Converting large numbers of DICOM image produces no results

[kwunh]

Converting ADNI dataset

Hello I am not sure if anyone else has run into this issue - so I've set up the heuristics file with no issues and it runs fine for the most part. That is, until I deal with a subject with large amounts of dicom files e.g. 9000+.

It gave me the error: Argument list too long. After a bit of googling, I think it may be due to a kernel limit on the amount of space for arguments to a command... so I tried a solution of setting a higher limit: ulimit -s 65536.

Whilst I no longer get an error, I am failing to get actual resultant nii files. Moreover, the logging on the command line leads me to believe the conversion was done properly:

INFO: Doing conversion using dcm2niix
INFO: Populating template files under /home/user/ADNI/Nifti/
INFO: PROCESSING DONE: {'subject': '0178', 'outdir': '/home/user/ADNI/Nifti/', 'session': 'itbs'}

It spawns in the typical BIDS files:

• dataset_description.json
• participants.json
• participants.tsv
• scans.JSON
• README
• CHANGES

Can someone please give suggestions of how to get around this? it may be that the original source dataset is a bit messed up because I'm not sure 9000+ files is very common. There are a number of patients that suffer from this limitation. Thank you!

Platform details:

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• Local environment

• Container

• Heudiconv version: 1.1.6