questions > Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?)
Showing 1-5 of 5 posts
Display:
Results per page:
Jan 10, 2025  10:01 PM | shanna1
Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?)

Dear all,


I encountered an error while using dcm2niix (v1.0.20241211):
Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?).


However, I was still able to obtain converted results for the task, T1, and fmap data. I searched online and found some suggestions to delete the localizer or scout files. Unfortunately, our scanning system was recently upgraded, and we can no longer identify subject IDs or series names from the raw data filenames (please refer to the screenshot for an example).


I’m wondering: Can I safely ignore this error and trust the results generated by dcm2niix? If not, what steps can I take to resolve this issue?


 

Thank you for your help!


Best,


Shanna

Jan 11, 2025  02:01 PM | Chris Rorden
RE: Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?)

Typically you get this error when you attempt to convert a localizer (scout) scan, where a single DICOM series includes different slice orientations. The NIfTI standard requires that all slices in a volume share the same angulation. For most neuroimaging tasks we discard the localizer scans, which are only used to plan subsequent images. If this is your intention, you can ignore this error, or you could use the `-i y` option to ignore localizer scans. If you do need the information from the localizer scans, you will want to retain these images. 


 


For more details, see issue 894


 


https://github.com/rordenlab/dcm2niix/issues/894

Jan 13, 2025  05:01 PM | shanna1
RE: Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?)

Hi Chris Rorden,


Thank you so much for your reply—I truly appreciate it.


You are correct that we do not intend to use the localizer and would like to remove it. However, based on the data we received from the scanner, I’m unable to identify which file corresponds to the localizer. As a result, I assume it can be safely ignored.


Thank you again for your assistance; your input has been incredibly helpful.


Best regards,


 


best regards,


Shanna

Jan 13, 2025  05:01 PM | Chris Rorden
RE: Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?)

Well in your case, I would certainly use the "-i y" option for dcm2niix to ignore derived and 2D images - this will likely eliminate or reduce these warning messages.

Jan 13, 2025  05:01 PM | shanna1
RE: Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?)

Got it. Thanks!


best,


Shanna