Hi Sean - This works on our redhat centos 4 and centos 6. I can dig around some more, but it'll have to wait for Monday b/c I'll be out of the office the next couple of days.

As for your other question, the symlink part has been moved to the -prep step, specifically to make it easier to then run bedpostx outside of trac-all if needed.

a.y

On Wed, 6 Mar 2013, Sean Hatton wrote:

Hi Anastasia,

FSLVersion is there and does create the variable. I believe it is a syntax error, is the bracket suppose to be there? I have also noticed in the bedp section of trac-all that the "Create links named as expected by bedposts" section is removed - is this correct? Is it called elsewhere? I am running CentrOS 4 (64bit) on Ubuntu 12.04.

Cheers,

Sean

On 7/03/13 3:29 AM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:

...

Hi Sean - Thanks for trying out the new version!

From what I've seen, the file $FSLDIR/etc/fslversion exists in FSL 5 as well. Does it exist in your distribution?

a.y

On Wed, 6 Mar 2013, Sean Hatton wrote:

...

Hi all,

I have installed FreeSurfer 5.2 to take advantage of improvements in TRACULA. When I run trac-all -bedp I get an error:

.../freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected

Looking at the programming it is faulting on line 131 where it is checking the FSL version.

fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`)

Is this syntax correct? Is TRACULA compatible with FSL 5+?

Sean Hatton Brain and Mind Research Institute University of Sydney _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.