Unsure how to utilize --dcmconfig flag to output uncompressed .nii files

1

Hello, I’m trying to modify my heudiconv output so that I get uncompressed .nii files from the dcm2niix step rather than the compressed format (.nii.gz).

According to git you can use a -dcmconfig flag pointing to a .json with {compress: “no”} as the sole text in the file to tell dcm2niix not to perform any compression. I’ve done that, as well as modifying my heuristic file to output as ‘nii’, although heudiconv is still generating compressed files.

Has anyone successfully used the --dcmconfig flag to convert their DCM’s into uncompressed Nifti’s? It would be helpful to see the steps you took for this process. Thanks!

2

@bhosseini there are a few things to try:

  • ensure the --dcmconfig json looks like:
{"compress": "n"}
  • remove heudiconv's cached grouping in <output-dir>/.heudiconv/<subject>

this will be fixed in an upcoming release

3

Thanks, this appears to fix the issue.

4

Hello. I’m interested in using additional dcm2niix options for the conversion (specifically: -m y and -i y).

Any idea on how these options should be specified in the dcmconfig json file?

Thanks!