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.kell...@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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
