Bill,

I'm runing your exact command with your exact filenames, and it's not reproducing your error (below). My best guess is something you-specific, like maybe you mistyped your input filename or your user doesn't have access to open that file. It doesn't seem to be an issue with your filenames, in your case.

Best,
Chris

$ time ./run_mri_reface_docker.sh test/t1_2.nii test_t1/ -imType T1
-------------------------------------------------------
Running mri_reface, version 0.3.5
By: Christopher G. Schwarz schwarz.christopher@mayo.edu
Temp directory: /tmp/tpaef8765c_ef9c_4d65_9334_d52aeb7ffcb8
Target file: /tmp/tmp.5YJ1Kh57kU/inputs/t1_2.nii
Output directory: /tmp/tmp.5YJ1Kh57kU/outputs
Target image type: T1
Template: /home/reface-user/.mcrCache9.12/mri_re0/mri_reface/images/MCALT_FaceTemplate_T1.nii
Face atlas: /home/reface-user/.mcrCache9.12/mri_re0/mri_reface/images/MCALT_FaceMask.nii
 
Calculating affine parameters to template. This will take some time.

[...]

Originally posted by wbbevis:

Originally posted by Christopher Schwarz:

Originally posted by Justin Kirby:

Thanks Chris, re-naming the files to use dashes instead of periods fixed the issue!

Thanks for reporting back! I'm glad it was an easy workaround. Please don't hesitate to reach out if you have more issues or feedback. If there's anything I can do to make mri_reface more usable for TCIA and similar projects, I would do my best to make that happen. 

Chris

Hello. I think I'm experiencing the same issue here: 

[panda_user@dom14044 mri_reface_docker]$ time ./run_mri_reface_docker.sh test/t1_2.nii test_t1/ -imType T1

Warning: ADIR_cp: the following warnings were produced:

> In ADIR_cp (line 171)

In ADIR_ReFace (line 271)

   cp: cannot open '/tmp/tmp.kufO28OHyS/inputs/t1_2.nii' for reading: Permission denied]

-------------------------------------------------------

Running mri_reface, version 0.3.5

By: Christopher G. Schwarz schwarz.christopher@mayo.edu

Temp directory: /tmp/tp74854768_777b_4317_bf48_f1b4b816c1a1

Error using load_nii_hdr

Cannot open file /tmp/tmp.kufO28OHyS/inputs/t1_2.nii.

 

Error in load_nii_noxform (line 13)

 

Error in ADIR_ReFace (line 322)

 

 

cp: cannot stat '/tmp/tmp.kufO28OHyS/outputs/*': No such file or directory

 

real 0m8.825s

user 0m0.017s

sys 0m0.033s

 

In my case, I can get pretty stripped down with the naming, but I'm still getting this ADIR_ReFace error. Oddly, this works on a T2 from the same session.

Any help would be much appreciated!

Thanks,

Bill