The command line is:
mris_glm --design $df --surfmeas thickness --hemi $h --trgsubj $ts --nsmooth 300 --beta beta.mgh --var var.mgh
And each column of the design file is:
subject_name 1
And then, when I try to run mris_convert -c beta.mgh beta.asc, it just gives me the usage instruction line. When I take out the -c, it does a segmentation fault.
Thanks,
-Aaron-
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From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, January 06, 2006 12:00 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness
what was your command-line? For mris_glm, specify --beta beta.mgh. btw, the rvar output will be the variance of the thickness.
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:greve@nmr.mgh.harvard.edu] 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:greve@nmr.mgh.harvard.edu] 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: aarong@mail.nih.gov
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