[caret-users] Brain extraction

[Jochen Ditterich]

Hi Hamied,

Here is what I had just sent to somebody else who had expressed interest:

I used an Erosion Size of 2 and activated the "Automatic" check mark 
next to "limit" (default values for the remaining parameters). "Do All" 
would not work for me since BSE ended up choosing the wrong set of 
pixels for the brain. I therefore had to use single steps ("Next") until 
the state "Finish Brain" was reached and I had to select the appropriate 
set of pixels (in this case the second largest set) for the brain. I was 
also interested in the skull surface. Thus, when reaching the "Finished" 
state, I would click on "Skull & Scalp", activate "Compute thresholds", 
and select "Do All". After having inspected the surfaces using the 
Surface Display Properties, they can be saved using "Surface Save" in 
the "Surface View Properties" dialog.

I don't think that caret can use these surfaces by default (community, 
please correct me if I am wrong). The reason we needed them is that we 
currently develop an extension for caret for anatomical planning of 
recording chamber placement and electrode trajectories (and the surfaces 
are read by our additional software).

Best,

Jochen.

Hamied Haroon wrote:
> Dear Jochen,
> 
> Thanks very much for your message.
> 
> I've just registered for and downloaded BrainSuite2. Please could you
> share the parameters you used to extract the brain surface in F99UA1
> using BSE? This sounds promising.
> 
> Many thanks.
> 
> Best wishes,
>  
> Hamied
>  
> 
> -----Original Message-----
> From: caret-users-bounces at brainvis.wustl.edu
> [mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Jochen
> Ditterich
> Sent: 15 July 2008 18:52
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] Brain extraction
> 
> 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
>>>
>>>  
>>>
>>>  
>>>
>>>
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-- 

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

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