Hi Colin, I'm not familiar with CARET, and I don't think that any of the
other FS developers are either. Maybe contact the wash u guys?
doug
On 12/27/13 12:54 PM, Colin Reveley wrote:
Hi - I actually sent this a couple of weeks back, but only just
noticed it was bounced back because I used the wrong address.
Happy new year!
Date: Sat, 14 Dec 2013 09:57:27 +0000
Subject: import from CARET
Hi -
If one has a surface that is aligned to a volume in CARET, is it
possible (or rather, is there a general procedure) to export the
volume and the surface into freesurfer?
The volume in CARET won't be conformed. It's header will define the
origin such that CARET interprets a specific voxel/coordinate as the
anterior commisure.
The surface will be aligned to the volume in the sense that it's
co-ordinates work with respect to that header/origin.
What I need to do is run mri_convert -c to conform the volume, and
then convert the surface to freesurfer format in such a way that it's
now aligned to the conformed volume in freesurfer.
Then I'd do some stuff (refine the surface) in freesurfer, and export
the surface back to CARET.
That's the general issue. Details include: the surface will need to be
transformed so that it appears to freesurfer to be 1mm data, and the
volume will have it's header changed so that it claims 1mm voxels (the
data is higher resolution than 1mm). that should be fine.
Also, there will be no ?h.orig surface, and the mesh is arbitrary wrt
the MRI data (not derived from it in any way). I don't know if that
matters.
The problem can be considered as finding the inverse of Van Essen's
Freesurfer to F99 pipeline. Pretty much.
It's some scaling, translating, conforming and format conversions.
connectome workbench, FS, CARET, FSL, MATLAB whatever are all
relevant/involved tools
hope can help
Colin Reveley
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