p.s. or you can just copy the relevant wm labels out of the
aparc+aseg.mgz (e.g. 2 and 41 are cerebral white matter from the
FreeSurferColorLUT.txt, but you probably want others such as brainstem
and cerebellar white matter)
On Tue, 18 May 2010, Bruce Fischl wrote:
> 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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