Hi Krista,

Try using the following command:

tksurfer BV2 lh inflated -overlay $SUBJECTS_DIR/BV2/surf/lh.pial_lgi -fthresh 1

The error you got is because the overlay needs the full path to the pial_lgi file. Then, not all regions are coloured because the default minimum threshold is 2, and you want to set it at 1 to see whether everything want fine (fthresh option).

If it's just for quality check it should not be a problem to transfer your subjects from one platform to another.

Hope it helps,

Marie

On Feb 12, 2014, at 9:50 AM, krista kelly krista.kelly16@gmail.com wrote:

Hello,

I am trying to do local gyrification with freesurfer and am having trouble. I have the image processing toolbox and have set the path. I ran recon-all -s BV21 -localGI and it exited without errors. Yet, when I try to view it in tksurfer using tksurfer BV21 lh inflated -overlay lh.pial_lgi, I get this error: cannot find rh.pial_lgi (even though it is in the surfs folder). I can open the inflated brain in tksurfer and overlay lh.pial_lgi but there seems to be a problem where not all of the brain is colored in (please see attached pictures).

I'm wondering if someone can help me with this problem, it's happened on more than one participant. When checking through the terminal, I found this at the beginning of the processing:

INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

I initially did recon-all -all using a linux on a virtual machine, however there wasn't enough working memory to do all of my analyses using linux, so I transferred all of my data to a mac and did the quality checks, extracted roi data (aparcstats2table) and ran glm analyses (qdec) from there. Do you think that the problem lies in the fact that recon-all was originally ran in Linux? I'd rather not do the local gyrification in Linux as I do not have matlab on that machine.

Thanks! Krista <Screen Shot 2014-02-12 at 12.49.23 PM.png><Screen Shot 2014-02-12 at 12.49.18 PM.png>_______________________________________________ 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.