Hi
I believe these must be the pial surfaces (lh.pial and rh.pial) which have been converted into GIFTI using Freesurfer’s mrs_convert tool.
Cheers
Saad
> On 5 Jun 2019, at 13:43, Samantha Baldi <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> I am considering the possibility of using WM/GM boundary surfaces to constrain my tractography in order to avoid spurious connections, as it is suggested in the FDT practical.
> However, I am very much new to this and especially Freesurfer so I'm experiencing some probably very basic difficulties.
> It is not clear to me how you obtained the ?h.cort.nii/?h.cortex.gii that are included in the files for the practical. I performed recon-all and I do not have such output so I wondered which file did you use? ?h.white or ?h.pial?
> Could you provide the basic steps/command that are needed in order to obtain these files starting from the Freesurfer output?
>
> Thanks in advance,
>
> Best
>
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