Hi,

I have been running mri_reface on my local machine and the error its throwing is as follows (also in attachment):

(base) userName:~/refacing/mri_reface_docker$ sudo ./run_mri_reface_docker.sh /home/userName/refacing/raw/mri/anat/BRS2023000P3_T1W_3D_TFE_SENSE2_20230711112735_301.nii.gz /home/userName/refacing/processed/
-------------------------------------------------------
Running mri_reface, version 0.3.5
By: Christopher G. Schwarz schwarz.christopher@mayo.edu
Temp directory: /tmp/tp82fcd62e_e76b_4fb1_ab77_23e4f348bd51
Error using load_nii_hdr
Cannot find file
"/tmp/tmp.dtbCzt1Zzu/inputs/BRS2023000P3_T1W_3D_TFE_SENSE2_20230711112735_301.gz.nii".

Error in load_nii_noxform (line 13)

Error in ADIR_ReFace (line 322)

cp: cannot stat '/tmp/tmp.dtbCzt1Zzu/outputs/*': No such file or directory

• I did chmod 777 on all directories being accessed by the program including my /tmp/ directory to help facilitate it.


• The problem seems to be in the docker run line of code. I placed "echo" statements throughout the code to catch this. (as seen in attachment)
  
  
  
  • docker run --rm -ti --mount type=bind,src=$tmpdir,target=$tmpdir mri_reface run_mri_reface.>
  
  
  
  


• I do not understand why its trying to access my /tmp/ directory instead of just accessing the nifti from the path specified, espcially because /tmp/ and the path where I am running mri_reface is in a different place.

Any help would be welcomed,

Sun