Hi, Stephanie-
Sorry for the delay in replying.
That is odd... I just ran FS on the Bootcamp subject (AFNI_data6/FT_analysis/FT/*anat*HEAD), and then (I have a different subject ID, but that shouldn't matter):
@SUMA_Make_Spec_FS \
-NIFTI \
-extra_annot_labels aparc.DKTatlas \
-sid sub-000 \
-fspath sub-000
... and I get *DKT* output files in the SUMA/ directory. That is, indeed, the correct way to run this command. (You didn't use "-fspath ..", because I guess you ran it from the directory made by recon-all, but that doesn't make a difference).
What version of FreeSurfer are you running?
If you run the command "-debug 2", it will be very verbose about what it is trying; and if you save all the text from the terminal, then I could take a look; to do that, you have to know if you are using: check with:
echo $0
... which should tell you bash/zsh or tcsh or something.
For bash or zsh, add the following to the end of your command line:
2>&1 | tee o.text_output_of_reconall.txt
... and for tcsh/csh, add the following:
|& tee o.text_output_of_reconall.txt
... and you can email me the output *.txt file.
--pt
Edited 1 time(s). Last edit at 03/17/2021 04:06PM by ptaylor.
