Emily Wrote:
-------------------------------------------------------
> I have tried to incorporate -init_xform
> AUTO_CENTER into my @auto_tlrc script because my
> centers were off by 40 mm when I ran the script
> without it. I am hoping it will help better align
> my GM masks onto an MNI template.
>
> This is the error message I get: Error: Anatomical
> dset
> pre../10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEA
> D not found
> […]
> Here is my script:
> foreach subject (10017)
>
> cd
> /home/AD/ebelleau/Desktop/nas/MRI/RumMR/FreeSurfer
> /${subject}/SUMA
>
> @auto_tlrc -base MNI_avg152T1.nii -input
> ${subject}.GM.nii -no_ss -rmode NN -init_xform
> AUTO_CENTER
> end

Hard to tell, but a few ideas:

- can you please paste the full output from @auto_tlrc?
- does the file '10017.GM.nii' exist in '/home/AD/ebelleau/Desktop/nas/MRI/RumMR/FreeSurfer/10017/SUMA'?