Hi Chris, the problem is that you do not have FSLDIR defined. Assuming
you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed
doug
On 11/06/2012 09:09 PM, Chris McNorgan wrote:
> Hi Doug,
>
> Attached are two plain-text files: fslog2.txt contains the redirected
> terminal outp
:32:30 CST 2012
> preproc-sess done
>
>
> Date: Mon, 05 Nov 2012 21:44:23 -0500
> From: Douglas Greve
> Subject: Re: [Freesurfer] fs-fast preprocessing resting state
> To:freesurfer@nmr.mgh.harvard.edu
> Message-ID:<50987987.7010...@nmr.mgh.harvard.edu>
> Content-Type: te
at Tue Nov 6 16:32:30 CST 2012
preproc-sess done
Date: Mon, 05 Nov 2012 21:44:23 -0500
From: Douglas Greve
Subject: Re: [Freesurfer] fs-fast preprocessing resting state
To:freesurfer@nmr.mgh.harvard.edu
Message-ID:<50987987.7010...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset
yes, that is probably best
cheers
Bruce
On Tue, 6 Nov 2012, Javeria Ali Hashmi wrote:
Hi there
I am running a program to generate a patient group specific template from T1
brains. I need to know which of the Free Surfer outputs will be best for
creating a patient brain template. The T1 images n
Hi there
I am running a program to generate a patient group specific template from
T1 brains. I need to know which of the Free Surfer outputs will be best for
creating a patient brain template. The T1 images need to be cleaned for
skull, meninges and neck. My guess is brain.finalsurfs.mgz.
thanks
Hi Chris, it should have been done with preproc-sess. What was your
preproc-sess command line? At some point, I had it set up so that it
would go to the bold directory by default unless you used "-fsd rest".
Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM,
Hello,
I'm getting started with freesurfer. I've played around with some of
the tutorial data for fs-fast
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was
able to follow along and successfully carry out the preprocessing
exercises (which sufficed for my purposes), which a
