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, 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")
2023-07-24 05:10:14,122 - JUNIFER - INFO - ===== Lib Versions =====
2023-07-24 05:10:14,122 - JUNIFER - INFO - numpy: 1.25.1
2023-07-24 05:10:14,122 - JUNIFER - INFO - scipy: 1.11.1
2023-07-24 05:10:14,122 - JUNIFER - INFO - pandas: 1.5.3
2023-07-24 05:10:14,122 - JUNIFER - INFO - nilearn: 0.10.0
2023-07-24 05:10:14,122 - JUNIFER - INFO - nibabel: 4.0.2
2023-07-24 05:10:14,122 - JUNIFER - INFO - junifer: 0.0.3
2023-07-24 05:10:14,122 - 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/3.10.12/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/3.10.12/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)
2023-07-24 05:10:14,151 - JUNIFER - INFO - Getting element sub-01
2023-07-24 05:10:14,151 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:14,151 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:14,151 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:14,152 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:14,153 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:14,153 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:14,153 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:14,153 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:14,153 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:14,153 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:14,155 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:15,027 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:15,083 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:15,084 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:15,084 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:15,084 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:15,084 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:15,084 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:15,084 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:15,087 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:15,989 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:16,087 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:16,087 - JUNIFER - INFO - Getting element sub-02
2023-07-24 05:10:16,087 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:16,087 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:16,087 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:16,089 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:16,089 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:16,089 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:16,089 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:16,090 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:16,090 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:16,090 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:16,093 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:16,947 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:17,004 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:17,004 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:17,005 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:17,005 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:17,005 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:17,005 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:17,005 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:17,009 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:17,882 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:17,984 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:17,984 - JUNIFER - INFO - Getting element sub-03
2023-07-24 05:10:17,984 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:17,984 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:17,985 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:17,986 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:17,986 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:17,986 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:17,986 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:17,987 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:17,987 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:17,987 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:17,989 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:18,860 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:18,920 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:18,920 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:18,920 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:18,920 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:18,920 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:18,920 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:18,920 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:18,923 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:19,784 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:19,877 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:19,877 - JUNIFER - INFO - Getting element sub-04
2023-07-24 05:10:19,877 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:19,877 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:19,877 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:19,878 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:19,878 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:19,879 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:19,879 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:19,879 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:19,879 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:19,879 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:19,881 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:20,726 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:20,779 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:20,779 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:20,779 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:20,779 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:20,779 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:20,779 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:20,780 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:20,782 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:21,650 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:21,747 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:21,747 - JUNIFER - INFO - Getting element sub-05
2023-07-24 05:10:21,748 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:21,748 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:21,748 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:21,750 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:21,750 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:21,750 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:21,750 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:21,750 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:21,750 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:21,751 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:21,754 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:22,611 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:22,666 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:22,666 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:22,666 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:22,667 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:22,667 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:22,667 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:22,667 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:22,670 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:23,566 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:23,663 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:23,663 - JUNIFER - INFO - Getting element sub-06
2023-07-24 05:10:23,664 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:23,664 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:23,664 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:23,665 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:23,665 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:23,666 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:23,666 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:23,666 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:23,666 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:23,666 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:23,669 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:24,570 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:24,629 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:24,629 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:24,629 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:24,630 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:24,630 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:24,630 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:24,630 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:24,633 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:25,514 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:25,619 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:25,619 - JUNIFER - INFO - Getting element sub-07
2023-07-24 05:10:25,619 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:25,619 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:25,619 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:25,621 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:25,621 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:25,621 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:25,621 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:25,621 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:25,621 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:25,621 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:25,624 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:26,491 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:26,552 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:26,553 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:26,553 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:26,553 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:26,553 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:26,553 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:26,554 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:26,557 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:27,394 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:27,488 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:27,488 - JUNIFER - INFO - Getting element sub-08
2023-07-24 05:10:27,489 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:27,489 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:27,489 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:27,490 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:27,490 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:27,491 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:27,491 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:27,491 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:27,491 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:27,491 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:27,494 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:28,306 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:28,361 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:28,361 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:28,362 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:28,362 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:28,362 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:28,362 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:28,362 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:28,364 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:29,219 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:29,317 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:29,317 - JUNIFER - INFO - Getting element sub-09
2023-07-24 05:10:29,317 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:29,317 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:29,317 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:29,319 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:29,319 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:29,319 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:29,319 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:29,319 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:29,319 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:29,319 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:29,322 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:30,236 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:30,296 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:30,296 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:30,297 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:30,297 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:30,297 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:30,297 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:30,297 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:30,299 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:31,172 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:31,264 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:31,264 - JUNIFER - INFO - Getting element sub-10
2023-07-24 05:10:31,264 - JUNIFER - INFO - Fitting pipeline
2023-07-24 05:10:31,264 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-07-24 05:10:31,265 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-07-24 05:10:31,266 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-07-24 05:10:31,266 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:31,266 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:31,267 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:31,267 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:31,267 - JUNIFER - INFO - n_rois: 100
2023-07-24 05:10:31,267 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:31,270 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:32,097 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:32,154 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-07-24 05:10:32,154 - JUNIFER - INFO - Computing VBM_GM
2023-07-24 05:10:32,155 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-07-24 05:10:32,155 - JUNIFER - INFO - Parcellation parameters:
2023-07-24 05:10:32,155 - JUNIFER - INFO - resolution: 2.0
2023-07-24 05:10:32,155 - JUNIFER - INFO - n_rois: 200
2023-07-24 05:10:32,155 - JUNIFER - INFO - yeo_networks: 17
2023-07-24 05:10:32,157 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-07-24 05:10:33,045 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpomu17qac/test.sqlite (multiple output)>
2023-07-24 05:10:33,139 - JUNIFER - INFO - Marker collection fitting done
2023-07-24 05:10:33,139 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2023-07-24 05:10:33,139 - JUNIFER - INFO - Collecting data from /tmp/tmpomu17qac/*test.sqlite
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2023-07-24 05:10:35,855 - 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 0.265640 0.034369 ... 0 509497eb21da473048117e0c6704d3ea
1 0.258639 0.033180 ... 1 509497eb21da473048117e0c6704d3ea
2 0.257170 0.034521 ... 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 22.952 seconds)