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")
2023-09-06 09:38:58,520 - JUNIFER - INFO - ===== Lib Versions =====
2023-09-06 09:38:58,521 - JUNIFER - INFO - numpy: 1.25.2
2023-09-06 09:38:58,521 - JUNIFER - INFO - scipy: 1.11.2
2023-09-06 09:38:58,521 - JUNIFER - INFO - pandas: 1.5.3
2023-09-06 09:38:58,521 - JUNIFER - INFO - nilearn: 0.10.0
2023-09-06 09:38:58,521 - JUNIFER - INFO - nibabel: 4.0.2
2023-09-06 09:38:58,521 - JUNIFER - INFO - junifer: 0.0.4.dev21
2023-09-06 09:38:58,521 - 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)
2023-09-06 09:38:58,545 - JUNIFER - INFO - Getting element sub-01
2023-09-06 09:38:58,545 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:58,545 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:58,545 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:58,546 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:38:58,546 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:58,546 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:58,546 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:58,546 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:38:58,546 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:38:58,546 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:38:58,548 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:59,139 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:38:59,183 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:38:59,183 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:59,183 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:59,183 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:59,183 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:38:59,183 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:38:59,184 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:38:59,186 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:38:59,812 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:38:59,888 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:38:59,889 - JUNIFER - INFO - Getting element sub-02
2023-09-06 09:38:59,889 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:38:59,889 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:38:59,889 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:38:59,890 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:38:59,890 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:38:59,890 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:38:59,890 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:38:59,890 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:38:59,890 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:38:59,890 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:38:59,892 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:00,508 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:00,550 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:00,550 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:00,550 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:00,550 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:00,550 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:00,550 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:00,551 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:00,553 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:01,175 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:01,252 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:01,252 - JUNIFER - INFO - Getting element sub-03
2023-09-06 09:39:01,252 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:01,252 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:01,252 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:01,253 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:01,253 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:01,254 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:01,254 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:01,254 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:01,254 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:01,254 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:01,256 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:01,912 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:01,956 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:01,956 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:01,956 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:01,956 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:01,956 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:01,956 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:01,956 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:01,959 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:02,683 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:02,761 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:02,761 - JUNIFER - INFO - Getting element sub-04
2023-09-06 09:39:02,761 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:02,761 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:02,761 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:02,762 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:02,762 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:02,763 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:02,763 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:02,763 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:02,763 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:02,763 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:02,765 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:03,463 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:03,507 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:03,507 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:03,507 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:03,507 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:03,507 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:03,507 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:03,507 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:03,510 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:04,121 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:04,199 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:04,199 - JUNIFER - INFO - Getting element sub-05
2023-09-06 09:39:04,199 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:04,199 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:04,199 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:04,200 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:04,200 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:04,200 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:04,200 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:04,200 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:04,201 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:04,201 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:04,203 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:04,798 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:04,839 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:04,840 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:04,840 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:04,840 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:04,840 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:04,840 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:04,840 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:04,842 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:05,458 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:05,535 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:05,535 - JUNIFER - INFO - Getting element sub-06
2023-09-06 09:39:05,536 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:05,536 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:05,536 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:05,537 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:05,537 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:05,537 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:05,537 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:05,537 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:05,537 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:05,537 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:05,539 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:06,131 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:06,175 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:06,175 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:06,175 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:06,175 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:06,175 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:06,175 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:06,175 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:06,177 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:06,847 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:06,924 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:06,925 - JUNIFER - INFO - Getting element sub-07
2023-09-06 09:39:06,925 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:06,925 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:06,925 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:06,926 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:06,926 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:06,926 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:06,926 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:06,926 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:06,926 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:06,926 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:06,928 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:07,526 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:07,568 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:07,568 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:07,569 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:07,569 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:07,569 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:07,569 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:07,569 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:07,571 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:08,197 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:08,275 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:08,275 - JUNIFER - INFO - Getting element sub-08
2023-09-06 09:39:08,275 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:08,275 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:08,275 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:08,276 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:08,276 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:08,276 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:08,277 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:08,277 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:08,277 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:08,277 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:08,279 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:08,857 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:08,901 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:08,901 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:08,902 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:08,902 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:08,902 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:08,902 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:08,902 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:08,904 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:09,539 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:09,616 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:09,617 - JUNIFER - INFO - Getting element sub-09
2023-09-06 09:39:09,617 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:09,617 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:09,617 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:09,618 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:09,618 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:09,618 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:09,618 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:09,618 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:09,618 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:09,618 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:09,620 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:10,247 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:10,289 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:10,289 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:10,290 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:10,290 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:10,290 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:10,290 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:10,290 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:10,292 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:10,909 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:10,984 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:10,985 - JUNIFER - INFO - Getting element sub-10
2023-09-06 09:39:10,985 - JUNIFER - INFO - Fitting pipeline
2023-09-06 09:39:10,985 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2023-09-06 09:39:10,985 - JUNIFER - INFO - VBM_GM is type NIFTI
2023-09-06 09:39:10,986 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2023-09-06 09:39:10,986 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:10,986 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:10,986 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:10,986 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:10,986 - JUNIFER - INFO - n_rois: 100
2023-09-06 09:39:10,986 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:10,988 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:11,581 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:11,625 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2023-09-06 09:39:11,625 - JUNIFER - INFO - Computing VBM_GM
2023-09-06 09:39:11,625 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2023-09-06 09:39:11,626 - JUNIFER - INFO - Parcellation parameters:
2023-09-06 09:39:11,626 - JUNIFER - INFO - resolution: 2.0
2023-09-06 09:39:11,626 - JUNIFER - INFO - n_rois: 200
2023-09-06 09:39:11,626 - JUNIFER - INFO - yeo_networks: 17
2023-09-06 09:39:11,628 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2023-09-06 09:39:12,235 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmptan61dl_/test.sqlite (multiple output)>
2023-09-06 09:39:12,312 - JUNIFER - INFO - Marker collection fitting done
2023-09-06 09:39:12,312 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2023-09-06 09:39:12,312 - JUNIFER - INFO - Collecting data from /tmp/tmptan61dl_/*test.sqlite
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2023-09-06 09:39:14,473 - 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 0.207180 0.028271 ... 0 509497eb21da473048117e0c6704d3ea
1 0.198519 0.028029 ... 1 509497eb21da473048117e0c6704d3ea
2 0.198791 0.027924 ... 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 16.920 seconds)