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")
2023-03-31 13:29:56,428 - JUNIFER - INFO - ===== Lib Versions =====
2023-03-31 13:29:56,428 - JUNIFER - INFO - numpy: 1.23.5
2023-03-31 13:29:56,428 - JUNIFER - INFO - scipy: 1.10.1
2023-03-31 13:29:56,428 - JUNIFER - INFO - pandas: 1.5.3
2023-03-31 13:29:56,428 - JUNIFER - INFO - nilearn: 0.10.0
2023-03-31 13:29:56,428 - JUNIFER - INFO - nibabel: 4.0.2
2023-03-31 13:29:56,428 - JUNIFER - INFO - junifer: 0.0.2
2023-03-31 13:29:56,428 - 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/3.10.10/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/3.10.10/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)
2023-03-31 13:29:56,453 - JUNIFER - INFO - Getting element sub-01
2023-03-31 13:29:56,453 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:56,453 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:56,453 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:56,454 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:29:56,454 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:56,454 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:56,454 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:56,454 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:29:56,454 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:29:56,454 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:56,456 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:57,144 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:29:57,187 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:29:57,187 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:57,187 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:57,187 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:57,188 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:29:57,188 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:29:57,188 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:57,190 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:57,839 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:29:57,915 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:57,915 - JUNIFER - INFO - Getting element sub-02
2023-03-31 13:29:57,916 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:57,916 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:57,916 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:57,917 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:29:57,917 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:57,917 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:57,917 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:57,917 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:29:57,917 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:29:57,917 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:57,919 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:58,548 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:29:58,589 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:29:58,589 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:58,590 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:58,590 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:58,590 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:29:58,590 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:29:58,590 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:58,592 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:59,238 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:29:59,313 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:29:59,313 - JUNIFER - INFO - Getting element sub-03
2023-03-31 13:29:59,313 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:29:59,313 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:29:59,313 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:29:59,314 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:29:59,314 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:59,315 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:59,315 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:59,315 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:29:59,315 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:29:59,315 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:59,317 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:29:59,934 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:29:59,976 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:29:59,976 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:29:59,977 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:29:59,977 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:29:59,977 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:29:59,977 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:29:59,977 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:29:59,979 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:00,640 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:00,717 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:00,717 - JUNIFER - INFO - Getting element sub-04
2023-03-31 13:30:00,717 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:00,717 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:00,717 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:00,718 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:00,718 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:00,718 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:00,719 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:00,719 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:00,719 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:00,719 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:00,721 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:01,334 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:01,378 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:01,378 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:01,379 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:01,379 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:01,379 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:01,379 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:01,379 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:01,381 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:02,038 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:02,117 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:02,117 - JUNIFER - INFO - Getting element sub-05
2023-03-31 13:30:02,117 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:02,117 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:02,117 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:02,118 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:02,119 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:02,119 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:02,119 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:02,119 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:02,119 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:02,119 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:02,121 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:02,784 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:02,829 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:02,829 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:02,829 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:02,829 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:02,829 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:02,829 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:02,829 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:02,831 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:03,525 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:03,603 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:03,604 - JUNIFER - INFO - Getting element sub-06
2023-03-31 13:30:03,604 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:03,604 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:03,604 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:03,605 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:03,605 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:03,605 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:03,605 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:03,605 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:03,605 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:03,605 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:03,608 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:04,248 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:04,291 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:04,291 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:04,292 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:04,292 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:04,292 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:04,292 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:04,292 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:04,294 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:04,957 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:05,034 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:05,035 - JUNIFER - INFO - Getting element sub-07
2023-03-31 13:30:05,035 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:05,035 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:05,035 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:05,036 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:05,036 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:05,036 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:05,036 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:05,036 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:05,036 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:05,036 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:05,039 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:05,685 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:05,729 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:05,730 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:05,730 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:05,730 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:05,730 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:05,730 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:05,730 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:05,732 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:06,405 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:06,483 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:06,483 - JUNIFER - INFO - Getting element sub-08
2023-03-31 13:30:06,483 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:06,483 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:06,483 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:06,484 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:06,484 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:06,484 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:06,484 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:06,484 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:06,484 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:06,485 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:06,487 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:07,114 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:07,157 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:07,157 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:07,157 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:07,157 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:07,157 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:07,157 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:07,157 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:07,160 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:07,802 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:07,879 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:07,879 - JUNIFER - INFO - Getting element sub-09
2023-03-31 13:30:07,879 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:07,879 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:07,879 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:07,880 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:07,880 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:07,880 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:07,880 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:07,881 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:07,881 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:07,881 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:07,883 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:08,562 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:08,607 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:08,608 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:08,608 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:08,608 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:08,608 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:08,608 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:08,608 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:08,610 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:09,276 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:09,354 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:09,354 - JUNIFER - INFO - Getting element sub-10
2023-03-31 13:30:09,354 - JUNIFER - INFO - Fitting pipeline
2023-03-31 13:30:09,354 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-03-31 13:30:09,354 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-03-31 13:30:09,355 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-03-31 13:30:09,355 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:09,356 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:09,356 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:09,356 - JUNIFER - INFO - n_rois: 100
2023-03-31 13:30:09,356 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:09,356 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:09,358 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:09,982 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:10,024 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-03-31 13:30:10,025 - JUNIFER - INFO - Computing VBM_GM
2023-03-31 13:30:10,025 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-03-31 13:30:10,025 - JUNIFER - INFO - Parcellation parameters:
2023-03-31 13:30:10,025 - JUNIFER - INFO - n_rois: 200
2023-03-31 13:30:10,025 - JUNIFER - INFO - yeo_networks: 17
2023-03-31 13:30:10,025 - JUNIFER - INFO - resolution: 2.0
2023-03-31 13:30:10,027 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-03-31 13:30:10,673 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp9k431lw0/test.sqlite (multiple output)>
2023-03-31 13:30:10,749 - JUNIFER - INFO - Marker collection fitting done
2023-03-31 13:30:10,749 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2023-03-31 13:30:10,749 - JUNIFER - INFO - Collecting data from /tmp/tmp9k431lw0/*test.sqlite
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2023-03-31 13:30:12,933 - 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 0.165060 0.024141 -0.799588 0 0
1 0.158438 0.023678 -313.683244 0 1
2 0.157643 0.023585 0.187337 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 17.270 seconds)