[caret-users] Brain extraction
Donna Dierker
donna at brainvis.wustl.edu
Wed Jul 16 09:43:12 CDT 2008
Hi Donald,
John Harwell is taking a vacation day today, and I'm unfamiliar with
BrainSuite's file format. But if BrainSuite is able to output one of
the following formats, Caret can read these: GIfTI, VTK, MNI OBJ,
Brainvoyager, BYU, Freesurfer, or STL.
GIfTI is the new standard that is to surfaces what NIfTI is for volumes.
Donna
On 07/15/2008 02:49 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 <mailto: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
> <mailto: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>
> > [mailto: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
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>
>
>
> --
> 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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