Alright, that was funny. It’s not a problem with those brighter intensities, Nagesh. Also ignore my guesses above; it’s something else entirely.
The problem is caused by 2 volumes in the dataset that can’t be assigned to a shell: volumes 21 and 22 have a b-value of 350, unlike the rest of the data which roughly has shells for b=0,1000,2000,3000. So best to check what’s up with those volumes, and whether their b-value should’ve been different. In any case, it runs without issues to completion if you first remove those volumes, e.g. via:
dwiextract dwi.mif newdwi.mif -shells 0,1000,2000,3000
…and then run everything (
dwi2response dhollander as well as any further processing, e.g.
dwi2fod msmt_csd) on
I tested both steps: got great responses (checked all internal workings of
dwi2response dhollander: all works robustly without issue on your data) and good CSD results using those responses. Nagesh, do check whether those 2 volumes should’ve had a different b-value or something. But if you don’t need them, get rid of them with the above command to resolve all problems.
Cheers & take care ,
The exact reason why it crashed initially can be traced back to a bug in
dwi2fod msmt_csd, which seems to produce all zero outputs under the very specific conditions of volume(s) not being able to be assigned to a shell combined with at least 2 tissues. No issues if it’s just one tissue.