Hello,

how to deal with the ‘Warning: Instance Number (0020,0013) order is not spatial.’ from dcm2niix? Will the images in Niftii still be stored in the correct order?

Many thanks in advance
Johanna

You will have to check by visual inspection. This error typically reflects that some files are missing or that the manufacturer does not consider the images spatial (e.g. derived color images from a Siemens diffusion sequence). I would try to ignore derived images (which are not useful for subsequent analyses) with

dcm2niix -i y /path/to/DICOMs

If you still get an error, check the provenance of your DICOMs - ideally get a dataset direct off of the instrument to prevent any data loss or corruption and unintended consequences of anonymization.