Mix of single and multishell data in a session

[ins0mniac2]

If there is a multishell acquisition split into N files, qsiprep by default combines them for a single reconstruction. If, in addition, there is also a single shell acquisition, what will it do ? Do I have control over whether in that case we would like it to 1) either combine them all, or 2) separately process the singleshell data ? To me it seems like the --separate_all_dwis option is all or none ?

[ajschadler12]

Although it's been over a year, I'd like to provide an answer.

This might be a simple fix: try to provide an acq- label to your dwi file names.

e.g. for single shell

sub-001_acq-single_dir-AP_dwi.nii.gz sub-001_acq-b1000_dir-AP_dwi.nii.gz

for multi shell

sub-001_acq-multi_dir-AP_dwi.nii.gz sub-001_acq-b1000b2000_dir-AP_dwi.nii.gz

You might find the b1000b2000 label a bit more descriptive.

[mattcieslak]

It's been much more than a year now, but I might suggest it's not a good idea to combine single and multishell data into a single processing stream.

[cookpa]

I think this is another use case for BIDS filters