Hi Jim, Donna and John,
Thanks very much for your replies. The segmentation I was working with did
contain fused sulci as you mention, and your feedback did clarify the process
for me. Much appreciated!
Bonnie.
________________________________________
From: caret-users-boun...@brainvis.wustl.edu
[caret-users-boun...@brainvis.wustl.edu] on behalf of Alexopoulos, Dimitrios
[alexopoulo...@kids.wustl.edu]
Sent: Thursday, April 30, 2015 1:45 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Cutting handles?
When generating our surfaces, we have never had to draw cuts. We simply modify
the volume segmentation until no handles are found by the automated Find
Handles' option or no topological errors are found after the surface
reconstruction using SureFit. Typically the handles we get are caused by fused
sulci that need to be opened.
Perhaps you can send a snapshot of the inflated surface showing the issue.
Jim
-----Original Message-----
From: caret-users-boun...@brainvis.wustl.edu
[mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
Sent: Wednesday, April 29, 2015 9:03 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Cutting handles?
Hi Bonnie,
With the cutting handles stuff, you are treading into territory I fear, so
can't help you there.
But with the term-12 atlas, I think you can just browse this paper:
Hill, J., Dierker, D., Neil, J., Inder, T., Knutsen, A., Harwell, J., Coalson,
T. and Van Essen, D. (2009) A surface-based analysis of hemispheric asymmetries
and folding of cerebral cortex in term-born human infants. J. Neuroscience
http://www.jneurosci.org/cgi/reprint/30/6/2268
... and then see which figure shows files you might want, and select a dataset
here:
http://sumsdb.wustl.edu:8081/sums/directory.do?id=7052056&dir_name=HILL_JNEUROSCIENCE_2010
Click the diskette shaped icon next to a particular dataset to download the zip
file containing the spec file and its contents.
Also search pubmed.org for Christopher Smyser and check out his papers. He
probably has some more current versions of the same atlas. He and the folks who
work for him are very helpful and knowledgeable.
Donna
On Apr 29, 2015, at 1:21 AM, Bonnie Alexander <bonnie.alexan...@mcri.edu.au>
wrote:
>
> Hi,
>
> I'm wondering whether there's an option to cut handles on a surface or volume
> rather than filling them? It appears the former is needed in some cases, but
> I haven't seen reference to it in the documentation. I tried using 'Draw
> Cuts' from the Surface menu, though when I use this on a .coord file it
> doesn't draw or cut, so I suspect I'm missing something here. Any suggestions
> on whether this is possible and how to go about it would be much appreciated.
>
> Also, I've been trying to locate the PALS-term12 atlas referred to in Hill et
> al. (2010), via SumsDB, though am as yet unable to find it. If someone could
> point me to this if it's still available, that would be great.
>
> Thanks,
>
> Bonnie.
>
>
>
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