dcm2niix_afni gives out too many warning messages

I am converting dcm to nii files. My dcm files are PET images from Siemens HRRT scanner. Somehow dcm2niix_afni doesn’t recognize the name of manufactory in the header of dcm files, and gives out tons of warning messages (one warning each slice) like below:
Warning: Unknown Manufacturer CPS
Warning: Unknown Manufacturer CPS
…(thousands of repeated warnings)…
Warning: Unknown Manufacturer CPS
Warning: Unable to determine manufacturer (0008, 0070) so conversion is not tuned for vendor.

I wonder if there is a way to suppress these warning messages?

By the way, currently dcm2niix_afni only takes folder as dcm input, is it possible to make dcm2niix_afni take tar files as dcm input as well? Just my suggestion.


dcm2niix is maintained by Chris Rorden. You could open an issue here: https://github.com/rordenlab/dcm2niix though I suspect he will be of the opinion that it’s better to spew too many messages than too few. It is packaged with AFNI for everyone’s convenience as it is a very popular and useful tool.

Practically speaking, the solution is probably just for you to use grep to filter out those warnings. You could try this:

dcm2niix_afni MY_DIR | grep -v “Unknown Manufacturer”

which will only display lines that do not contain the substring “Unknown Manufacturer”

Lastly, dcm2niix is not designed to read compressed files, to my knowledge. The most common solution is to programatically or manually un-archive the dicom files and then run the program.