[Freesurfer] Displaying cortical thickness

Hi, I would really appreciate a help (steps or a link to description) on how to display cortical thinning on an inflated surface. I ran a subject through recon-all -autorecon3 and now I would basically want to see, where (s)he has abnormal thickness of the cortex. Thanks a lot in advance, Mar

RE: [Freesurfer] Displaying cortical thickness

Martin, I'm working on this too. I think you may want to do a group analysis so the pointer is: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferGroupAnalysis The recon-all process should pass step 1, 2 and 3 and not just 3. So you should run: recon-all -all -s subjid Also you can use the file

Re: [Freesurfer] problems

Hi, Pedro Paulo Oliveira: Thank you for your answers. But, I'm a rookie of Linux. I don't know what do you mean and how to do that for the answer 2? Can you tell me detail and get me some command lines? Thank you again. 2007/10/4, Pedro Paulo Oliveira Jr <[EMAIL PROTECTED]>: > 1) Yes. mri

RE: [Freesurfer] problems

You can execute: cd /usr/lib ln -s libstd++.so.6 libstd++.so.5 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Feng-Xian Yan Sent: segunda-feira, 8 de outubro de 2007 10:27 To: Pedro Paulo Oliveira Jr Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Free

[Freesurfer] Question on fs-fast

I'm trying to use fs-fast to analysis the PET data, but found that the first level analysis is specially designed for fmri. Is there any way to use fs-fast to analysis the PET data? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] problems

Feng-Xian, If you have fedora core 4, then you should the centos4 build of freesurfer which is built against the libstdc++.so.6 libs, unlike the rh9 build of freesurfer, which it appears you are using, which is built against the libstdc++.so.5 libs. Nick > Hi, Pedro Paulo Oliveira: >Tha

[Freesurfer] preproc-sess failure on Mac

I'm trying to use freesurfer/fsfast on Mac Pro and found preproc-sess fails in mcparams2etreg. The problem seems actually in Mac version of MATLAB, which does not terminate properly when it finishes processing the piped code without an explicit 'exit' at the end of it (I asked Mathworks and

[Freesurfer] how to apply transformation into other dataset?

I have some functional data coregistered to MRI, is it possible to apply linear and nonlinear transformation that we got at MRI recon-all to those functional data? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] how to apply transformation into other dataset?

yes, I think mri_vol2vol will do this. cheers, Bruce On Mon, 8 Oct 2007, lan lin wrote: I have some functional data coregistered to MRI, is it possible to apply linear and nonlinear transformation that we got at MRI recon-all to those functional data?

Re: [Freesurfer] Displaying cortical thickness

Hi Martin, do you want to display an individual thickness map or do a group study? If the former, you can load the ?h.thickness file from the subject's surf directory using file->overlay->load overlay. If the latter, you want to use Doug's group analysis tools. cheers, Bruce On Mon, 8 Oct 2