----- Forwarded Message ----- From: "Kushal Kapse" <kka...@mail.med.upenn.edu> To: "Douglas N Greve" <gr...@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" <gr...@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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
