[caret-users] Brain extraction

[Donna Dierker]

Hi Hamied,

This detail is helpful:  Yeah, registering a skull-intact source to a 
skull-stripped target hasn't worked well for me, either; no surprise, there.

Given that you are using a nonlinear method, the differences between 
source and target become more important.  You could try just using FSL's 
bet on F6.  This will leave brainstem, cerebellum, etc., whereas the 
surface-to-segmentation-to-mask route described below will exclude such 
non-cortical structures.  Does your brain-only MRI volume have these 
structures?

Like you, I would guess it's better to use F6 than F99UA12, for a 
fascicularis macaque.  Off-list, I'll copy some busy residents and grad 
students who may already have a BET version of the F6.

Donna


On 07/15/2008 11:20 AM, Hamied Haroon wrote:
> Hi Donna,
>
> Thanks so much for your kind reply.
>
> I'm actually particularly interested in the F6 volume. I want to
> non-linearly register the F6 MRI volume to a brain-only MRI volume I
> have of an ex-vivo Macaca fascicularis. I then want to apply the same
> non-linear warp to the cortical partitioning schemes available in Caret
> to spatially match them to my dataset. Non-linear registration of a
> brain-only volume to a whole-head volume doesn't work well, so that's
> why I need to extract the brain in the F6 MRI volume. I'm guessing that
> it's best to register the Caret atlas associated with the same species
> (M. fascicularis) as the dataset I have. Would you agree? Or would it be
> valid to use the F99UA12 dataset in this case?
>
> I look forward to hearing from you.
>
> 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 Donna
> Dierker
> Sent: 15 July 2008 17:01
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] Brain extraction
>
> 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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