Dear Mrtrix3 team,
I’d like to request for an additional module involving automatic QC of raw DWI data in the near or far future. I’m aware that some tools already do exist, but it would be really helpful to perform the whole analysis pipeline within the same platform and the same image format (.mif)
Regards,
Archith
Hi Archith,
I think this would be a great project to which various community members could contribute. Previous discussions have shown that different individuals have different ideas about what this would actually entail / contain / provide. The development team additionally all have their own research / development specialties, whereas in other software teams there are researchers who are dedicated to QC development.
One enhancement in the coming update is the ability to export image data directly to PNG. I’m hoping this will assist anyone interested in QC report generation to produce the images required for such.
When it comes to DWI QC though, it’s worth bearing in mind that QC and pre-processing are intimately linked. There are a lot of issues with raw DWI data that can now be reasonably well detected & corrected, and the parameters related to that detection & correction are themselves QC metrics. This is the philosophy behind FSL’s eddyqc. Following the coming update, if dwipreproc is run with one of the “-eddyqc_*” command-line options provided, and EddyQC is installed, dwipreproc will execute the relevant command internally, and provide its outputs in the user-specified location (in addition to the raw eddy outputs that are already provided when using those options).
Rob
Hi Dr Smith,
Thank you very much for the response and the update information. Also, regarding the EddyQC, I’m currently able to run them successfully with the -eddyqcdir option to store eddy qc outputs in a separate user specified directory.
Thanks and Regards,