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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