Note
Click here to download the full example code
7.7. 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")
2022-12-20 14:34:34,271 - JUNIFER - INFO - ===== Lib Versions =====
2022-12-20 14:34:34,272 - JUNIFER - INFO - numpy: 1.23.5
2022-12-20 14:34:34,272 - JUNIFER - INFO - scipy: 1.9.3
2022-12-20 14:34:34,272 - JUNIFER - INFO - pandas: 1.5.2
2022-12-20 14:34:34,272 - JUNIFER - INFO - nilearn: 0.9.2
2022-12-20 14:34:34,272 - JUNIFER - INFO - nibabel: 4.0.2
2022-12-20 14:34:34,272 - JUNIFER - INFO - junifer: 0.0.1
2022-12-20 14:34:34,272 - 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/3.10.9/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:774: 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/3.10.9/x64/lib/python3.10/site-packages/nilearn/datasets/struct.py:774: 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)
2022-12-20 14:34:34,297 - JUNIFER - INFO - Getting element sub-01
2022-12-20 14:34:34,297 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:34,298 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:34,298 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:34,299 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:34,299 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:34,299 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:34,299 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:34,299 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:34,299 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:34,299 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:34,301 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:35,140 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:35,196 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:35,196 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:35,197 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:35,197 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:35,197 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:35,197 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:35,197 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:35,199 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:36,048 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:36,140 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:36,141 - JUNIFER - INFO - Getting element sub-02
2022-12-20 14:34:36,141 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:36,141 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:36,141 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:36,142 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:36,142 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:36,142 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:36,142 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:36,142 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:36,143 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:36,143 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:36,145 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:36,975 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:37,031 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:37,031 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:37,031 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:37,031 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:37,031 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:37,031 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:37,031 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:37,034 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:37,900 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:37,989 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:37,989 - JUNIFER - INFO - Getting element sub-03
2022-12-20 14:34:37,990 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:37,990 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:37,990 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:37,991 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:37,991 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:37,991 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:37,991 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:37,991 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:37,991 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:37,992 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:37,994 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:38,825 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:38,877 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:38,878 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:38,878 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:38,879 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:38,879 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:38,879 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:38,879 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:38,881 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:39,742 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:39,833 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:39,834 - JUNIFER - INFO - Getting element sub-04
2022-12-20 14:34:39,834 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:39,834 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:39,834 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:39,835 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:39,835 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:39,835 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:39,835 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:39,835 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:39,835 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:39,835 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:39,838 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:40,668 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:40,722 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:40,722 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:40,722 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:40,723 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:40,723 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:40,723 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:40,723 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:40,725 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:41,567 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:41,658 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:41,658 - JUNIFER - INFO - Getting element sub-05
2022-12-20 14:34:41,658 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:41,658 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:41,658 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:41,659 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:41,660 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:41,660 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:41,660 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:41,660 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:41,660 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:41,660 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:41,662 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:42,487 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:42,540 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:42,540 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:42,540 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:42,540 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:42,540 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:42,541 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:42,541 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:42,543 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:43,408 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:43,499 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:43,499 - JUNIFER - INFO - Getting element sub-06
2022-12-20 14:34:43,499 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:43,499 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:43,500 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:43,501 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:43,501 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:43,501 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:43,501 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:43,501 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:43,501 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:43,501 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:43,503 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:44,363 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:44,423 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:44,423 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:44,423 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:44,423 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:44,423 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:44,424 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:44,424 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:44,426 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:45,286 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:45,375 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:45,375 - JUNIFER - INFO - Getting element sub-07
2022-12-20 14:34:45,375 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:45,375 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:45,375 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:45,376 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:45,377 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:45,377 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:45,377 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:45,377 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:45,377 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:45,377 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:45,379 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:46,206 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:46,261 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:46,261 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:46,262 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:46,262 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:46,262 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:46,262 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:46,262 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:46,264 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:47,098 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:47,187 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:47,187 - JUNIFER - INFO - Getting element sub-08
2022-12-20 14:34:47,187 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:47,188 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:47,188 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:47,189 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:47,189 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:47,189 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:47,189 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:47,189 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:47,189 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:47,189 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:47,191 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:48,015 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:48,069 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:48,069 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:48,070 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:48,070 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:48,070 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:48,070 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:48,070 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:48,073 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:48,911 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:48,998 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:48,998 - JUNIFER - INFO - Getting element sub-09
2022-12-20 14:34:48,998 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:48,999 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:48,999 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:49,000 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:49,000 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:49,000 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:49,000 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:49,000 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:49,000 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:49,000 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:49,003 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:49,878 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:49,931 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:49,932 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:49,932 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:49,932 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:49,932 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:49,932 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:49,932 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:49,934 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:50,807 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:50,893 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:50,893 - JUNIFER - INFO - Getting element sub-10
2022-12-20 14:34:50,893 - JUNIFER - INFO - Fitting pipeline
2022-12-20 14:34:50,893 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2022-12-20 14:34:50,894 - JUNIFER - INFO - VBM_GM is type NIFTI
2022-12-20 14:34:50,895 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2022-12-20 14:34:50,895 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:50,895 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:50,895 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:50,895 - JUNIFER - INFO - n_rois: 100
2022-12-20 14:34:50,895 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:50,895 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:50,897 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:51,717 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:51,770 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2022-12-20 14:34:51,770 - JUNIFER - INFO - Computing VBM_GM
2022-12-20 14:34:51,770 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2022-12-20 14:34:51,770 - JUNIFER - INFO - Parcellatikon parameters:
2022-12-20 14:34:51,771 - JUNIFER - INFO - n_rois: 200
2022-12-20 14:34:51,771 - JUNIFER - INFO - yeo_networks: 17
2022-12-20 14:34:51,771 - JUNIFER - INFO - resolution: 2.0
2022-12-20 14:34:51,773 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2022-12-20 14:34:52,623 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp1znc2mn6/test.sqlite (multiple output)>
2022-12-20 14:34:52,710 - JUNIFER - INFO - Marker collection fitting done
2022-12-20 14:34:52,711 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2022-12-20 14:34:52,711 - JUNIFER - INFO - Collecting data from /tmp/tmp1znc2mn6/*test.sqlite
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2022-12-20 14:34:55,172 - 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 0.183844 0.024389 -0.872465 0 0
1 0.181063 0.024316 -139.601195 0 1
2 0.178574 0.024312 -0.261410 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 21.740 seconds)