[Freesurfer] Freesurfer and Gaussian Random field theory

Hello all I have computed and smoothed some thickness maps using Freesurfer. Next I would like to make inference using Gaussian Random Field theory (GRFT). How can I do it in Freesurfer? If it is not implemented in freesurfer , is there any thing that I have to take into account when applying an

Re: [Freesurfer] Freesurfer and Gaussian Random field theory

It is implemented, but I'm just not sure of the results. My results differ from those of Don Hagler from UCSD, and I'd like to track down the discrpancy before releasing it. You can always use the simlation approach (monte carlo or permutation). Use the --sim option to mri_glmfit followed mri_sur

[Freesurfer] error.. help?

after autorecon2, I sometimes get this error: preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: nan +- nan [10.0 --> -10.0] GM: nan +- nan [1000

[Freesurfer] parcellation problem

Hello, Group, After I manually removed the skull around cerebellum in the brainmask.mgz, the parcellation of the final inflated brain is totally messed up. Manual corrections of talairach transform and white matter surface did not mess up the parcellation. Could anyone tell me what is wrong?

Re: [Freesurfer] parcellation problem

can you send us an image to show what you mean by "completely messed up"? On Mon, 10 Sep 2007, Wang, Xin wrote: Hello, Group, After I manually removed the skull around cerebellum in the brainmask.mgz, the parcellation of the final inflated brain is totally messed up. Manual corrections of t

Re: [Freesurfer] variability

Hi Leila, I just wanted to let you know that I took a look at the parcellation snap shots you sent along (the rostro-lateral views of the frontal cortex) using V3 and V4 and it seems from these that at least for the superior, and middle frontal gyri, the V4 image is indeed more accurate (i.e. foll

[Freesurfer] running time v4

Hi, I would like to ask if there's already a benchmark performance of V4 compared to V3. In my environment V3 run a full recon-all in 21 hours full brain. How long I should expect the running time of V4 if I install it? Thanks, Pedro Paulo Oliveira Jr. ___

Re: [Freesurfer] running time v4

v4 should be comparable, except in cases where the old topology fixer fails (mris_fix_topology). In this case it runs the newer one (mris_topo_fixer), and everything downstream will take longer, maybe an additional 5-10 hours On Mon, 10 Sep 2007 [EMAIL PROTECTED] wrote: Hi, I would like to