Hi - yes, if you can't get BET to give you what you want then you
still may be able to get it to generate reasonable skull estimates
(note that this needs to be an image of the external skull surface
only). Assuming that you can get images ready:
A
A_brain
A_brain_mask
A_brain_skull
Then you can change the following lines in the $FSLDIR/bin/siena
script (just take a local copy and edit and run that):
change
${FSLDIR}/bin/imcp $Ao ${outdir}/A
to
${FSLDIR}/bin/imcp $Ao ${outdir}/A
${FSLDIR}/bin/imcp ${Ao}_brain ${outdir}/A_brain
${FSLDIR}/bin/imcp ${Ao}_brain_mask ${outdir}/A_brain_mask
${FSLDIR}/bin/imcp ${Ao}_brain_skull ${outdir}/A_brain_skull
likewise for:
${FSLDIR}/bin/imcp $Bo ${outdir}/B
and then delete:
${FSLDIR}/bin/bet $A ${A}_brain -s -m $betopts >> report.siena
${FSLDIR}/bin/bet $B ${B}_brain -s -m $betopts >> report.siena
Cheers.
On 29 Nov 2007, at 16:32, MCLAREN, Donald wrote:
> Dear All,
>
> I'd like to use SIENA; however, BET seems to consistently fail on my
> subjects. A couple of quick questions:
> (1) I have images that have been deskulled (and could easily get
> images of the skulls);
> (2) I have a customized deskulled template (and could create a skulled
> template).
>
> Is there anyway to use SIENA with images that have been deskulled
> outside of the SIENA processing stream and to use a different
> template.
>
> Any thoughts would be appreciated.
>
> --
> 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.
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
|