[Freesurfer] inspecting images

Dear freesurfer users, I am a beginner in freesurfer. I have run the recon-all command for all my images, but in some of them the program aborted before completing (and even if I try to re-run recon-all). After that, inspecting the segmentation with tkmedit and tksurfer, many images have smal

Re: [Freesurfer] Intensity Problem

Hi matt Does the parcellation look correct? If so you might be ok if you stay away from the affected regions. It's hard to tell from one slice. Cheers Bruce On Mar 3, 2011, at 9:47 PM, Matt Russell wrote: > Dear FreeSurfer Experts, > > I'm currently working with a data set that seems to have

Re: [Freesurfer] inspecting images

Hi Alfredo It depends on why it aborted. Can you send us the error message you get? Cheers Bruce On Mar 4, 2011, at 8:25 AM, Alfredo Damasceno wrote: > Dear freesurfer users, > > > I am a beginner in freesurfer. I have run the recon-all command for all my > images, but in some of them the

Re: [Freesurfer] Counting Gyri

mris_curvature -max -w /lh.white will write out the max curvature at each vertex to a file named lh.white.max. Load this into tksurfer as a using the file->load curvature menu. You can then create a path in tksurfer by clicking on two end points, and type plot_curv 0 at the tcl (%) prompt. T

Re: [Freesurfer] DODS and DOSS

Hi Chris, There really shouldn't be a "thickness-age correlation group difference" result with the DOSS model. I have FS 4.1 (rather than 5.0 on my system) but running an analogous model, I see that I do indeed get a verbal "Description" for such a contrast. However, if I compare that to the "th

[Freesurfer] BBRegister mincost and B0 Masking

Hey Doug, When using the bbregister feature to mask areas with b0 distortion, I find noticeably lower registration cost values (as revealed by the first number in the .mincost file that gets generated). When this number is calculated, does it take into account the registration in the areas affect