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.