questions > Empty Protocol Name(s) (0018,1030)
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Apr 16, 2020  06:04 AM | krumb_snatcher
Empty Protocol Name(s) (0018,1030)
Hello,

Using the dm2niix nipype module I am converting DICOM images of about 40 subjects to NIfTI (and later BIDS).

For most subjects it works flawless - many thanks for such a great tool.

However, for 4 subjects I receive a warning that the protocol name is empty and  a protocol name cannot be appended, after which conversion is aborted:


200416-15:02:26,934 nipype.interface INFO:
stdout 2020-04-16T15:02:26.933785:Chris Rorden's dcm2niiX version v1.0.20190902 (JP2:OpenJPEG) GCC7.3.0 (64-bit Linux)
200416-15:02:26,938 nipype.interface INFO:
stdout 2020-04-16T15:02:26.933785:Found 2618 DICOM file(s)
200416-15:02:26,940 nipype.interface INFO:
stdout 2020-04-16T15:02:26.933785:Warning: Empty protocol name(s) (0018,1030)
200416-15:02:26,942 nipype.interface INFO:
stdout 2020-04-16T15:02:26.933785:Warning: Unable to append protocol name (0018,1030) to filename (it is empty).
200416-15:02:26,943 nipype.interface INFO:
stdout 2020-04-16T15:02:26.933785:Convert 192 DICOM as /data/leo/NNIP/NNIP_conv/sub-13/NNIP013__20190829083426_2 (256x256x192x1)
200416-15:02:33,40 nipype.interface INFO:
stderr 2020-04-16T15:02:33.040766:*** buffer overflow detected ***: dcm2niix terminated
200416-15:02:33,257 nipype.interface INFO:
stderr 2020-04-16T15:02:33.257049:Aborted (core dumped)

The data was not collected by myself, but I have been told that the same protocol has been used for all subjects.

What is the best way to deal with it? I have been searching through the forums and questioned whether the following thread contains an answer to my issue: https://github.com/rordenlab/dcm2niix/issues/341? Or is there a different way to allow for conversion of these images?

Thanks,


Leo
Apr 16, 2020  06:04 AM | Chris Rorden
RE: Empty Protocol Name(s) (0018,1030)
Hello-

1.)  I suspect this is an issue with nipype and not dcm2niix. You should report this as an issue with nipype
    https://github.com/nipy/nipype
  You can verify this by converting a file without a Protocol Name (0018,1030) and Series Description (0008,103e, which dcm2niix uses as a surrogate for protocol name if series description is empty) using dcm2niix from the command line (example posted below). While dcm2niix generates a warning, it converts the images (it does not generate an error), even if the output filename was based solely on protocol name ("-f %p").

2.) Can I suggest you upgrade to the latest version of dcm2niix v1.0.20200331 
       https://github.com/rordenlab/dcm2niix/releases

3.) If dcm2niix from the command line fails, it suggests these DICOM images may have been corrupted. The lack of a protocol name suggests an over-agressive anonymization tool was applied. In my experience, poorly implemented DICOM anonymization is one of the leading causes of data loss. For example, the Matlab function dicomanon removes the Siemens CSA header and other details crucial for accurate conversion. 
  https://www.mathworks.com/help/images/ref/dicomanon.html
If this is the case, you need to check the provenance of your images and get copies of the images prior to corruption.


-------------------------

>dcm2niix -f %p -s y ./in.dcm
Chris Rorden's dcm2niiX version v1.0.20200331 (JP2:OpenJPEG) (JP-LS:CharLS) Clang11.0.0 (64-bit MacOS)
Convert 1 DICOM as ./sag_int_36slb (64x64x36x1)
Conversion required 0.006616 seconds (0.006603 for core code).
>gdcmanon --dumb --empty 0018,1030 --empty 0008,103e in.dcm out.dcm
>dcm2niix -f %p -s y ./out.dcm
Chris Rorden's dcm2niiX version v1.0.20200331 (JP2:OpenJPEG) (JP-LS:CharLS) Clang11.0.0 (64-bit MacOS)
Warning: Unable to append protocol name (0018,1030) to filename (it is empty).
Convert 1 DICOM as ./dcm2nii_invalidName (64x64x36x1)
Conversion required 0.008707 seconds (0.008692 for core code).
Apr 22, 2020  09:04 AM | krumb_snatcher
RE: Empty Protocol Name(s) (0018,1030)
Dear Chris,

Thank you for your reply, and please forgive my delayed response.

Running dcm2niix from command line, I was able to convert the images.

I will report this issue with nipype.

Thanks again,

Leo