[caret-users] Brain extraction; F6 segmentation

David Van Essen vanessen at brainvis.wustl.edu
Thu Jul 17 00:19:32 CDT 2008 

To all,

In case it is useful to anyone following this email thread, the  
macaque F6 segmentation volumes (in *.nii format, plus the standard- 
mesh surfaces) have now been uploaded to SumsDB and made publicly  
available in the following archive:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6684885&archive_name=Macaque.F6.BOTH.Std-MESH_Segment.73730.spec

in the directory  http://sumsdb.wustl.edu/sums/directory.do?id=6614663&dir_name=MACAQUE_F6

David


On Jul 15, 2008, at 2:49 PM, MCLAREN, Donald wrote:

> John, Donna, etc.
>
> Is it possible to import these surfaces into CARET?
>
> On Tue, Jul 15, 2008 at 2:48 PM, MCLAREN, Donald <mclaren.donald at gmail.com 
> > wrote:
> John, Donna, etc.
>
> Is it possible to import these surfaces into CARET?
>
>
> On Tue, Jul 15, 2008 at 2:17 PM, Jochen Ditterich <jd at shadlen.org>  
> wrote:
> 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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> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>>
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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
> _______________________________________________
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> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
>
> -- 
> Best Regards, Donald McLaren
> =====================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Tel: (773) 406 2464
> =====================
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>
>
> -- 
> Best Regards, Donald McLaren
> =====================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Tel: (773) 406 2464
> =====================
> This e-mail contains CONFIDENTIAL INFORMATION which may contain  
> PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED  
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