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

[Krishna Srihasam]

Hi,

I tried setting the AC as origin. It resulted in the volume getting 
segmented. But the output of the segmentation was really bad. I am 
uploading two scans (under the zip file Abe_scans.zip. It contains 
Abe_axial.[hdr, img] and Abe_saggital.[hdr,img]) on to the site. I tried 
segmenting right and left hemispheres separately on both the volumes and 
I am missing lot of sulci. Any help would be greatly appreciated.

regards,
krishna


Donna Dierker wrote:
> 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.
>>>
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>
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>
>
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