[caret-users] constantly getting either Error in hind brain segmentation or segmentation fault

[Donna Dierker]

Hi Krishna,

The very first thing I would check is whether volume is centered near 
the anterior commissure (AC); if not, then failure of the sort you 
describe is one of many sorts of trouble that could be expected.

Analyze volumes are notorious for lacking origin information, so unless 
you explicitly set the origin to the AC, or this information was somehow 
embedded into the .hdr file (e.g., by SPM, then it's unlikely that it 
would be set properly by chance.

The attached capture shows a volume with the crosshairs located at the 
AC, along with the corresponding Volume: Edit Volume Attributes 
coordinates settings (i.e., origin setting).

As David suggests, if you upload the volume, I can rule this issue in or 
out.

Donna

On 02/24/2008 09:31 PM, David Van Essen wrote:
> Krishna,
>
> Caret's segmentation algorithm was originally generated for humans and 
> has not yet been fully customized for the macaque.  However, i would 
> not expect the behavior you describe.
>
> Try uploading your dataset to
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> Then let Donna Dierker (donna at brainvis.wustl.edu)  know the filename.  
> We may be able to debug from our side.
>
> David VE
>
> On Feb 23, 2008, at 6:33 PM, Krishna Srihasam wrote:
>
>> Hi Everyone,
>>
>> I am new to CARET . As a first project, I've been trying to segment a 
>> hemisphere in Caret 5.5 ( using the instructions from Caret 5 
>> tutorial : Segmentation, Flattening, and Registration).
>>
>> I have a 0.5mm isotropic anatomical image of a macaque in Analyze 
>> format and where ever I set the gray and white peaks I  get a 
>> hindbrain  segmentation error. If I disable disconnect hind brain I 
>> get a segmentation fault repeatedly.
>>
>> I have tried several different combinations of Gray and White peak 
>> values:
>>
>> Gray 34, White 38;
>> Gray 38, White 42;
>> Gray 43, White 46;
>> All these peak values give a Hindbrain Error and disabling Disconnect 
>> Hindbrain in SureFit Segmentation operations  gives me a segmentation 
>> fault.
>>
>> I tried using Gray 29, White 61 as peaks.  The segmentation went 
>> through when i set low threshold for hindbrain. But the output after 
>> this had most of occipital lobe missing.
>>
>> Any help me would be greatly appreciated.
>>
>> Thanks in advance.
>> regards,
>> Krishna.
>>
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>
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