├── .github └── workflows │ └── osl-cicd-actions.yml ├── .gitignore ├── .readthedocs.yaml ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── doc └── source │ ├── Makefile │ ├── conf.py │ ├── documentation.rst │ ├── faq.rst │ ├── index.rst │ ├── install.rst │ └── tutorials │ ├── README.rst │ ├── glm_sensor.py │ ├── glm_sensor_solution.py │ ├── glm_simulation.py │ ├── glm_simulation_solution.py │ ├── preprocessing_automatic.py │ ├── preprocessing_batch.py │ ├── preprocessing_manual.py │ ├── source-recon_batch.py │ ├── source-recon_coreg.py │ ├── source-recon_deleting-headshape-points.py │ └── source-recon_subject.py ├── envs ├── README.md ├── bmrc.yml ├── hbaws.yml └── osle.yml ├── examples ├── README.md ├── ctf │ ├── ctf_with_headshape_pos │ │ ├── 1_preprocess.py │ │ ├── 2_coregister.py │ │ ├── 3_source_reconstruct.py │ │ ├── 4_sign_flip.py │ │ ├── 5_save_npy.py │ │ └── README.md │ └── ctf_with_smri_fid │ │ ├── 1_preprocess.py │ │ ├── 2_coregister.py │ │ ├── 3_source_reconstruct.py │ │ ├── 4_sign_flip.py │ │ └── README.md ├── eeg │ ├── 1_preprocess.py │ ├── 2_coregister.py │ ├── 3_move_sensors.py │ ├── 4_source_reconstruct.py │ ├── 5_sign_flip.py │ └── README.md ├── elekta │ ├── 1_maxfilter.py │ ├── 2_preprocess.py │ ├── 3_coregister.py │ ├── 4_source_reconstruct.py │ ├── 5_sign_flip.py │ └── README.md ├── misc │ ├── beamformer_comparison_paper.py │ ├── delete_headshape_points.py │ ├── fix_smri_files.py │ ├── freesurfer_source_recon.py │ ├── sign_flipping_matlab_files.py │ └── spectrum_analysis_walkthrough.py ├── opm │ ├── 0_convert_files.py │ ├── 1_preprocess.py │ ├── 2_coregister.py │ ├── 3_source_reconstruct.py │ ├── 4_sign_flip.py │ └── README.md ├── oxford │ └── README.md ├── parallelisation │ ├── README.md │ ├── parallel_preprocess.py │ ├── parallel_source_reconstruct.py │ ├── serial_preprocess.py │ └── serial_source_reconstruct.py └── toolbox-paper │ ├── 1_preprocessing.py │ ├── 2_source-reconstruct.py │ ├── 3_sign-flip.py │ ├── 4_stats.py │ ├── README.md │ └── osl-toolbox-paper.yml ├── osl_ephys ├── README.md ├── __init__.py ├── glm │ ├── README.md │ ├── __init__.py │ ├── glm_base.py │ ├── glm_epochs.py │ └── glm_spectrum.py ├── maxfilter │ ├── README.md │ ├── __init__.py │ └── maxfilter.py ├── preprocessing │ ├── README.md │ ├── __init__.py │ ├── batch.py │ ├── ica_label.py │ ├── mne_wrappers.py │ ├── osl_wrappers.py │ └── plot_ica.py ├── report │ ├── README.md │ ├── __init__.py │ ├── preproc_report.py │ ├── src_report.py │ └── templates │ │ ├── raw_subject_panel.html │ │ ├── raw_summary_panel.html │ │ ├── src_subject_panel.html │ │ ├── src_summary_panel.html │ │ ├── subject_report.html │ │ └── summary_report.html ├── source_recon │ ├── README.md │ ├── __init__.py │ ├── batch.py │ ├── beamforming.py │ ├── files │ │ ├── Glasser50_space-MNI152NLin6_res-8x8x8.nii.gz │ │ ├── Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz │ │ ├── Glasser52_binary_space-MNI152NLin6_res-8x8x8.txt │ │ ├── Glasser52_binary_space-MNI152NLin6_res-8x8x8.xml │ │ ├── HarvOxf-sub-Schaefer100-combined-2mm_4d.nii.gz │ │ ├── HarvOxf-sub-Schaefer100-combined-2mm_4d.xml │ │ ├── HarvOxf-sub-Schaefer100-combined-2mm_4d_ds8.nii.gz │ │ ├── HarvOxf-sub-Schaefer100-combined-2mm_4d_ds8.xml │ │ ├── HarvardOxford-sub-prob-bin-2mm.nii.gz │ │ ├── MNI152_T1_2mm_brain.nii.gz │ │ ├── MNI152_T1_8mm_brain.nii.gz │ │ ├── Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm_4d.nii.gz │ │ ├── Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm_4d.xml │ │ ├── Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm_4d_ds8.nii.gz │ │ ├── Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm_4d_ds8.xml │ │ ├── WTA_fMRI_parcellation_ds2mm.nii.gz │ │ ├── WTA_fMRI_parcellation_ds8mm.nii.gz │ │ ├── aal_cortical_merged_8mm_stacked.nii.gz │ │ ├── dk_cortical.nii.gz │ │ ├── dk_full.nii.gz │ │ ├── fMRI_parcellation_ds2mm.nii.gz │ │ ├── fMRI_parcellation_ds8mm.nii.gz │ │ ├── fmri_d100_parcellation_with_PCC_reduced_2mm.nii.gz │ │ ├── fmri_d100_parcellation_with_PCC_reduced_2mm_ss5mm_ds8mm.nii.gz │ │ ├── fmri_d100_parcellation_with_PCC_tighterMay15_v2_2mm.nii.gz │ │ ├── fmri_d100_parcellation_with_PCC_tighterMay15_v2_6mm_exclusive.nii.gz │ │ ├── fmri_d100_parcellation_with_PCC_tighterMay15_v2_8mm.nii.gz │ │ ├── giles_39_binary.nii.gz │ │ ├── reduced_hcp-mmp_2mm.nii.gz │ │ └── reduced_hcp-mmp_8mm.nii.gz │ ├── freesurfer_utils.py │ ├── minimum_norm.py │ ├── nii.py │ ├── parcellation.py │ ├── rhino │ │ ├── __init__.py │ │ ├── coreg.py │ │ ├── forward_model.py │ │ ├── fsl_utils.py │ │ ├── polhemus.py │ │ ├── surfaces.py │ │ └── utils.py │ ├── sign_flipping.py │ └── wrappers.py ├── tests │ ├── __init__.py │ ├── test_00_package_canary.py │ ├── test_batch_api.py │ ├── test_batch_preproc.py │ ├── test_file_handling.py │ ├── test_glm.py │ └── test_parallel.py └── utils │ ├── README.md │ ├── __init__.py │ ├── create_neuromag306_info.py │ ├── file_handling.py │ ├── logger.py │ ├── misc.py │ ├── neuromag306_info.yml │ ├── 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