DWIConvert usage

Hello everyone!

I’m trying to convert the scan files from DICOM to NIFTI using DWIConvert. Since the files come from the reformatting process of a sagittal scan the folder contains, as first slice, a schematic representation of the process showing where the axial slices were located.

Using dcm2niix or mcverter two NIFTI files are generated, one for this first slice and the other one for the volume. When I repeat the process using DWIConvert a strange volume is generated due to the DICOM tags of this first file, I guess.

Do you know if there is a workaround for this? This conversion is a step of an automated pipeline which cannot detect the first disturbing slice.

Thank you beforehand for your comments!!


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For the moment the best bet is probably to sort the files in a temp directory and run DWIConvert on that. DWIConvert examines every file in a directory and doesn’t do much general sorting or validation, so the program behavior is basically undefined if you have mixed series or non-DICOM data in the directory. Sometimes it just crashes. See this related comment about CLI file communication.

Thanks @ihnorton, I’ll keep this information in mind when I use DWIConvert.

Best regards.