Hi Elsie,
Yes Caret5 can read FreeSurfer files. You will need to know if the
file is ASCII (usually ends with "asc") or binary. You will also need
to know if the file is a "patch" file which usually has "patch" in its
name. If the file is a patch file, you must open it AFTER opening a
non-patch file such as an "orig" file.
In Caret5:
* Select File Menu->Open Data File.
* Set the File Type to "Free Surfer Ascii Surface File" or "Free
Surfer Binary Surface File". Select your file and press the Open
Button.
On the command line, using caret_command (run caret_command -file-
convert for help information):
Convert the free surfer surface into closed topology and
fiducial
coordinate files. Create a spec file for a left cortex.
-file-convert -sc -is FSS lh.orig.asc -os CARET
fiducial.coord \
closed.topo FIDUCIAL CLOSED -spec file.spec -
struct LEFT
Convert the free surfer patch into cut topology and flat
coordinate files. Create or add to the spec file as left
cortex.
Write the coord and topo files in text format.
-file-convert -sc -is FSP lh.oc.flat.asc lh.orig.asc \
-os CARET flat.coord cut.topo FLAT CUT -spec
file.spec \
-struct LEFT -outtext
By the way, there is a committee (GIFTI, www.nitrc.org/projects/gifti)
that has developed a common surface file format for neuroimaging file
formats. Both Caret and FreeSurfer are part of this committee. In
the not too distant future you, and others, should be able to use the
GIFTI format for your data and move between different neuroimaging
software applications without having to do any file format conversion.
-----------------------------------
John Harwell
[email protected]
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave Box 8108
Saint Louis, MO 63110
On Nov 25, 2009, at 10:34 AM, Dickinson, Annelise (NIH/NIMH) [F] wrote:
> Hello,
>
> Sorry in advance if the answer to this question is already up
> somewhere!
>
> I was just wondering if there is any way to import flat maps made in
> Freesurfer into Caret for viewing and editing? If so, how would this
> process be carried out?
>
> Please let me know, thanks so much and happy Thanksgiving!
>
> Best,
>
> Elsie
>
> *****************************************************
> Annelise Dickinson
> Post-Bac IRTA
> Laboratory of Brain and Cognition, NIMH/NIH/DHHS
> Building 10, Room 4C212
> 10 CENTER DR MSC 1366
> BETHESDA MD 20892-1366
> *****************************************************
> Phone: (301) 435-4941
> FAX: (301) 402-0921
> E-Mail : [email protected]
>
> _______________________________________________
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>
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