Include CNR in eddy_qc ouputs

[donnagift]

The automated eddy_qc framework currently does not include the CNR metrics and therefore outputs the CNR in qc.json files as -1 for all runs.

The --cnr_maps flag can be added to the 02_proc-dwi.sh module, line 372-373, so that when eddy_quad is executed in line 386, the CNR will be included.

echo -e "COMMAND --> dwifslpreproc $dwi_4proc $dwi_corr $opt -pe_dir $pe_dir -readout_time $ReadoutTime -eddy_options \" --data_is_shelled --slm=linear --repol\" -nthreads $threads -nocleanup -scratch $tmp -force"
     dwifslpreproc "$dwi_4proc" "$dwi_corr" $opt -pe_dir "$pe_dir" -readout_time "$ReadoutTime" -eddy_options " --data_is_shelled --slm=linear --repol" -nthreads "$threads" -nocleanup -scratch "$tmp" -force

For more info:
https://git.fmrib.ox.ac.uk/nichols/docdev/-/blob/add-eddy-qc/docs/diffusion/eddyqc.md