Jennifer,
BET has quite a number of options, it's likely doing a bad job since
you don't have the entire brain. Easy things to do is first just type
"bet" at the command line and get the numerous options
the -f option sometimes helps:
-f <f> fractional intensity threshold (0->1); default=0.5;
smaller values give larger brain outline estimates
probably even better would be
-c <x y z> centre-of-gravity (voxels not mm) of initial mesh surface.
you can use FSLVIEW, figure out a good starting point somewhere in the
middle of whatever brain you have, and then feed the x,y,z voxel
indexes from FSLVIEW into the BET command and see if that makes things
better.
DG
On Thu, Oct 2, 2008 at 11:36 AM, Perrin, Jennifer <[log in to unmask]> wrote:
> Hi Matt,
>
> Thanks for your response. I have tried to use the data but when I try to run BET on it to generate the no_dif_brain_mask it all goes wrong. Any suggestions on how to get around this issue?
>
> Thanks,
> Jennifer
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matt Glasser
> Sent: 02 October 2008 16:26
> To: [log in to unmask]
> Subject: Re: [FSL] FDT with limited slices
>
> Yes, it is possible.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Jennifer Perrin
> Sent: Thursday, October 02, 2008 7:44 AM
> To: [log in to unmask]
> Subject: [FSL] FDT with limited slices
>
> Hi,
>
> I was wondering if anyone has used FSL to process DTI data with a limited number of slices that do not span the entire brain? Is this possible?
>
> Any help would be greatly appreciated.
>
> Regards,
> Jennifer
>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
>
--
David A Gutman, M.D. Ph.D.
Department of Psychiatry & Behavioral Sciences
Emory University School of Medicine
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