Fibre density and cross-section - Multi-tissue CSD Guide


I am running through the documentation notes for fibre density and cross-section (multi-tissue CSD - Fibre density and cross-section - Multi-tissue CSD — MRtrix 3.0 documentation).

In step 18 for computing a combined measure of fibre density and cross-section (FDC), it has the following code;

for_each * : mrcalc …/template/fd/IN.mif …/template/fc/IN.mif -mult …/template/fdc/IN.mif

I have followed the guide exactly and nowhere is a fd/IN.mif file created. If anyone can provide me any help I’d be very appreciative.


hello Archie
May be this Batch processing with for_each — MRtrix 3.0 documentation will help you understand the result.


Hi Archie,

If this is not a misunderstanding with respect to the operation of for_each, these files should correspond with what is generated at step 16:

for_each * : fixelcorrespondence IN/fixel_in_template_space/fd.mif ../template/fixel_mask ../template/fd PRE.mif

It looks different because the (current) interface to fixelcorrespondence takes output directory and file names separately, and a different for_each substitution string is used. But if the files are genuinely not there, we’d need to look closer.