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-

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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-

 

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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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-- 

Douglas N. Greve, Ph.D.

MGH-NMR Center

greve@nmr.mgh.harvard.edu

Phone Number: 617-724-2358 

Fax: 617-726-7422

-- 

Douglas N. Greve, Ph.D.

MGH-NMR Center

greve@nmr.mgh.harvard.edu

Phone Number: 617-724-2358 

Fax: 617-726-7422

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422