[caret-users] To all,

David Van Essen vanessen at brainvis.wustl.edu
Tue Aug 23 18:41:21 CDT 2005


Joe,

You can have many topo files loaded at one time, and each coord file  
can be associated with its own topo file.  If things don't look right,  
then use Surface: Topology: Assign Topology to Surface to make sure you  
have the desired matchup (e.g., cut topo for FLAT map).  I'm guessing  
this pairing got out of whack in your data set.

David


On Aug 23, 2005, at 6:21 PM, Joe Munson wrote:

> Dr. Van Essen,
>
> Thank you! The bordercolor file seems to be successful. However, I  
> double-checked my CLOSED and CUT .topo files. They were loaded when I  
> took the screenshot of the flat surface.  I'm resegmenting my volume,  
> so I don't think it is an issue for me anymore.  However, it may be  
> nice to figure out the cause of it for future reference.  I can still  
> load up the distorted volume if you would like to pursue the problem  
> further.  If it happens again, I'll be in touch.
>
> Thanks again,
> Joe
>
> Joseph Munson
> Maryland Psychiatric Research Center
> Functional Neuroimaging Laboratory
> Syshelp
> x7105
> 410-206-5139
>
>>>> vanessen at brainvis.wustl.edu 8/23/2005 6:53 PM >>>
> Joe,
>
> If you're doing spherical registration to the PALS atlas, then the
> bordercolor file you want should be the following one that can be
> downloaded from SumsDB:
>
> ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor
> http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=5993911
>
> If that doesn't work, then I'm puzzled.  The next step would be to
> click on any borders that aren't properly colored, and see what their
> name is in the ID window report.  Then you can (i) add new border
> colors of your own using Layers: Borders: edit border colors; (ii)
> change the names of your borders using Layers: Borders: edit border
> Attributes; or (iii)  email back to us with a more precise articulation
> of what the problem is and why the first two options didn't work.
>
> Donna's explanation about the topology file seems likely to be on
> target.
>
> David VE
>
> On Aug 23, 2005, at 3:29 PM, Joe Munson wrote:
>
>> Donna,
>>
>> I'm using v5.3.  You may be right about deselecting the other .topo
>> file.  I'll double check and get back to you.
>>
>> I did try to load both of the bordercolor files included in the
>> PALS-B12 set, but to no avail.  Is there one that you use, that you
>> could send me?  I'm working on the right hemisphere (PALS-B12).
>>
>> Thanks Donna,
>> Joe
>>
>> Joseph Munson
>> Maryland Psychiatric Research Center
>> Functional Neuroimaging Laboratory
>> Syshelp
>> x7105
>> 410-206-5139
>>>>> donna at brainvis.wustl.edu 08/23/05 3:42 PM >>>
>> Hi Joseph,
>>
>> Which version of Caret are you running?
>>
>> Your capture looks like you have only the CLOSED topo file loaded, but
>> the current version of Caret should have the CUT topo selected by
>> default.  Did you deselect the CUT topo?
>>
>> I believe the bordercolors used during flattening are generated
>> automatically, but the ones you use during registration are not.  When
>> drawing registration borders, I always navigate to my atlas target
>> directory and load the bordercolor file found there.
>>
>> Donna
>>
>> On 08/23/2005 02:34 PM, Joe Munson wrote:
>>
>>> To all,
>>>
>>> After generating an aligned flat surface (and save), I exit Caret.
>>> When I return, the flat surface appears as it does in the attached
>>> .jpeg file.  It seems as if the borders have distorted the image.
>>> Any reason as to why this happens?
>>>
>>> Also, when/how is the .bordercolor file created?  Is the Draw Border
>>> dialog supposed to prompt me for color selection?
>>>
>>> Help!
>>>
>>> Joseph Munson
>>> Maryland Psychiatric Research Center
>>> Functional Neuroimaging Laboratory
>>> Syshelp
>>> x7105
>>> 410-206-5139
>>>
>>>
>>>
>>>
>>> --------------------------------------------------------------------- 
>>> -
>>> --
>>>
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>>> -
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>>>
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>>>
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>>
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