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June 09, 2021 05:17PM
Hi, Yash-

I suspect that there might be some spaces to the right of the continuation-of-line character "\" in one or more lines. If that happens, the shell won't keep on reading the next line as part of the current command, and then it will try to start reading the next line instead as a whole new command. That is why I think the following "Command not found"s occurred:
[Yashs-Air:~] yashkommula% -gltsym 'SYM: unpleasant -neutral' \
-gltsym: Command not found.
[Yashs-Air:~] yashkommula% -glt_label 2 U-N \
-glt_label: Command not found.
[Yashs-Air:~] yashkommula% -regress_motion_per_run \
? -regress_censor_motion 0.3 \
? -regress_censor_outliers 0.05 \
? -regress_3dD_stop \
? -regress_reml_exec \
? -regress_compute_fitts \
? -regress_make_ideal_sum sum_ideal.1D \
? -regress_est_blur_epits \
? -regress_est_blur_errts \
? -regress_run_clustsim no \
? -html_review_style pythonic \
? -execute
-regress_motion_per_run: Command not found.

You also have missing file errors:
** missing run 1 dataset: Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz
A lot of your input file paths are started with "Users" or "Volumes"---that looks like you are using a Mac, then. Typically, those are top level directories on a Mac, and those should each start with the following character to denote the start of an absolute path: "/". So, the above file should actually be input as:
/Users/yashkommula/Desktop/E4BH/AES101/EXERCISE/AES101EXpicviewing_shft.nii.gz

Try fixing those things, and see how it goes. Note that while you are trying to sort these issues out, you might want to leave out the "-execute" option from your afni_proc.py script---At the moment, the scripts is failing, but then some things are still trying to run. Once these issues are sorted, you could stick that "-execute" back in.

On a more "style" note: usually "/Users/" starts a path on your OS, and "/Volume/" starts one on an externally attached hard drive. You might want to have all your data on your OS together, so if you want to re-run things, it is easier to find all the pieces. Or, if you accidentally bump the external drive connector, that won't interrupt your processing. This isn't necessary, but just something I would probably do. It would also make it easier for you to move all your data later if you decide to process on another system. And scriptily, things will have more similar paths, making typos or bugs with paths less likely.

--pt
Subject Author Posted

errors running afni_proc.py

yk40_ June 09, 2021 04:37PM

Re: errors running afni_proc.py

ptaylor June 09, 2021 05:17PM

Re: errors running afni_proc.py

yk40_ June 10, 2021 08:04AM

Re: errors running afni_proc.py

ptaylor June 10, 2021 06:41PM

Re: errors running afni_proc.py

yk40_ June 24, 2021 02:13PM



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