[caret-users] Brain extraction

[Hamied Haroon]

Hi Donna,

Thanks very much for your reply.

Yes, my brain-only MRI volume does include brainstem, cerebellum,
thalamus, etc.

I'll have a go at BET-ing the F6 atlas but if someone at your place has
already done this then that would be awesome. I'm attempting to manually
extract the brain at the moment but the relatively low quality of the F6
MRI volume makes it quite difficult.

Many thanks for all your help.

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 17:39
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Brain extraction

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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