Separate MRI and CT pipeline and add Prep Pipeline
adam2392 opened this issue · comments
It would be nice to just run the freesurfer/fsl commands on MRI and CT be allowed separately.
To make sure all the data from dicoms, go through the same conversion step (e.g. BIDS first and rotation), add a PREP step that uses mne-bids to write_anat.
Also should perform rotation of the image to a hardcoded orientation. Similar to #8.
@TheBrainChain I believe, you suggested RAS?
@adam2392, I believe Freesurfer's normal output is LIP, but all the raw data we receive is in LPS. Since RAS is the neurological convention I would suggest that.