On Tue, Feb 1, 2011 at 5:28 PM, Bruce Fischl
<fischl@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 <fischl@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
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