmp/tmpy1zu7qf6/*test.sqlite
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2024-02-09 10:12:28,947 - 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 0.158449 0.022290 ... 0 509497eb21da473048117e0c6704d3ea
1 0.156348 0.022035 ... 1 509497eb21da473048117e0c6704d3ea
2 0.155115 0.021825 ... 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: (0 minutes 16.925 seconds)