No output files in helper directory using dcm2bids_helper

Software Support
1

Hi there, I’ve come across a problem regarding the command dcm2bids_helper.

The codes that I use are as follow:

dcm2bids_helper -d sourcedata/202512124_mm

And the INFO from the terminal:

INFO    | --- dcm2bids_helper start ---
INFO    | Running the following command: /media/ubuntu/Work2/anaconda3/bin/dcm2bids_helper -d sourcedata/202512124_mm
INFO    | OS version: Linux-6.8.0-90-generic-x86_64-with-glibc2.35
INFO    | Python version: 3.11.7 (main, Dec 15 2023, 18:12:31) [GCC 11.2.0]
INFO    | dcm2bids version: 3.2.0
INFO    | dcm2niix version: v1.0.20250505
INFO    | Checking for software update
INFO    | Currently using the latest version of dcm2bids.
WARNING | A newer version exists for dcm2niix: v1.0.20250506
WARNING | You should update it -> https://github.com/rordenlab/dcm2niix.
INFO    | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /home/ubuntu/NAS_zoc/hy/aphantatia_reconstruction/BIDS/tmp_dcm2bids/helper sourcedata/202512124_mm
INFO    | Check log file for dcm2niix output

INFO    | Helper files in: /home/ubuntu/NAS_zoc/hy/aphantatia_reconstruction/BIDS/tmp_dcm2bids/helper

INFO    | Log file saved at /home/ubuntu/NAS_zoc/hy/aphantatia_reconstruction/BIDS/tmp_dcm2bids/log/helper_20260119-170826.log
INFO    | --- dcm2bids_helper end ---

Everything seems fine, except that there’s no output files in:

/home/ubuntu/NAS_zoc/hy/aphantatia_reconstruction/BIDS/tmp_dcm2bids/helper

The command dcm2bids_helper was working properly before and successfully generated NIfTI and JSON files, but at some point it stopped working.

2

Hi @Yan_Huang,

What if you run the internal helper command directly? E.g.,

INFO    | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /home/ubuntu/NAS_zoc/hy/aphantatia_reconstruction/BIDS/tmp_dcm2bids/helper sourcedata/202512124_mm

Best,
Steven

3

Hi @Steven,

I followed your suggestion and ran the following command:

dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /home/ubuntu/NAS_zoc/hy/aphantatia_reconstruction/BIDS/tmp_dcm2bids/helper sourcedata/202512124_mm

I got the following error:

Chris Rorden's dcm2niiX version v1.0.20250505  GCC14.3.0 x86-64 (64-bit Linux)
Error: Input folder invalid: sourcedata/202512124_mm

This made me realized that the correct input folder should be:

sourcedata/sub-1/202512124_mm

I had been missing the subject field the whole time. But it seems a bit strange that the dcm2bids_helper command did not report any error, which made me think the input folder was fine.