Note
Go to the end to download the full example code.
8.7. Run junifer and julearn.¶
This example uses a ParcelAggregation marker to compute the mean of each parcel of the Tian subcortical parcellation (scale II, 32 ROIs) 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
from julearn import run_cross_validation, PipelineCreator
import junifer.testing.registry # noqa: F401
from junifer.api import collect, run
from junifer.storage import HDF5FeatureStorage
from junifer.testing.datagrabbers import UCLACNPVBMTestingDataGrabber
from junifer.utils import configure_logging
Set the logging level to info to see extra information:
configure_logging(level="INFO")
2026-10-19 21:14:37 [info ] ===== Lib Versions ===== [junifer] pkg=utils
2026-10-19 21:14:37 [info ] click: 8.5.0 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] numpy: 2.4.6 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] scipy: 1.17.1 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] datalad: 1.7.1 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] pandas: 3.0.6 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] nibabel: 5.4.2 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] nilearn: 0.14.1 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] sqlalchemy: 2.1.5 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] ruamel.yaml: 0.19.1 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] h5py: 3.16.0 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] tqdm: 4.70.1 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] templateflow: 25.1.2 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] lapy: 1.7.0 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] junifer_data: 1.6.1 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] junifer: 0.0.8 [junifer] pkg=utils
2026-10-19 21:14:37 [info ] ======================== [junifer] pkg=utils
Define the markers you want:
marker_dicts = [
{
"name": "TianxS2_TrimMean80",
"kind": "ParcelAggregation",
"parcellation": "TianxS2x3TxMNInonlinear2009cAsym",
"method": "trim_mean",
"method_params": {"proportiontocut": 0.2},
},
{
"name": "TianxS2_Mean",
"kind": "ParcelAggregation",
"parcellation": "TianxS2x3TxMNInonlinear2009cAsym",
"method": "mean",
},
]
Define target and confounds for julearn machine learning:
Load the phenotype data of the UCLA CNP subjects (OpenNeuro ds000030) for machine learning:
with UCLACNPVBMTestingDataGrabber() as dg:
participants = dg.get_participants()
2026-10-19 21:14:37 [info ] Parameters: {'types': ['VBM_GM'], 'datadir': '/tmp/tmpmc101b16', 'resolution': 2.0} [junifer] component=UCLACNPVBMTestingDataGrabber pkg=datagrabber step=datagrabber
Create a temporary directory for junifer feature extraction:
with tempfile.TemporaryDirectory() as tmpdir:
storage = {"kind": "HDF5FeatureStorage", "uri": f"{tmpdir}/test.hdf5"}
# run the defined junifer feature extraction pipeline
run(
workdir="/tmp",
datagrabber={"kind": "UCLACNPVBMTestingDataGrabber"},
markers=marker_dicts,
storage=storage,
)
# read in extracted features and add confounds and targets
# for julearn run cross validation
collect(storage)
db = HDF5FeatureStorage(uri=storage["uri"])
df_vbm = db.read_df(feature_name="VBM_GM_TianxS2_Mean_aggregation")
df_vbm.index = [x[0] for x in df_vbm.index]
2026-10-19 21:14:37 [info ] Parameters: {'types': ['VBM_GM'], 'datadir': '/tmp/tmpmc101b16', 'resolution': 2.0} [junifer] component=UCLACNPVBMTestingDataGrabber pkg=datagrabber step=datagrabber
2026-10-19 21:14:37 [info ] Parameters: {'on': ['T1w', 'T2w', 'BOLD', 'VBM_GM', 'VBM_WM', 'VBM_CSF', 'fALFF', 'GCOR', 'LCOR'], 'name': 'TianxS2_TrimMean80', 'parcellation': ['TianxS2x3TxMNInonlinear2009cAsym'], 'method': 'trim_mean', 'method_params': {'proportiontocut': 0.2}, 'time_method': None, 'time_method_params': None, 'masks': None} [junifer] component=TianxS2_TrimMean80 pkg=markers step=marker
2026-10-19 21:14:37 [info ] Parameters: {'on': ['T1w', 'T2w', 'BOLD', 'VBM_GM', 'VBM_WM', 'VBM_CSF', 'fALFF', 'GCOR', 'LCOR'], 'name': 'TianxS2_Mean', 'parcellation': ['TianxS2x3TxMNInonlinear2009cAsym'], 'method': 'mean', 'method_params': None, 'time_method': None, 'time_method_params': None, 'masks': None} [junifer] component=TianxS2_Mean pkg=markers step=marker
2026-10-19 21:14:37 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/test.hdf5', 'single_output': False, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:37 [info ] Validating Marker Collection [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] DataGrabber output type: ['VBM_GM'] [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Validating Data Reader: [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Data Reader output type: ['VBM_GM'] [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Validating Marker: TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Marker output type: [<StorageType.Vector: 'vector'>] [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Validating storage for TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Validating Marker: TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Marker output type: [<StorageType.Vector: 'vector'>] [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Validating storage for TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Getting element ('sub-10206',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:37 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10206/anat/sub-10206_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:37 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:37 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:37 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:37 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:37 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:37 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:37 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:37 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:37 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:37 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:37 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:37 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:37 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:37 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:37 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:37 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:37 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:37 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:37 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:37 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:37 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:38 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:38 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10206_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:38 [info ] Getting element ('sub-10339',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:38 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:38 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10339/anat/sub-10339_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:38 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:38 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:38 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:38 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:38 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:38 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:38 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:38 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:38 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:38 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:38 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:38 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:38 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:38 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:38 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:38 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:38 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:38 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:38 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:38 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:38 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10339_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Getting element ('sub-10388',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:39 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10388/anat/sub-10388_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:39 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:39 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:39 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:39 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:39 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:39 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:39 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:39 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:39 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:39 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:39 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:39 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:39 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:39 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:39 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:39 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:39 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:39 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10388_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:39 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Getting element ('sub-10429',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:39 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10429/anat/sub-10429_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:39 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:39 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:39 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:39 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:39 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:39 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:39 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:39 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:39 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:40 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:40 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:40 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:40 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:40 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:40 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:40 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:40 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:40 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:40 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:40 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10429_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:40 [info ] Getting element ('sub-10460',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:40 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:40 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10460/anat/sub-10460_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:40 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:40 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:40 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:40 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:40 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:40 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:40 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:40 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:40 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:40 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:40 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:40 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:40 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:40 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:40 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:40 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:40 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:40 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:40 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:41 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:41 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10460_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Getting element ('sub-10471',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:41 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10471/anat/sub-10471_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:41 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:41 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:41 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:41 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:41 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:41 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:41 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:41 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:41 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:41 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:41 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:41 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:41 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:41 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:41 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:41 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:41 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:41 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10471_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:41 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Getting element ('sub-10527',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:41 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10527/anat/sub-10527_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:41 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:41 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:41 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:41 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:41 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:41 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:41 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:41 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:41 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:42 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:42 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:42 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:42 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:42 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:42 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:42 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:42 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:42 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:42 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:42 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10527_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:42 [info ] Getting element ('sub-10696',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:42 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:42 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-10696/anat/sub-10696_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:42 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:42 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:42 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:42 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:42 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:42 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:42 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:42 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:42 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:42 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:42 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:42 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:42 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:42 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:42 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:42 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:42 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:42 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:42 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:43 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:43 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-10696_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Getting element ('sub-11059',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:43 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-11059/anat/sub-11059_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:43 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:43 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:43 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:43 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:43 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:43 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:43 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:43 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:43 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:43 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:43 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:43 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:43 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:43 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:43 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:43 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:43 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:43 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11059_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:43 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Getting element ('sub-11105',) [junifer] pkg=datagrabber step=datagrabber
2026-10-19 21:14:43 [info ] Fitting pipeline [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Reading VBM_GM from /home/docker/nilearn_data/ds000030/ds000030_R1.0.4/uncompressed/derivatives/fmriprep/sub-11105/anat/sub-11105_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue_res-2mm.nii [junifer] pkg=datareader step=datareader
2026-10-19 21:14:43 [info ] VBM_GM is of type NIFTI [junifer] pkg=datareader step=datareader
2026-10-19 21:14:43 [info ] Fitting marker TianxS2_TrimMean80 [junifer] pkg=pipeline
2026-10-19 21:14:43 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:43 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:43 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:43 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:43 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:43 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:43 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:44 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:44 [info ] Writing HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Wrote HDF5 metadata for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Writing HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Wrote HDF5 data for 69e41733a704faeb52f016d2ba28515a to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Fitting marker TianxS2_Mean [junifer] pkg=pipeline
2026-10-19 21:14:44 [info ] Computing DataType.VBM_GM [junifer] pkg=markers step=marker
2026-10-19 21:14:44 [info ] Parcellation parameters: [junifer] pkg=data
2026-10-19 21:14:44 [info ] resolution: 2.0 [junifer] pkg=data
2026-10-19 21:14:44 [info ] scale: 2 [junifer] pkg=data
2026-10-19 21:14:44 [info ] space: MNI152NLin2009cAsym [junifer] pkg=data
2026-10-19 21:14:44 [info ] magneticfield: 3T [junifer] pkg=data
2026-10-19 21:14:44 [info ] Loading parcellation: /home/docker/junifer_data/v8/parcellations/Melbourne/v1.4/3T/Subcortex-Only/Tian_Subcortex_S2_3T_2009cAsym.nii.gz [junifer] pkg=data
2026-10-19 21:14:44 [info ] Storing in <HDF5FeatureStorage @ /tmp/tmpox5tdhkg/test.hdf5 (multiple output)> [junifer] pkg=markers step=marker
2026-10-19 21:14:44 [info ] Writing HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Wrote HDF5 metadata for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Writing HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Wrote HDF5 data for 18cd403f00a3f00fbe724002fee3b88e to: /tmp/tmpox5tdhkg/element_sub-11105_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Marker collection fitting done [junifer] pkg=pipeline
2026-10-19 21:14:44 [info ] Collecting data using HDF5FeatureStorage [junifer] pkg=api
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/test.hdf5', 'single_output': False, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Collecting metadata from /tmp/tmpox5tdhkg/*_test.hdf5 [junifer] pkg=storage step=storage
file-metadata: 0it [00:00, ?it/s]2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10339_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-11059_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10460_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10388_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-11105_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10471_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10527_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10206_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10429_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
2026-10-19 21:14:44 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/element_sub-10696_test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
file-metadata: 10it [00:00, 96.76it/s]
file-metadata: 10it [00:00, 96.29it/s]
2026-10-19 21:14:44 [info ] Writing metadata to HDF5 file ... [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Collecting data from /tmp/tmpox5tdhkg/*_test.hdf5 [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Will collect 2 features. [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Collecting 10 files for feature MD5: 69e41733a704faeb52f016d2ba28515a. [junifer] pkg=storage step=storage
2026-10-19 21:14:44 [info ] Collecting 10 files for feature MD5: 18cd403f00a3f00fbe724002fee3b88e. [junifer] pkg=storage step=storage
feature: 0%| | 0/2 [00:00<?, ?it/s]
file-data: 0%| | 0/10 [00:00<?, ?it/s]
file-data: 50%|█████ | 5/10 [00:00<00:00, 41.44it/s]
file-data: 100%|██████████| 10/10 [00:00<00:00, 41.97it/s]
file-data: 100%|██████████| 10/10 [00:00<00:00, 41.75it/s]
feature: 50%|█████ | 1/2 [00:00<00:00, 3.81it/s]
file-data: 0%| | 0/10 [00:00<?, ?it/s]
file-data: 50%|█████ | 5/10 [00:00<00:00, 42.43it/s]
file-data: 100%|██████████| 10/10 [00:00<00:00, 46.19it/s]
file-data: 100%|██████████| 10/10 [00:00<00:00, 45.46it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 3.99it/s]
feature: 100%|██████████| 2/2 [00:00<00:00, 3.96it/s]
2026-10-19 21:14:45 [info ] Collect done [junifer] pkg=api
2026-10-19 21:14:45 [info ] Parameters: {'uri': '/tmp/tmpox5tdhkg/test.hdf5', 'single_output': True, 'overwrite': 'update', 'compression': 7, 'force_float32': True, 'chunk_size': 100} [junifer] component=HDF5FeatureStorage pkg=storage step=storage
Using julearn for machine learning: We predict the age given our vbm features and sex as a confound.
X = list(df_vbm.columns)
# Match the phenotypes to the subjects by their identifier
df_vbm[y] = participants.loc[df_vbm.index, "age"].to_numpy()
df_vbm[confound] = (
participants.loc[df_vbm.index, "gender"] == "F"
).to_numpy(dtype=int)
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,
scoring="r2",
)
print(scores[["fold", "test_score"]])
2026-10-19 21:14:45 [info ] Adding step zscore that applies to ColumnTypes<types={'features', 'confound'}; pattern=(?:__:type:__features|__:type:__confound)> [julearn]
2026-10-19 21:14:45 [info ] Step added [julearn]
2026-10-19 21:14:45 [info ] Adding step confound_removal that applies to ColumnTypes<types={'features'}; pattern=(?:__:type:__features)> [julearn]
2026-10-19 21:14:45 [info ] Setting hyperparameter confounds = confound [julearn]
2026-10-19 21:14:45 [info ] Step added [julearn]
2026-10-19 21:14:45 [info ] Adding step ridge that applies to ColumnTypes<types={'features'}; pattern=(?:__:type:__features)> [julearn]
2026-10-19 21:14:45 [info ] Step added [julearn]
2026-10-19 21:14:45 [info ] ==== Input Data ==== [julearn]
2026-10-19 21:14:45 [info ] Using dataframe as input [julearn]
2026-10-19 21:14:45 [info ] Features: ['aHIP-rh', 'pHIP-rh', 'lAMY-rh', 'mAMY-rh', 'THA-DP-rh', 'THA-VP-rh', 'THA-VA-rh', 'THA-DA-rh', 'NAc-shell-rh', 'NAc-core-rh', 'pGP-rh', 'aGP-rh', 'aPUT-rh', 'pPUT-rh', 'aCAU-rh', 'pCAU-rh', 'aHIP-lh', 'pHIP-lh', 'lAMY-lh', 'mAMY-lh', 'THA-DP-lh', 'THA-VP-lh', 'THA-VA-lh', 'THA-DA-lh', 'NAc-shell-lh', 'NAc-core-lh', 'pGP-lh', 'aGP-lh', 'aPUT-lh', 'pPUT-lh', 'aCAU-lh', 'pCAU-lh', 'sex'] [julearn]
2026-10-19 21:14:45 [info ] Target: age [julearn]
2026-10-19 21:14:45 [info ] Expanded features: ['aHIP-rh', 'pHIP-rh', 'lAMY-rh', 'mAMY-rh', 'THA-DP-rh', 'THA-VP-rh', 'THA-VA-rh', 'THA-DA-rh', 'NAc-shell-rh', 'NAc-core-rh', 'pGP-rh', 'aGP-rh', 'aPUT-rh', 'pPUT-rh', 'aCAU-rh', 'pCAU-rh', 'aHIP-lh', 'pHIP-lh', 'lAMY-lh', 'mAMY-lh', 'THA-DP-lh', 'THA-VP-lh', 'THA-VA-lh', 'THA-DA-lh', 'NAc-shell-lh', 'NAc-core-lh', 'pGP-lh', 'aGP-lh', 'aPUT-lh', 'pPUT-lh', 'aCAU-lh', 'pCAU-lh', 'sex'] [julearn]
2026-10-19 21:14:45 [info ] X_types:{'features': ['aHIP-rh', 'pHIP-rh', 'lAMY-rh', 'mAMY-rh', 'THA-DP-rh', 'THA-VP-rh', 'THA-VA-rh', 'THA-DA-rh', 'NAc-shell-rh', 'NAc-core-rh', 'pGP-rh', 'aGP-rh', 'aPUT-rh', 'pPUT-rh', 'aCAU-rh', 'pCAU-rh', 'aHIP-lh', 'pHIP-lh', 'lAMY-lh', 'mAMY-lh', 'THA-DP-lh', 'THA-VP-lh', 'THA-VA-lh', 'THA-DA-lh', 'NAc-shell-lh', 'NAc-core-lh', 'pGP-lh', 'aGP-lh', 'aPUT-lh', 'pPUT-lh', 'aCAU-lh', 'pCAU-lh'], 'confound': ['sex']} [julearn]
2026-10-19 21:14:45 [info ] ==================== [julearn]
2026-10-19 21:14:45 [info ] [julearn]
2026-10-19 21:14:45 [info ] = Model Parameters = [julearn]
2026-10-19 21:14:45 [info ] ==================== [julearn]
2026-10-19 21:14:45 [info ] [julearn]
2026-10-19 21:14:45 [info ] = Data Information = [julearn]
2026-10-19 21:14:45 [info ] Problem type: regression [julearn]
2026-10-19 21:14:45 [info ] Number of samples: 10 [julearn]
2026-10-19 21:14:45 [info ] Number of features: 33 [julearn]
2026-10-19 21:14:45 [info ] ==================== [julearn]
2026-10-19 21:14:45 [info ] [julearn]
2026-10-19 21:14:45 [info ] Target type: int64 [julearn]
2026-10-19 21:14:45 [info ] Using outer CV scheme KFold(n_splits=3, random_state=None, shuffle=False) [julearn]
fold test_score
0 0 -1.177497
1 1 -22.392046
2 2 -8.400203
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 9.430 seconds)