Re: [caret-users] Cutting handles?

2015-05-21 Thread Bonnie Alexander
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=7052056dir_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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Re: [caret-users] Cutting handles?

2015-04-29 Thread John Harwell
Hi Bonnie,

The surface cuts are intended for use on a flat surface.

It is best to remove all handles in the segmentation volume prior to generating 
a surface.  There are several modes for editing segmentation voxels that 
include both adding voxels (filing the handle) and removing voxels (essentially 
cutting the handle).

* Use Volume Menu-Segmentation-Find Handles to automatically identify handles 
in the segmentation volume.
* Use Volume Menu-Segmentation-Edit Voxels  to edit segmentation voxels to 
repair handles.
* Use Volume Menu-Segmentation-Topology Report to help verify handles have 
been removed.
* Surface Menu-Topology-Correct Fiducial Surface Topology can remove handles 
from a surface.  However, there is the possibility of undesired changes to the 
surface especially when there are large handles.  

These items may be helpful:

*   http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Segmentation 
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Segmentation
*   
http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf
 
http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf

John Harwell

 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.
 
  http://www.mcri.edu.au/
 
 
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