wrongs when using @SUMA_Make_Spec_FS

AFNI Message Board
1

Dear AFNI experts:
I’m trying to convert FreeSurfer surfaces to afni, however there are something wrongs in this process. I tried to download a new FreeSurfer license but I still encountered the same problem.

The code I used in Freesurfer as follow:

export FREESURFER_HOME=~/Downloads/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export path_p_ss=~/Downloads/T1/sub-001
export ss_id=$path_p_ss:t
recon-all
-all
-sd $path_p_ss
-subjid sub-001
-i $path_p_ss/sub-001.nii

It said nothing wrong when running this program.
And the code I used to convert FreeSurfer surfaces to afni is that:

@SUMA_Make_Spec_FS
-NIFTI
-fspath $path_p_ss/sub-001
-sid $ss_id

Here is the error in this program:

writing to /home/p1/Downloads/T1/sub-001/sub-001/./SUMA/wm.seg.nii…
– running ‘mris_convert lh.smoothwm lh.smoothwm.asc’
Saving lh.smoothwm.asc as a surface
Error ConvertSurface: volume /home/p1/Downloads/T1/sub-001/sub-001/./SUMA//home/p1/Downloads/T1/sub-001:t_SurfVol.nii not found.
failure: could not create surface lh.smoothwm.gii

→ is your FreeSurfer license installed?
program failure: exiting…

2

To be sure, what does “afni -ver” show?

  • rick
3

Hello:
Thanks for your reply. When I keyed “afni -ver” to the afni, it showed that “Precompiled binary linux_ubuntu_16_64: Nov 22 2019 (Version AFNI_19.3.14 ‘Nero’)”

4

Nothing is leaping out at me. Would you please (remove the SUMA directory and) run it again, but include the option, “-debug 2”?

The output can be sent via email (click on my name), or I can PM you with upload instructions if you prefer.

Would that be okay?

Thanks,

  • rick
5

Thanks you so much. I will run it again and send the output to your email! thanks again!