Thanks for the detailed report @JMaller1. The images shown do look completely normal indeed. I was about to ask you to share the data so we could have a look at it, until I did a quick test myself over here. I figured out that I’d made a mistake suggesting the CSF would be the problem here (I reasoned the tissue index started counting from 0, but I think I had originally changed that in the code myself to start counting from one). Essentially, tissue index 2 relates to your second input tissue type, which in your case is GM. That, together with the CSF and WM images you posted, makes me suspect the GM is actually going to be zero (or very close to it). I’m quite used to looking at multi-tissue reconstructions these days, and your CSF looks like it is a tiny bit brighter in GM regions that I would expect it to be; but more importantly, your WM looks like it gets a lot of GM. What I suspect is a de facto 2-tissue reconstruction… which may be a realistic guess if you’ve potentially only used single-shell data to do multi-tissue CSD.
So, long story short: can you also check your GM input image? I predict it’s going to be all zero or amazingly small magnitudes (both positive as well as slightly negative potentially).
If that is the case, and you only have single-shell data, then at the moment (until I release SS3T-CSD at some point) you’re limited to 2-tissue WM and CSF CSD. There’s other good news there for you though: I did start to test extensively whether
mtnormalise still works and makes sense on 2-tissue WM and CSF reconstructions, and the answer so far is “yes”. So essentially, you can just (consistently) provide only the WM and CSF to
mtnormalise, and it would make sense. Also, you don’t have to ask
dwi2fod msmt_csd for the GM in this scenario, since it won’t give you any by definition. Those subjects where it did succeed to run, may have had quite weird or problematic outputs as well with a GM compartment that is numerically very close to zero.
If you want more information on such a 2-tissue strategy, I recommend to read this post and all the replies, as well as all the links to other posts I have given in the replies I made to that post: Fixel-Based Analysis on single shell data
Hope this helps!