search

nih-megcore / nih_to_mne

General functions for NIH data to work with MNE python
Other
2 stars 3 forks source link

Is Freesurfer required to get to BIDS #5

Open jstout211 opened 2 years ago

jstout211 commented 2 years ago

Currently the BIDS anatomical locations (NAS,LPA,RPA) are created on the Freesurfer MRI according to the directions on the mne_bids website. This requires creating a freesurfer import and T1.mgz reconstruction. This may be unecessary and can take some time (even though the skullstrip is avoided).

Investigate if there is a more direct way to go from BRIK or nii directly to voxelwise fiducial locations in anatomy json

jstout211 commented 2 years ago

Possibly use this command: mne.channels.make_dig_montage

    landmarks = mne.channels.make_dig_montage(
            lpa=spm_fids['lpa'],     #<< this is from the meg_fiducials_extract package - just fids in voxel space
            nasion=spm_fids['nas'],
            rpa=spm_fids['rpa'],
            coord_frame='mri_voxel')

    t1w_bids_path = write_anat(
        image=t1_fname,  # path to the MRI scan
        bids_path=t1w_bids_path,
        landmarks=landmarks,  # the landmarks in MRI voxel space
        verbose=True  # this will print out the sidecar file
    )
jstout211 commented 2 years ago

Check code for the camcan conversion - this should work without needing an FS import. Just provide the landmarks.

Need to confirm AFNI registered are accounted for or recut to orthogonal space before voxel entries are used.