Canon classic DICOM SeriesInstanceUID bug #495
Comments
neurolabusc
added a commit
that referenced
this issue
Mar 17, 2021
yarikoptic
added a commit
to neurodebian/dcm2niix
that referenced
this issue
Apr 6, 2021
* tag 'v1.0.20210317': (23 commits) CI: Travis updates submodules always from remote. Update dcm_qa_nih submodule. Remove diagnostic message help should describe accession number (rordenlab#496) Describe and provide kludge for mangled Canon DICOMs (rordenlab#495) Update Philips notes (rordenlab#493) Update dcm_qa submodule. Support Canon Enhanced DICOM (rordenlab#491) Use first recognized manufacturer tag (rordenlab#487) If mosaics where ANY volume is non-planar, save ALL volumes as 3D(rordenlab#481) Add notes Kludge to separate vNav files as 3D (rordenlab#481) Tell user to override merging (-m o) to separate coils, specific with fmrib usage that disrupts Siemens DCE processing (rordenlab#187) Forbid semicolon in filenames as Linux uses this for command concatenation and Windows function GetOpenFileName will truncate (rordenlab#425) report totalReadoutTime once EstimatedEffectiveEchoSpacing -> EffectiveEchoSpacing (rordenlab#480) GE Round factor for Total Readout Time Update explicit naming of DICOMs (rordenlab#252), GE file naming changes (rordenlab#476) Update issue templates GE TotalReadouTime, BEP009 fixes (rordenlab#476) ...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
PUBLIC SERVICE ANNOUNCEMENT
Users of Canon MRI systems should avoid saving data as classic 2D DICOMs. Export data from the console in enhanced DICOM format.
DETAILS
The describes an issue with Canon MRI saved in classic (2D) format. This was observed in Canon SoftwareVersions (0018,1020) V6.0SP2001*. Specifically, 4D sequences like fMRI and DTI use a different SeriesInstanceUID for each slice in the series (with the final number in the UID reflecting the slice number). Therefore, the first and second slice of the volume will appear as:
and
respectively. Note that SeriesInstanceUID (0020,000E) is a Type 1 tag and the usage here conflicts with the definition of the DICOM standard. Therefore, these are technically not valid DICOM images. This is a limitation of the Canon classic DICOMs, not of dcm2niix. This is in addition to the issues with Canon classic DICOMs previously described. These issues have not been observed in the limited number of Canon enhanced DICOMs provided to me.
This error will impact any tool that uses the SeriesInstanceUID to distinguish series. To help users with mangled data, the upcoming release of dcm2niix will include the
-m 2command that will set the SeriesInstanceUID to be equal to the Series number. For example:This option should only be used a last resort. While this will allow Canon series to be stacked correctly, it is possible that series from different sessions might not be disambiguated. One possible solution would be to rename DICOMs (e.g. using
dcm2niix -r y -f %t/%s_%p/%4r_%o.dcm ~/Desktop/canon) and then converting the appropriate sub-folders one at a time.The text was updated successfully, but these errors were encountered: