FBA question regarding FD PRE and IN

1

Hi MRtrixers,

In the FBA analysis instructions (https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mt_fibre_density_cross-section.html ), Step 16 (Assign subject fixels to template fixels), the output is “../template/fd PRE.mif”.

However in Step 18. (Compute a combined measure of fibre density and cross-section (FDC)), the last command is “mrcalc ../template/fd/IN.mif ../template/fc/IN.mif -mult ../template/fdc/IN.mif”.

Hence, there is no IN.mif file in the ../template/fd directory. Does that ../template/fd/IN.mif file refer to the ../template/fd PRE.mif ?

Thanks!

Jerome

2

Hi Jerome,

Files “IN.mif” and “PRE.mif” are not supposed to exist. The keywords “IN” and “PRE” are substitution strings that are manipulated by for_each in the construction of the multiplicity of commands to be executed across participants at each step.

If there’s some inconsistency in how these are used in the sequence of commands executed, then we can correct that, but my suspicion is that there’s an upstream misinterpretation.

Regards
Rob

3

Hi Rob,

Thankyou so much for your fast response.

So to clarify: the fd/input (Step 18) for mrcalc is the output from Step 16 (Assign subject fixels to template fixels)?

Regards,

Jerome