[Freesurfer] Visualizing individual ROI labels

2014-10-04 Thread Elissa McIntosh
Hello freesurfer experts, I am hoping that someone can tell me how I can create 3D representations of individual cortical ROIs (labels based on the Desikan/Killiany Atlas) to be used in figures. I'm trying to make figures that show the ROIs that I investigated (like this figure in Desikan et al.

[Freesurfer] order of edits and autorecon commands

2014-04-28 Thread Elissa McIntosh
This is a basic question about the process for manual edits and the autorecon commands. I am going to follow the recommended reconstruction page (on fs wiki) to make manual edits on my data. The page says that you can make all the manual edits at once. But my question is, how do you go about

[Freesurfer] freeview invalid drawable

2013-10-23 Thread Elissa McIntosh
Hi, When trying freeview command (see below) from the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the bert data too. What does invalid drawable mean?

[Freesurfer] tkmedit error message

2013-10-16 Thread Elissa McIntosh
Hello, I am a new freesurfer user. I tried to view subject data with tkmedit for the first time after the recon-all process finished without errors. Here is what I typed and the message I got: [ariana:~/Desktop/ELISSA_ THESIS/ATO] cmurphy% tkmedit ATO brainmask.mgz -aux T1.mgz -surfs -aseg Wed