I was not able to locate the …/template/fd/IN.mif.
Image “…/template/fd/IN.mif” does not exist. The text string “IN” is a substitution to be manipulated by the for_each command.
I’m having the same issue as this user and can’t seem to find an answer anywhere;
Can you please add a link to the thread / post to which you are referencing.
In Step 18,
Since the documented example pipeline can change between software versions—and I can tell that you’re referencing an out-of-date version of MRtrix3 as foreach was renamed to for_each—could you please also verify that you are looking at the version of the online documentation that matches the version of MRtrix3 that you are using, and quote for us here that version (more info on versioned documentation here).
However, I’m not actually using the batch processing function and am just trying to process a single subject at the moment using - mrcalc …/template/fd/IN.mif …/template/fc/IN.mif -mult …/template/fdc/IN.mif
The problem I’ve encountered is that I can’t find anywhere in the Fibre Density and Cross Section (Multi-Tissue CSD) documentation where the fd/IN.mif file is created to complete the above line of code. I’m using Matrix 3.0 as well.
unique part of the input after removing any common prefix
and common suffix. For example, if the target list contains files:
“folder/001dwi.mif”, “folder/002dwi.mif”, “folder/003dwi.mif”, any
occurrence of “UNI” will be substituted with “001”, “002”, “003”.