You can also run the defect-seg program to help locate the places where the automatic topology fixer fixed defects. Run it with --help to get more info.
doug Bruce Fischl wrote: > Hi Nikolas > > the spiked by themselves aren't a problem, it's only if the surface isn't > accurately following the true gray/white boundary that you need to > intervene. It's a bit hard to tell in this case without being able to > scroll back and forth, but I suspect the segmentation is a bit inaccurate > in this region, which results in an incorrectly fixed topological defect. > If you want to, you can tar and gzip the entire subject dir and ftp it for > us and I'll take a look. > > cheers > Bruce > > On Tue, 1 Feb 2011, Nikolas > Borrel-Jensen wrote: > > >> Hi everybody. >> >> I have done all the auto-recon steps on my data, and I have some questions >> about the quality of the resulting images. I am aware of the troubleshooting >> tutorials, but I don't think these are covering my questions. >> >> I have uploaded some images of the surfaces and segmentations of a subject >> to http://freesurfer.nikolasborrel.com, and my question is about the spikes >> in the inflated surfaces. I have selected two spikes on the surface (green >> mark), one for each hemisphere, and have found the corresponding location in >> tkmedit in each of the three directions (s,h,c). >> >> For the spike in the left hemisphere (spike1_lh), I can't see what should be >> causing the spike. The segmentation looks correct. >> >> For the spike in the right hemisphere (spike_rh), it seems like there are >> many 'isles of segmentations, but are these causing the spike? If yes, how >> should these isles be corrected? >> >> Finally, how smooth is the inflated surface expected to be in a 'correct' >> case? Should a small amount of spikes be allowed, as long as they are not >> 'too severe'? >> >> I can upload more images if needed, thanks in advance! >> >> Kind regards >> Nikolas >> >> > _______________________________________________ > 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.
