Dear Christopher Schwarz,

It looks like I'm having similar issues to multiple other individuals in the thread and I am having trouble diagnosing the problem.

So far I have attempted:

1) used gunzip to convert my .nii.gz into .nii;

2) simplified input .nii file name;

3) placed the .nii and output directory files in the same directory as run_mri_reface_docker.sh

My current input (from the appropriate working directory) is as follows:

$ time ./run_mri_reface_docker.sh CHUM039.nii mri_reface_output/ -imType CT

The resulting output is as follows:

Error using ADIR_ReFace
File not found: C:/.../AppData/Local/Temp/tmp.p0YZ69tric/inputs/CHUM039.nii

cp: cannot stat '/tmp/tmp.p0YZ69tric/outputs/*': No such file or directory

real    0m21.212s
user    0m0.384s
sys     0m0.613s

I am unsure what additional steps I can take to help troubleshoot this issue and any assistance would be greatly appreciated. Thank you!

(I am more used to working with Python scripts so a lot of this is something I'm learning as I go; I do not know how to create a complete console output as referenced previously in this thread.)

Best,

Anthony Kang