Hi Antonin that's a good point and something we probably need to fix.
Bruce On Fri, 24 Jul 2015, Antonin Skoch wrote: > Dear Kalyan, > > do you use standard pial surface reconstruction via T1 images, or optional > pial > surface refinement with T2/FLAIR images? > > I had similar problems with FLAIRpial surface refinement. The corrected pial > surface appeared jagged and some areas were artificially cut out (whereas they > were included in original woFLAIR.pial surface). By inspection of my data I > found > that these were areas with very high voxel intensity. By some reason my FLAIR > images have voxels with inexpectedly high signal (outlying values in the > intensity values histogram). I have solved the problem by increasing > nsigma_above > parameter in mris_make_surfaces from 3 to 8 (in several exceptional subjects > this > value had to be even higher). > > By the way - question to the experts - is there any option how to alter > nsigma_above parameter apart from directly editing recon-all script? I > suppose it > is not possible to do it via expert.options file since mris_make_surface is > called more times in processing stream. > > Regards, > > Antonin Skoch > _______________________________________________ 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.
