----- Forwarded Message ----- From: "Kushal Kapse" kkapse@mail.med.upenn.edu To: "Douglas N Greve" greve@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:45:14 AM Subject: Re: [Freesurfer] fMRI time series in surface space

run preprocessing of FS-FAST and do sampling on surface seems a good way to give a try....i am having confusions with directory structure for FS-FAST....Project/sess01/bold/001/f.nii

this is how my anatomical directory structure is originally: data/server/controls/14987_4589/ 14987_4589 is one of the subject in controls folder

for me i m confused with following thing around FS-FAST:

1- the "project" directory of FS-FAST is supposed to be within 14987_4589 directory???? because as per the tutorial, "sess01" directory is supposed to be subjects directory with bold folder containing functional runs of that subject called as "sess".......

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

Hi Everyone,

I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation.

My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space?

Many thanks, kk

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