Argument list too long

[hieukien212]

Summary

I was trying to run heudiconv in bash script with an input as below:

-d ${dataset-dir}/scans/resources/DICOM/files/*.dcm

The error was Argument list too long, which I know is the kernel limit problem.

There are about 40,000 dicom files in total, and I'm expecting to operate on datasets of 90,000 files each.

Is there a way to get around this? I have tried increasing size limit ($ulimit -s 65536) but it did not work. And I assume the commonly given solutions using find and for loop will not work with heudiconv.

Platform details:

Choose one:

• Local environment

• Container: apptainer version 1.3.4-1.el8

• Heudiconv version: 1.2.0

[yarikoptic]

did you try to just -d ${dataset-dir}/scans/resources/DICOM/files/ ?

[hieukien212]

Yes, it will give an unrecognized argument error, because the directories don't end at dicom files.