[caret-users] Voxels size ??

Donna Hanlon donna at brainvis.wustl.edu
Mon Aug 22 08:13:47 CDT 2005


Dr. Giffard,

I forgot that Caret checks to make sure the voxdims are cubic 1mm.  If 
the algorithm refuses to proceed for this reason, you might try lying to 
Caret, by telling it the species is not human (select other).  If this 
doesn't work, then let me know.

If the eye fat or hindbrain disconnect fails, then turn off the 
offending option.  Turning off hindbrain disconnection causes Caret to 
crash, but John put a patched version here before he left for vacation:

http://brainvis.wustl.edu/pub/john/
login pub
password

Donna

On 08/22/2005 08:07 AM, Cyrille Giffard wrote:

>Dear Ms Hanlon,
>
>Thanks a lot for your answer.
>
>Regards
>
>Cyrille
>
>Quoting Donna Hanlon <donna at brainvis.wustl.edu>:
>
>  
>
>>Dear Dr. Giffard,
>>
>>I haven't tried this (on purpose, anyway), so I'm not sure, but here
>>are 
>>some guesses:
>>
>>* Minor deviations (e.g., cubic 0.9) are unlikely to cause trouble,
>>but 
>>0.5mm voxels (e.g., colin27) almost certainly will.  My sense is that
>>
>>somewhere around .75-.8mm things would start to turn ugly.
>>* Parts of the algorithm that disconnect eye fat (skull), hindbrain,
>>and 
>>contralateral hemisphere (corpus callossum cut) are most likely to be
>>
>>vulnerable to significant deviations from cubic 1mm voxel dimensions,
>>
>>because they use landmarks that are based on number of slices from
>>the 
>>anterior commissure along each axis.  (Someday, we hope to improve
>>the 
>>way these routines work.)
>>* Any resulting surface probably will need to be scaled (using
>>Surface: 
>>Transform) accordingly, so that they reflect true mm coordinates.  
>>Unless John Harwell has made a change I don't know about (he's on 
>>vacation for another week), then such scaling is required.
>>
>>Of course, you can always resample to cubic 1mm, but I assume you
>>have a 
>>good reason for wanting to do otherwise.  I'm sure you realize there
>>are 
>>ways to apply affine transforms to functional data (e.g., fMRI, CSM 
>>sites, or cells) you want to map onto the surface.
>>
>>Hope this helps,
>>
>>Donna
>>
>>On 08/22/2005 04:44 AM, Cyrille Giffard wrote:
>>
>>    
>>
>>>Dear all,
>>>
>>>Please could you tell me if it is possible to use human anatomical
>>>      
>>>
>>MRI 
>>    
>>
>>>with an isotropic voxel size lower than 1 mm3 ??
>>>
>>>Thanks in advance for your answer
>>>
>>>Cyrille Giffard
>>>
>>>Faculteit der Geneeskunde
>>>Laboratorium voor Neuro- en Psychofysiologie
>>>Campus Gasthuisberg
>>>Herestraat 49, B. 801, B-3000 LEUVEN (Belgium)
>>>Tel. +32 (0) 16 34 59 62
>>>_______________________________________________
>>>caret-users mailing list
>>>caret-users at brainvis.wustl.edu
>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>
>>> 
>>>
>>>      
>>>
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>>caret-users mailing list
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>>
>>    
>>
>
>
>Cyrille Giffard
>
>Faculteit der Geneeskunde
>Laboratorium voor Neuro- en Psychofysiologie
>Campus Gasthuisberg
>Herestraat 49, B. 801, B-3000 LEUVEN (Belgium)
>Tel. +32 (0) 16 34 59 62
>_______________________________________________
>caret-users mailing list
>caret-users at brainvis.wustl.edu
>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
>  
>




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