what did you call it? On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
> Thanks for the fast reply. I have uploaded the entire subject directory and > would appreciate if you could take a look. > > /Nikolas > > On Tue, Feb 1, 2011 at 3:17 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu>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 >>> >>> >> >> 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. >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
