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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.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Robert Austin Bruce Benn robertaustinbruce.benn@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?
thanks!
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