subj1dir.tar.gz <http://freesurfer.nikolasborrel.com/subj1dir.tar.gz> in the outermost directory.
On Tue, Feb 1, 2011 at 5:28 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > 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. >>> >>> >>> >>
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