[caret-users] Brain extraction

[Jochen Ditterich]

Dear all,

I have been successful extracting the brain surface from the F99UA1 
volume (FullHead) using the automatic BSE algorithm implemented in 
BrainSuite2 (http://brainsuite.usc.edu/). Please let me know if you need 
help with setting up the parameters.

Best,

Jochen.

Donna Dierker wrote:
> Hi Hamied,
> 
> If you mean generate output similar to FSL's BET, then I'd say, no -- 
> not automatically.
> 
> In the case of F99UA12, the AFNI volume 
> Macaque.F99UA1.BOTH.SEGMENT.clean+orig.HEAD in the September 2006 
> tutorial 
> (http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030), 
> MACAQUE subdirectory, is in the ballpark.  It is a segmentation of both 
> hemispheres, but it aims for the cortical midthickness, rather than the 
> pial surface.  Also, the sulci are not filled in, the way a BET-style 
> mask would be.  Using utilities in Caret's Window: Caret Command Script 
> Builder: VOLUME DILATE and ERODE you could fill in the sulci, and then 
> zero out all voxels outside the resulting mask.
> 
> In the case of F6, I could find no segmentation volume, but this dataset 
> contains both fiducial coord files:
> 
> Macaque.F6.BOTH.VincentEtAl_Nature07_Fig2.73730.spec
> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6621813
> 
> You could project these surfaces to volumes; fill the cavity; and get a 
> segmentation not unlike the F99UA12 volume described above.  You'd need 
> to similarly dilate and erode to fill the sulci.
> 
> The situation looks similar for M3:  Fiducial surfaces exist and could 
> be back projected to volumes; dilated; eroded; and extra-mask voxels set 
> to zero.
> 
> With the exception of F99UA12, these volumes are affine means of 
> multiple subjects.  While you could segment them in Caret, I wouldn't 
> describe this process as automatic.  While you'd probably have a handle 
> or two to patch with F99UA12, your work would be far easier with that 
> volume, not only because it is a single subject, but also because the 
> quality is spectacular.  But why do it when it has been done, and the 
> segmentation volume is available?
> 
> How were you planning to use the extracted brains?
> 
> Donna
> 
> On 07/15/2008 09:50 AM, Hamied Haroon wrote:
>> Hi,
>>
>>  
>>
>> Is there any way in Caret (v5.502) to automatically extract the brain 
>> in the MRI volumes of the F99UA12, F6 and M3 macaque atlases, please?
>>
>>  
>>
>> Many thanks.
>>
>>  
>>
>> Best wishes,
>>
>>  
>>
>> Hamied
>>
>>  
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>   
> 
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users

-- 

-------------------------

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95618
USA

office: +1 (530) 754-5084
lab:    +1 (530) 754-6987
fax:    +1 (530) 757-8827