Dear Chris,

My name is Rosie,

You answered me a question in the FSL forum about Canon dicom files.

I am new to Canon and I am a bit lost in relation to some issues you pointed out.

I wonder if the latest dcm2niix will guarantee that I will get the correct bvals and bvecs to work with FSL.

Should I download the qa Canonand go through the scrippting or is not needed?

Also,I am unsure about what do you mean with not storing dicom 2D un the Canon scanner and save them as 4D dicom enhanced.

Best,
Rosie

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 ....

See issue https://github.com/rordenlab/dcm2niix/issues/495
This describes the error in the Canon classic DICOM files and a desperate kludge in dcm2niix 1.0.20210317 to handle these mangled images. This seems like a clear contravention of the DICOM standard. Please report this to your Canon Research Collaboration manager to have it resolved. Based on this issue and the issue with diffusion tensors, I strongly urge users of Canon MRI systems to only export to enhanced DICOM. This is a limitation with the classic DICOM images generated by this system, not my software.