mriconvert: File does not contain image data

[Jolinda Smith]

Hi Roman! Hope you are well.

This means that mcverter is reading it as DICOM, but it can't find the "photometric interpretation" tag (0028, 0004). For MR images this is usually "MONOCHROME2". If you have dcmtk installed, you can look for this tag by running dcmdump +P PhotometricInterpretation [filename]. If it's not found, mcverter assumes this isn't an image file.

I've mostly switched to dcm2niix myself since I haven't had time to work on mriconvert and it's gotten behind. I'm currently working on a python-based front end for dcm2niix that converts to bids format, if you are interested.

If you really want to use mcverter and not dcm2niix, the first thing I can think of to try is to rewrite the dicoms using something like dcmconv from dcmtk: https://support.dcmtk.org/docs/dcmconv.html. This should correct any missing required elements in the dicom files.

Jolinda

From: Roman Fleysher <roman.fleysher at einsteinmed.edu>
Sent: Thursday, December 29, 2022 11:55 AM
To: 'MRIConvert user's list' <mriconvert at lists.uoregon.edu>; Jolinda Smith <jolinda at uoregon.edu>
Subject: File does not contain image data

Dear Jolinda,
Dear All,

I have not had any issues with mcverter in a long time. I am installing a new system and new versions of software and some of the old DICOM files do not convert. New DICOMs are fine.

I get error message (when using -v option for verbose output):

Not added File does not contain image data

I use  mcverter version 2.1.0 build 434

The DICOM files are not that old, only few years, so this should not be any major change in format. What could this error mean and how to get mcverter to convert these DICOMs to NIFTI?

Thank you, and wishing you a Happy New Year,

Roman


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