Hi Hitoshi
I am afraid I don’t understand what the problem is. Could you try to rephrase please?
Thanks
Saad
> On 17 Mar 2016, at 05:39, Hitoshi Sasaki <[log in to unmask]> wrote:
>
> Dear Saad
>
> When I used .gii or .gii.nii.gz, in protbrackx2, results were different.
> Tracking ( using .gii.nii.gz file) only got fdt_paths.nii.gz.
> I wonder if nodif_brain_mask.nii.gz( in diffusion space) was not good, I don't know whether the way below was correct or wrong.
>
> To make a nodif_brain_mask_diffusion.nii.gz (-m,--mask Bet binary mask file in diffusion space) I used the following script.
>
> flirt -in $dti_subjects_dir/$D/bedpostx.bedpostX/nodif_brain_mask.nii.gz -ref $dti_subjects_dir/$D/bedpostx.bedpostX/nodif_brain.nii.gz -out $dti_subjects_dir/$D/bedpostx.bedpostX/nodif_brain_mask_diffusion.nii.gz -omat $dti_subjects_dir/$D/bedpostx.bedpostX/xfms/str2diff.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
>
> Is it correct?? struct2fa.mat is correct?
>
> and
>
> If I want to change surface from .gii to diffusion, Can I use flirt, freesurfer2fa.mat, nodif_brain??
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