Intersection mask using mrmath min

1

Dear Mrtrix users/developers,

I am performing the fixel-based analysis for my dataset, but have a question for calculating the intersection mask…
On the information page the following mrmath command is mentioned with ‘min’ option:
mrmath input_all_warped_masks_multiple_inputs min output_template_mask_intersection

However, if I inspect this intersection image, it rather looks like a sum image (the ‘sum’ option creates exactly the same image by the way)…
Whereas if I use the option ‘product’ instead of ‘min’, this rather looks like the intersecting mask that is appropriate in all subjects…
Is this possible?

A second question I have regarding group comparisons of FC, FD and FDC is:
Should only FC be log-transformed to be normally distributed, or FD also?
And should the multiplication of both (FDC) be log_FC x log_FD <=> rather FC x FD <=> rather log_FC x FD ?

Thank you in advance!
With kind regards,
Charlotte

2

Hi @Charlotte,

I just tested this scenario for you, and there’s indeed something wrong. Thanks for reporting; it’s clearly a bug!

Strangely, what does seem to work correctly is:

mrcat input_all_warped_masks_multiple_inputs - -axis 3 | mrmath - min output_template_mask_intersection -axis 3

Until the bug has been looked into and resolved, I’d personally advise to go with this one as a quick fix. The bug seems to at least relate in a way to the multiple input behaviour of mrmath, so even though the product option seems to work correctly, I wouldn’t fully trust it for now…

For your other question, let’s see if we can grab @Dave’s attention to write a good post about this. :wink:

Cheers,
Thijs

3

Hi Charlotte,
Only FC should be log transformed for analysis. However when computing FDC use the raw FC values (i.e. not log transformed).

I’ll be improving the documentation for fixel-based analysis of FD, FC and FDC in the near future, after we have made a switch to a new file format for storing fixels and associated data. I’ll post about it when I do.

In case you have not already seen it, Fig. 2 of our recent paper may help to explain the flow of the FBA steps in the MRtrix documentation.

Cheers,
Dave

4

Hi Thijs and Dave,

Thank you both for your fast responses!
@Dave , I read the paper indeed and very much appreciate your work!
I’m really enthusiastic about Mrtrix btw :slight_smile: !

Cheers,
Charlotte

5

No worries @Charlotte. By the way, the bug you discovered has been resolved in the mean time; if you update your MRtrix installation, the “min” operator should now work correctly in the scenario you described!