Re: [Freesurfer] Fwd: talairach_afd failed

2008-08-11 Thread Bruce Fischl
Hi Tim, can you tell us what form the data that you started with was in? Something is wrong with the direction cosines as tkmedit is displaying the brain upside-down (and it thinks that sagittal is horizontal). cheers, Bruce On Mon, 11 Aug 2008, [GB2312] ÀîÈÕ wrote: Hello: I am a new to

[Freesurfer] longitudinal stuff

2008-08-11 Thread Sky Raptentsetsang
Hi Bruce, From the processing that's been performed we're fairly certain that the issue is only with the -long script. So I just wanted to verify with you if I processed our many baseline subjects with version4 (cross-sectionally), while the -long script is being bug-fixed, I could simply star

Re: [Freesurfer] longitudinal stuff

2008-08-11 Thread Bruce Fischl
yes, it's only with -long, so you should be fine. On Mon, 11 Aug 2008, Sky Raptentsetsang wrote: Hi Bruce, From the processing that's been performed we're fairly certain that the issue is only with the -long script. So I just wanted to verify with you if I processed our many baseline subjec

[Freesurfer] cortical thickness at different locations

2008-08-11 Thread Al-Radaideh Ali
Hi, I managed to measure the cortical thickness for different subjects and to display their maps. Bu t I am not sure if I can measure the cortical thickness at some points in the cortex or at least the cortical thickness for some cortical regions. Best regards Ali Al-Radaideh PhD student S

[Freesurfer] cortical thickness for a ROI

2008-08-11 Thread Deniz KATIRCIOGLU
Hi, I want to learn if there exists a way of overlaying the "cortical thickness output" of "recon-all -*autorecon3*" stage with a ROI drawing (a 3D image file with non-zero values for ROI and zero for the remaining parts) performed in AFNI, so that we can better restrict the cortical thickness to o