Estephan Moana wrote: > So what I need to do is to run the 1st level FEAT as usual for the FSL > pipeline, and repeat this analysis for FS with the only difference > been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab > of the FEAT GUI? yes > > Also, can you explain if this smoothing on the FEAT GUI is the 3D you > refer to? And how 2D smoothing is accomplished? Yes, this the 3D smoothing. 2D smoothing on the raw data is more difficult inside of feat. You'd have to use MC and then run mris_volsmooth (FS program) outside of FEAT, then pass FEAT the preprocessed data and tell it not to do MC or smoothing. > > Thank you. > > Estephan > > Douglas N Greve wrote: >> The example_func does not actually get smoothed, so smoothing itself >> will not affect the registration. 3D smoothing will smooth values >> from WM and CSF into gray and from across sulci into functionally >> distinct regions. For this reason we recommend not using 3D smoothing >> (or doing 2D smoothing on the surface). Unfortunately, this requires >> two different analyses. >> >> doug >> >> Estephan Moana wrote: >>> Hello all, I took the FS course last June at the OHBM in San >>> Francisco, and am now playing with it to get to know it better. One >>> of the slides on the talk about FSL-FS integration mentioned that >>> the input data (from FEAT) for the reg-feat2anat command should have >>> not been smoothed prior to registering to FS. >>> >>> Considering that FEAT 1st level analysis has a default of 5mm >>> spatial smoothing (and that's what I used on my data), it seems >>> counterintuitive to need to run a 1st level analysis again so the >>> output files are not spatially smoothed. >>> >>> So my questions are: 1) having the example_func file spatially >>> smoothed will necessarily hinder a proper registration to the FS >>> anatomical?; 2) if so, should I re-run all my FEAT 1st level >>> analysis without smoothing or is there any other way? >>> >>> I know this is quite a beginners question, but I could not find the >>> answers on the FS FAQ or the mailing list archives. I appreciate any >>> light on this. >>> >>> Regards, >>> >>> Estephan Moana, DDS >>> Graduate Student >>> Oral Biology PhD Program - Neurobiology track >>> School of Dentistry, UNC- Chapel Hill >>> 2140 Old Dental Building, CB# 7455 >>> Chapel Hill, NC 27599 >>> Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 >>> mo...@email.unc.edu <mailto:mo...@email.unc.edu> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
