Error: Too many NIFTI images with the name

1

Hello all,

After an update of the MRI, we now have DICOM files in the enhanced mode.
When trying to use dcm2bids on this new format, I have the following errors:

Error: Too many NIFTI images with the name */tmp_dcm2bids/sub-x_ses-x/026_x_x_wip_20221209094910_e1
Error: Too many NIFTI images with the name */tmp_dcm2bids/sub-x_ses-x/026_x_x_wip_20221209094910_e1
Error: Too many NIFTI images with the name */tmp_dcm2bids/sub-x_ses-x/026_x_x_wip_20221209094910_e1
Error: Too many NIFTI images with the name */tmp_dcm2bids/sub-x_ses-x/026_x_x_wip_20221209094910_e1
Error: Too many NIFTI images with the name /tmp_dcm2bids/sub-x_ses-x/026_x_x_wip_20221209094910_e1
Error: Too many NIFTI images with the name/tmp_dcm2bids/sub-x_ses-x/026_x_x_wip_20221209094910_e1
Error: Converted 69038 of 130530 files
Traceback (most recent call last):
File “/home/elena/anaconda3/bin/dcm2bids”, line 114, in
sys.exit(main())
File “/home/elena/anaconda3/bin/dcm2bids”, line 110, in main
return app.run()
File “/home/elena/anaconda3/lib/python3.8/site-packages/dcm2bids/dcm2bids.py”, line 103, in run
dcm2niix.run(self.forceDcm2niix)
File “/home/elena/anaconda3/lib/python3.8/site-packages/dcm2bids/dcm2niix.py”, line 91, in run
self.execute()
File “/home/elena/anaconda3/lib/python3.8/site-packages/dcm2bids/dcm2niix.py”, line 104, in execute
output = run_shell_command(cmd)
File “/home/elena/anaconda3/lib/python3.8/site-packages/dcm2bids/utils.py”, line 109, in run_shell_command
return check_output(shlex.split(commandLine))
File “/home/elena/anaconda3/lib/python3.8/subprocess.py”, line 411, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File “/home/elena/anaconda3/lib/python3.8/subprocess.py”, line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command ‘[‘dcm2niix’, ‘-b’, ‘y’, ‘-ba’, ‘y’, ‘-z’, ‘y’, ‘-f’, ‘%3s_%f_%p_%t’, ‘-o’, ‘tmp_dcm2bids/sub-x_ses-x’, ‘/DICOM/x/x_x/’]’ returned non-zero exit status 8.

I think the issue is that I have images acquired with multiple echo times (32) and there are not enough alphabet letters to assign a new name to the nifti file (for now in my tmp folder I have from a to y, 26 images and 6 from the error that could not be assigned).

I am trying now to run directly the dcm2niix function adding the echo time in the name to see whether this could solve the issue, as follow:

dcm2niix -b y -ba y -z y -f ‘%3s_%f_%p_%t_%e’ -o … …

Still, if this works, I am not sure how I to add the option when running the dcm2bids command.
Do you have any suggestion?

Thank you very much in advance,
Elena

3

Hi @ebeanato ,

Check this section of the documentation Use advanced commands - Dcm2Bids

Let us know if it helps you fix your issue.
Best,
Arnaud

1 Like
4

Thank you, I managed to add the option I wanted by adding

“dcm2niixOptions”: “-b y -ba y -z y -f ‘%3s_%f_%p_%t_%b’”

to the config file.

Just to notice, the “Error: Too many NIFTI images with the name” was solved by adding %b in the name in order to differentiate the images of the different echo times since %e was just taking into account the echo number which was fixed.

Thank you again!

1 Like