He wants to convert to the ascii surface format, so he needs
mris_convert (which will read all our "volume" formats).
Bruce Fischl wrote:
use mri_convert, not mris_convert (the version with the "s" is for
surfaces, not volumes)
Bruce
On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote:
Hi, I downloaded the new version of mris_convert, but I'm having
trouble getting it to run successfully. When I start with bfloats it
says freadFloat: fread failed a bunch of times, and starting with a
COR file it says it can't allocate memory. How do I specify the mgh
format you recommended when I run mris_glm?
Thanks,
-Aaron-
________________________________
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Thursday, January 05, 2006 4:30 PM
To: Goldman, Aaron (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average thickness
I'd recommend using mgh instead of bfloat, but in either case you'd
do something like:
mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white
beta.asc
(or use beta.bhdr for bfloat).
The ability of mris_convert to read any "volume" format was added
fairly recently, so if yours does not do it, you can get a new one from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert
doug
Goldman, Aaron (NIH/NIMH) [F] wrote:
Great, thanks.
One more question. Doing it the mris_glm way, is there somehow I can
turn the beta files (bfloat) into ascii surface format? Thanks,
-Aaron-
________________________________
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Thursday, January 05, 2006 3:08 PM
To: Goldman, Aaron (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average thickness
The easiest way is probably to build an average subject
(make_average_subject). This will create ?h.thickness in the surf dir
which will be the average across the input subjects. You could also
use mris_glm with a design matrix of all 1s. The beta output will
then be the average thickness.
Goldman, Aaron (NIH/NIMH) [F] wrote:
Hi, I feel like I used to know this, but how do I make a map of
average thickness for a group of subjects? Also, is there a way I can
make a similar map showing the variance of thickness values? Thanks,
-Aaron-
Aaron L. Goldman
Post-Bacc IRTA
Genes, Cognition and Psychosis Program, NIMH
Building 10, Room 3C108
Phone: (301) 435-0944
Email: [EMAIL PROTECTED]
________________________________
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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