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Were the images acquired with the animal in a funny position relative to 
humans?  That might be the issue.  I would convert DICOMs to NIFTI prior to 
FreeSurfer, make sure the image is oriented as RPI or LPI and that the labels 
match the brain (e.g. in a tool like FSLView) and then run FreeSurfer.


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Robert Austin Bruce 
Benn <robertaustinbruce.b...@cnic.es>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 13, 2019 at 7:06 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] c_ras for HCP compatibility

        External Email - Use Caution
Hi Y’all,

I was wondering if Y’all could tell me how c_ras is calculated in the x_form 
matrix for orig.mgz?

I’ve been using some animal brains, and the pipeline works very well at 
creating surfaces and aligning them to their coresponding image for freeview.
Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to 
remove the offset for use in wb_view.

The commands for applying the transforms work fine.
However I end up getting a surface that is either inverted, or perpendicular to 
the nifti volume in wb_view.

The animal image does have a large field of view, with a relatively small brain.
I think the cras matrix isn’t getting calculated correctly, but that the images 
I’m using may not have a standered cras so I may need to hack around that.

Could you explain to me how c_ras is calculated?
Also if I need to edit c_ras how would I go about doing it? is it derived from 
the q and s forms?


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