you can use mris_fwhm with the mask option. Just give it a maks of the places that are NOT NaNs doug
On 05/21/2013 09:37 AM, Glen Lee wrote: > Inline image 1 > > > Hi freesurfer experts, > > I'm dealing with an issue with smoothing on surface data that > unfortunately contain 'NaN' in the ventral temporal region (which > is a region that we are interested in). > > This may be due to the slab data acquisition, where the bottom of > the slice meant to be at the bottom of the tomporal lobe for every > subject. Apparently, we didn't quite succeed in this as we saw > missing data points that are filled with 'NaN' during 2D > reconstruction in some subjects' 2D data. > > In the cartoon above, the yellow color depicts vertices with 'NaN' > in the ventral temporal region , and you can easily see how this > is affected by smoothing (4mm FWHM), such that a large swath of > ventral regions have NaNs after smoothing. > > I've tried smoothing both with and without --cortex flag, but the > results were the same regardless. > > So, the best bet would be masking out those NaN vertices before > smoothing and I wonder if there is any way of doing it in freesurfer. > Otherwise, I may need to consider smoothing outside of the > freesurfer using Matlab (but I have no experience about this > approach). > > If anyone has previously dealt with this issue (hope I'm not the > only one) and know how to get around with it either inside or > outside of the freesurfer, please help me. > -Glen > > > > > > > > > _______________________________________________ > 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: 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 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.
