Hi Theodor,
you should be able to use mris_fill to create the interior of the white
matter surface. If you specify the output volume as having the extension
.nii (or .nii.gz) it will be written in nifti format.
cheers,
Bruce
On Tue, 18 May 2010, Theodor R?ber
wrote:
> Dear FSL experts,
>
> I am trying to track the Pyramidal Tract in healhty subjects, and found
> fibers escaping the brain as well as fibers in areas with very low FA values.
> Going through several discussions in the FSL archive, I surmised that the
> best way to get rid of these unwanted fibers would be a Freesurfer-generated
> white matter mask to be used as nodif_brain_mask. Consequently, I generated a
> few white matter masks with Freesurfer and found that these masks were not
> only in a different space, but also has a different x-y-z orientation from
> the normalized dti_FA. What steps are necessary to turn the Freesurfer output
> into a FSL-FDT compatible white matter mask?
>
> Thank you very much for in advance. Your help will be greatly appreciated.
>
> Best,
>
> Theodor
>
>
>
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