AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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February 23, 2020 08:16PM
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...
Subject Author Posted

wrongs when using @SUMA_Make_Spec_FS

wallypsy February 23, 2020 08:16PM

Re: wrongs when using @SUMA_Make_Spec_FS

rick reynolds February 23, 2020 10:45PM

Re: wrongs when using @SUMA_Make_Spec_FS

wallypsy February 24, 2020 06:34PM

Re: wrongs when using @SUMA_Make_Spec_FS

rick reynolds February 25, 2020 08:46AM

Re: wrongs when using @SUMA_Make_Spec_FS

wallypsy February 25, 2020 06:58PM