On 09/26/2013 02:54 PM, Connor Lane wrote: > Great, thanks so much for the advice. Can you say a little about why > pre-whitening needs to be turned off? I thought the process operated on > each voxel's timeseries independently, so it wouldn't matter that the > spatial relations are jumbled in the surface format. This isn't the case? The FEAT prewhitening spatially smooths the autocorrelation function, and that will assume volumetric geometry. > > As far as writing a converter, my plan was to just modify the freesurfer > tool to reshape with a remainder. E.g. The modified tool would convert > between N x 1 x 1 x t surfaces and ceil(N/10) x 10 x 1 x t nifti files > (with a 10 - remainder vector of 0s in each volume). Would this work? (It > is a little beside the point, since I'm perfectly fine going straight to > fsaverage.) Yes, that should work, but you'll have to do the bookkeeping doug > > Connor > > On 9/26/13 2:14 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >> I would actually put the data straight onto fsaverage, smooth there, >> and do the FSL analysis there. You will need to put it on fsaverage >> eventually for group analysis, and you're better off doing that before >> doing the FEAT analysis. Remember to turn off temporal pre-whitening >> when running FEAT. >> >> For nifti1, there is no solution to the prime number of vertices >> problem. The problem is fixed in nifti2, so, assuming that FSL is >> reading nifti2, you could write a mgh to nifti2 converter. But I would >> do it on fsaverage anyway >> >> doug >> >> >> On 09/26/2013 01:53 PM, Connor Lane wrote: >>> Hmm, that's unfortunate. >>> >>> The reason I'm interested in this surface to nifti conversion is that >>> I'm trying to incorporate surface based pre-stats smoothing into my FSL >>> fMRI analysis stream. My strategy has been: preprocess with FSL --> map >>> to surface space and smooth --> convert mgh surface to nifti surface and >>> continue with FSL analysis. >>> >>> Do you think the surface smoothing benefits of this kind of stream >>> justify the trouble associated with either a) modifying the data as you >>> suggest every time this factoring issue shows up, or b) writing an mgh >>> <-> nifti utility that avoids the issue? >>> >>> Some other possible answers I've thought of are: >>> -After surface smoothing, map the functional data to fsaverage and >>> then convert back to nifti (since we know there's no factoring problem >>> with fsaverage). The drawback here is we never get to see statistics in >>> subject-specific space. >>> -Switch from FSL to FsFast, where surface smoothing is built in. >>> >>> Or maybe I should forget about surface based smoothing altogether, and >>> actually volumetric smoothing works just fine? >>> >>> I would really appreciate hearing your overall recommendation on this. >>> >>> Connor >>> >>> >>> >>> >> -- >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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. >> > >
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
