[caret-users] Brain extraction; F6 segmentation
Donna Dierker
donna at brainvis.wustl.edu
Thu Jul 17 16:17:46 CDT 2008
Hamied,
If you haven't already extracted the F6 with BrainSuite, Tom Malone
(Snyder Lab) located the BET output with help from Gaurav Patel. This
volume, plus the GM and WM segmentations from FAST are here:
http://brainmap.wustl.edu/pub/donna/WUSTL/SNYDER/MacaqueF6_BET.zip
login pub
password download
(I considered putting them in sumsdb in the same directory as DVE used
below, but decided things were already crowded there; I'll confer with
DVE when he returns next week.)
The volumes are in NIfTI format (both nii and hdr forms) with the origin
set to match the Macaque.F6.LR.nii.gz volume included in DVE's dataset
below.
Donna
On 07/17/2008 12:19 AM, David Van Essen wrote:
> 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
> <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
> <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 <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
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >
>> ------------------------------------------------------------------------
>> >>> _______________________________________________
>> >>> caret-users mailing list
>> >>> caret-users at brainvis.wustl.edu
>> <mailto:caret-users at brainvis.wustl.edu>
>> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>> >>>
>> >> _______________________________________________
>> >> caret-users mailing list
>> >> caret-users at brainvis.wustl.edu
>> <mailto:caret-users at brainvis.wustl.edu>
>> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>> >
>>
>> --
>>
>> -------------------------
>>
>> 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
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> <mailto:caret-users at brainvis.wustl.edu>
>> 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
>> =====================
>> This e-mail contains CONFIDENTIAL INFORMATION which may contain
>> PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY
>> PRIVILEGED and which is intended only for the use of the
>> individual or entity named above. If the reader of the e-mail is
>> not the intended recipient or the employee or agent responsible
>> for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and
>> privileged information. Any unauthorized use, disclosure, copying
>> or the taking of any action in reliance on the contents of this
>> information is strictly prohibited and may be unlawful. If you
>> have received this e-mail unintentionally, please immediately
>> notify the sender via telephone at (773) 406 2464 or email.
>>
>>
>>
>>
>> --
>> 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
>> and which is intended only for the use of the individual or entity
>> named above. If the reader of the e-mail is not the intended
>> recipient or the employee or agent responsible for delivering it to
>> the intended recipient, you are hereby notified that you are in
>> possession of confidential and privileged information. Any
>> unauthorized use, disclosure, copying or the taking of any action in
>> reliance on the contents of this information is strictly prohibited
>> and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone
>> at (773) 406 2464 or email.
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu <mailto:caret-users at brainvis.wustl.edu>
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
More information about the caret-users
mailing list