Issue running dcm2niix container: “Unable to find any DICOM images in /input (or subfolders 5 deep)”

[Filippo Manini]

Hello everyone,

Here’s my setup:

• XNAT: 1.8.10

• Container Service: 3.5.0

• OHIF Viewer: 3.7.1

• OS: Linux

• Installation: via Docker using NRG XNAT Docker Compose

I installed the following container: NRG XNAT dcm2niix

However, when I try to run it on a DICOM session, I get this error in Command History:

View stdout (from file):

However, when I try to run it on a DICOM session, I get this error in Command History:

View stdout (from file):

Compression will be faster with 'pigz' installed Chris Rorden's dcm2niiX version v1.0.20211006 (JP2:OpenJPEG) GCC9.3.0 x86-64 (64-bit Linux)

View stderr (from file):

Error: Unable to find any DICOM images in /input (or subfolders 5 deep)

  File organization:

To verify if the problem was with my DICOM data, I also installed dcm2niix locally, and it successfully generated the .nii file.

So I suspect the issue is not with XNAT itself, but with the dcm2niix container.
It seems that the /input directory mounted by XNAT doesn’t contain valid DICOMs, or it’s not being mounted as expected inside the container.

Has anyone experienced a similar issue?
How did you solve it?

Thanks in advance for your help!  

[Moore, Charlie]

Hi there,

Have you set up Path Translation for the container service? There's a section in the readme of the docker compose project explaining why it's needed and how to set it up.

Thanks,

Charlie Moore

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Subject: [XNAT Discussion] Issue running dcm2niix container: “Unable to find any DICOM images in /input (or subfolders 5 deep)”

 

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[Filippo Manini]

Hi Charlie,

thanks — I’ve resolved the issue by configuring the path translation as follows:

XNAT Path Prefix: /data/xnat
Server Path Prefix: /home/myName/projects/xnat-docker-compose/xnat-data

Everything works correctly now.

Thanks again for your help!

Filippo