kymata-atlas / kymata-core

Core Kymata codebase, including statistical analysis and plotting tools
https://kymata.org
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Create BEMs within the preproc pipeline #198

Open caiw opened 8 months ago

caiw commented 8 months ago

Removed the comment # todo - AT has used the commandline version to create the BEMSs: do and then compare from create_current_estimation_prerequisites() as part of #173/#184.

This includes Flash BEMs.

There's a large commented-out section which should be removed or implemented.

Contexts:

    # Computing the 'BEM' surfaces (needed for coregistration to work)
    for participant in list_of_participants:
        #        # andy is using:
        #        https://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing
        #        # todo -  AT has used the commandline version to create the BEMSs: do and then compare
        #
        #        if mri_structural_type == 'T1':
        #            mne.bem.make_watershed_bem(  # for T1; for FLASH, use make_flash_bem instead
        #                subject=participant,
        #                subjects_dir=mri_structurals_directory,
        #                copy=True,
        #                overwrite=True,
        #                show=True,
        #            )
        #
        #            mne.bem.make_scalp_surfaces(
        #                subject=participant,
        #                subjects_dir=mri_structurals_directory,
        #                no_decimate=True,
        #                force=True,
        #                overwrite=True,
        #            )
        #        elif mri_structural_type == 'Flash':
        #            # todo add & test flash
        #            # mne.bem.make_flash_bem().
        #            print("Flash not yet implemented.")