Dcm2niix: Weird CSA 'ProtocolSliceNumber' & Check that 2D images are not mirrored

Dear community,

I’m converting my DICOM images (32 subjects) into Nifti using dcm2niix. The code I used is the following:

for x in {1…32}; do echo “THIS IS SUBJECT $x”; dcm2niix -o /sub_$x/func /sub_$x/DICOM; done; echo “I’m done”

Once the conversion is over, I see that for every participant I get the following warnings:

*WARNING n. 1:  Weird CSA 'ProtocolSliceNumber' (System/Miscellaneous/ImageNumbering reversed): VALIDATE SLICETIMING AND BVECS
*WARNING n. 2: Check that 2D images are not mirrored. 

How should I make sure that the slice timing is correct and that the images are not mirrored?

Best and thanks for the support.

The issue with the ProtocolSliceNumber is described here. The scans were specified on the console with reversed slice numbering. This only impacts how slices are ordered in the 2D mosaic, not how images are acquired. I would urge you to heed Siemens warnings on acquiring data this way. While I assume dcm2niix works correctly, I have not tested all the possible edge cases. You will want to rigorously evaluate the data to ensure it is correct. The big fear is that the slice timing numbers might be reversed or the diffusion gradients reversed.

For MRI image processing, we are only concerned with 3D scans, in general the 2D scans are localizers that are used to plan subsequent scans. I always use the dcm2niix -i y to ignore these scans.

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