[caret-users] errors during segmentation

krishna chaluvadi chkaushik at gmail.com
Mon Aug 10 09:41:01 CDT 2009


Thanks Donna, that worked. I am getting another error saying " out of
memory, caret terminating". This happens while i am trying to segment the
volume. Kindly let me know what could be a possible solution
thanks
kaushik

On Thu, Aug 6, 2009 at 4:14 PM, Donna Dierker <donna at brainvis.wustl.edu>wrote:

> Kaushik,
>
> Something went horribly wrong when the volume got rescaled.  See attached
> capture.
>
> The omniscient Tim Coalson believes you started with an input volume that
> was long or float that got written as char or unsigned byte.  But the data
> was just truncated rather than scaled.
>
> I didn't see the original volume in our upload area, but the cropped volume
> was there.
>
> Try rescaling again on your end.
>
> Load the original anatomy volume.
>
> Select Volume: Edit volume attributes: Data: Rescale Voxels Values.
>
> Leave the current range alone.
>
> Next to output range, click Set and select Byte unsigned.
>
> Save the resulting rescaled volume by a different filename (not yet
> cropped, because you'll need the rescaled version for both hems).
>
> Donna
>
> On 08/06/2009 10:26 AM, krishna chaluvadi wrote:
>
>> Thanks Donna
>>
>> i have uploaded the original volume file, the cropped volume file and the
>> params file, kindly let me know if the problem(cropping or the
>> thresholding?). if one of these are the problems, kindly let me know the
>> correct peaks and limits that should be used
>>  the file names are
>>
>> original volume file
>> 20060407_114706IM-0001-0001EPILEPSYSEIZUREDISORDAnonymizeds007a1001A.nii.gz
>>
>> cropped volume file
>> Human.case10.R.Right_Hem+orig.nii.gz
>>
>> params file
>> Human.case10.R.params_file_22.params
>>
>> thanks
>> kaushik
>>
>> On Thu, Aug 6, 2009 at 7:33 AM, Donna Dierker <donna at brainvis.wustl.edu<mailto:
>> donna at brainvis.wustl.edu>> wrote:
>>
>>    Hi Kaushik,
>>
>>    Thank you for posting to caret-users; I really appreciate it.
>>    Asynchronous communication is a must right now, given very tight
>>    deadlines. But it is always preferrable.
>>
>>    The easiest way for me to diagnose your trouble is for you to upload
>>    your cropped *anatomy* volume here:
>>
>>    http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>>    It wouldn't hurt to upload the params file, if you did take a stab at
>>    setting the peaks. I can give you feedback there.
>>
>>    Three possible causes come to mind when I see this error:
>>
>>    * You didn't crop to left or right hemisphere.
>>
>>    * Your volume's origin is offset significantly from the AC.
>>
>>    * There is a bridge of eye fat connecting the eyeball to the cortex.
>>
>>    Looking at your volume will tell me immediately which, if any of these
>>    causes, is the culprit.
>>
>>    Donna
>>
>>    On 08/05/2009 02:43 PM, krishna chaluvadi wrote:
>>    >
>>    > Hello sir
>>    >
>>    > This is kaushik. I am a beginner with caret and have a few problems
>>    > during segmentation. I am having trouble with determining the
>>    > threshold limit for gray and white peaks. I am constantly
>>    getting the
>>    > error “ threshold limit reached before eye disconnected”. Kindly
>>    help
>>    > me on this
>>    >
>>    > thanks
>>    >
>>    >
>>
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