Rosie-
 The Canon scanner console should allow you to export data as either classic DICOM (each 2D slice is a separate file) or enhanced DICOM (the entire series saved as a single file). I strongly encourage you to export data as enhanced images, as this retains gradient information for DWI data. This data can not be recovered if you save classic DICOMs.

 The Canon enhanced DICOM is a new format, so it is not supported by prior versions of dcm2niix. You will want to make sure you use dcm2niix v1.0.20210308 or later. As with any new feature for a complex format, please validate the resulting conversion and report any issues on Github. I developed support for this format with a handful of images (https://github.com/neurolabusc/dcm_qa_ca...), and it is possible that some sequences will not be handled correctly.
  I expect that there will be a new stable release of dcm2niix in the next few days, but until then you will need to compile dcm2niix from the development branch using the following commands:


git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
cd dcm2niix/console
g++ -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG
./dcm2niix ....