Hi Alistair
This should now be explained better in the new FSL5 doc (released yesterday). Please have a look at the freesurfer section and let me know if you have issues.
saad
On 5 Sep 2012, at 04:23, Alistair Perry wrote:
> Hello FSL experts,
>
> I know this has been posted elsewhere with the original probtrackx.
>
> I am basically trying to create a surface file from the aseg+aparc.mgz cortical parcellation created when running recon-all. I wish to use this surface file as the seed reference file when performing probtrackx2.
>
> I have succeeded sucessfully in transforming the cortical parcellation into diffusion space, and have created a label file for it.
>
> However, I am having difficulty understanding converting the label file into ascii format, as required for probtrackx2. I am aware that you can convert a label file into ascii format using mri_convert, but you have to specify the lh.white surface file created when performing recon-all. This does not make sense to me for one this label file is not in diffusion space. Plus, why would I only specify one surface hemisphere when I have a label file that lists vertices across both hemispheres?
>
> In the end I am asking whether it is possible/and the best method in creating an ascii surface file of the whole cortical parcellation in diffusion space?
>
> Regards,
>
> Alistair
>
--
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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