Hi
You might want to have a look at the latest FDT documentation under "surface tracking". You will find some useful instructions on how to take a volume from the freesurfer conformed space into diffusion space (1. Registering FreeSurfer conformed structural space to diffusion space)
Cheers,
Saad.
On 18 May 2010, at 03:06, Matt Glasser wrote:
> As more recent discussions have covered, using a white matter mask as
> nodif_brain_mask was a hack that is not optimal. It is better to use the
> inverse of the white matter as the stop mask (use fslmaths <wmmask> -sub 1
> -mul -1 <invwmmask> to generate, use the flag --stop= in probtrackx).
>
> As for creating a NIFTI file white matter mask with the same dimensions and
> orientation as your original structural image with FreeSurfer, this should
> be easy to do. You might try asking that on the FreeSurfer list, as I
> convert my FreeSurfer data to Caret formats before doing stuff like this
> (which is hardly necessary in your case) so I don't actually know the
> command to do this in FreeSurfer. As far as FSL goes, once you have the
> white matter mask in structural space, you will need to provide a
> transformation matrix between structural and diffusion space, and your seeds
> will need to be in structural space to use this method. Otherwise, if your
> seeds are in diffusion space, you will need to transform the mask into
> diffusion space first, because the --stop mask needs to be in the same space
> as the seed mask.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Theodor R?ber
> Sent: Monday, May 17, 2010 6:15 PM
> To: [log in to unmask]
> Subject: [FSL] white matter mask - Freesurfer
>
> 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
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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