Hi Kushal, if they are already analyzed in FEAT, then you don't need to sample the time series, just the copes. Alternatively, you can sample the time series to the surface and analyze it in FEAT as long as you turn off the temporal whitening. If you want to resample the copes, you can use reg-feat2anat to create the registration file, then use feat2surf. We have a tutorial on interfacing with FEAT on-line. doug
On 05/24/2012 09:51 AM, Kushal Kapse wrote:
----- Forwarded Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Bruce Fischl"fischl@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 9:14:55 AM Subject: Re: [Freesurfer] fMRI time series in surface space
hi Bruce,
what if I have .feat files from FSL which have already been processed for functional analysis......how can i use transformation tools for going from 4D time series-functional to FS average template surface space for FSL output?.....
----- Original Message ----- From: "Bruce Fischl"fischl@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 8:50:43 AM Subject: Re: [Freesurfer] fMRI time series in surface space
Hi KK,
mri_vol2surf will take it to individual subject space, then mri_surf2surf can be used to bring it into average space if you want.
cheers Bruce
On Thu, 24 May 2012, 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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