You can use the GIFTI file directly in probtrackx. If you want to "visualise" the GIFTI file, then you need to use a surface viewer like Workbench. Alternatively, you can resample the surface file onto voxels using surf2volume, which will make up a NIFTI file that you can view with FSLview.

On 27 Sep 2013, at 17:12, Stefano Delli Pizzi <[log in to unmask]> wrote:

Thanks Saad.

A last question (hopefully). I have obtained a GII file. How can I trasfom it to NII.GZ? And I should apply surf2surf command?

Stefano

----Messaggio originale----
Da: [log in to unmask]
Data: 27-set-2013 17.37
A: <[log in to unmask]>
Ogg: Re: [FSL] Where are and what are the input surface for label2surf

Hi

I've updated the wiki page to make this clearer (hopefully). See https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Label_files

Cheers,
Saad.

On 27 Sep 2013, at 16:23, Stefano <[log in to unmask]> wrote:

Hi list,

I'd like to transform cortical label form FS to FSL.

I'm running this command:

label2surf -s <surface> -o <outputsurface> -l <labels>

      -s,--surf       input surface
      -o,--out        output surface
      -l,--labels     ascii list of label files

I have .label files previously created with mri_annotatiion2label, but where are and what are the input surface?

I have ask an help to FS list but they have the same difficult to understand this command.

Thanks,

Stefano

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi