# FBA question regarding FD PRE and IN

**URL:** <https://community.mrtrix.org/t/fba-question-regarding-fd-pre-and-in/8629>\
**Category:** Uncategorized\
**Created:** [December 7, 2025, 5:02pm UTC](https://community.mrtrix.org/t/fba-question-regarding-fd-pre-and-in/8629 "2025-12-07T17:02:25Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![JMaller1](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/j/4da419/32.png) [@JMaller1](https://community.mrtrix.org/u/JMaller1)\
**Post date:** [December 7, 2025, 5:02pm UTC](https://community.mrtrix.org/t/fba-question-regarding-fd-pre-and-in/8629/1 "2025-12-07T17:02:25Z")

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Hi MRtrixers,

In the FBA analysis instructions ([https://mrtrix.readthedocs.io/en/latest/fixel\_based\_analysis/mt\_fibre\_density\_cross-section.html](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

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**Author:** ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)\
**Post date:** [December 9, 2025, 1:37am UTC](https://community.mrtrix.org/t/fba-question-regarding-fd-pre-and-in/8629/2 "2025-12-09T01:37:24Z")

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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

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**Author:** ![JMaller1](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/j/4da419/32.png) [@JMaller1](https://community.mrtrix.org/u/JMaller1)\
**Post date:** [December 9, 2025, 2:16pm UTC](https://community.mrtrix.org/t/fba-question-regarding-fd-pre-and-in/8629/3 "2025-12-09T14:16:27Z")

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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