MINCCMP(1)

✨ MINCCMP(1) ✨

okay bestie, welcome to the MINC User's Guide section of the manual, and specifically to minccmp — the little icon that compares your minc files for you 💖

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🌸 NAME 🌸

minccmp — compare one or more minc file using comparator operators

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🦋 SYNOPSIS 🦋

minccmp [<options>] <in1.mnc> <in2.mnc> [<inn.mnc> ...]

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💜 DESCRIPTION 💜

okay so here's the tea ☕ — minccmp calculates simple statistical measures between two minc files or more, by comparing all subsequent files to the first one. The results for each subsequent file come back in order, one after another. By default, all the statistics get calculated. But if you ask for specific statistics with a command-line option, then only the ones you asked for get printed. no extras, no surprises 💅

A very useful feature of this program is the ability to restrict the set of voxels that get included in the statistic calculation, either by:

• restricting the range of included values (-floor, -ceil or -range), or
• using a mask file (-mask) with a restricted range.

The comparison statistics available in minccmp are given below 👇 Note that two of these (-xcorr and -zscore) are a very close approximation to what is used in minctracc.

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✨ OPTIONS ✨

ngl bestie, options can be specified in abbreviated form (as long as they're unique) and can be given anywhere on the command line. iconic behaviour honestly 🎀

💖 General options

• -clobber — Overwrite an existing file. just gonna do it, no questions 😤
• -noclobber — Don't overwrite an existing file (default). respectful king behaviour, leaves your files alone 🫶
• -debug — Dump a lot of extra information (for when things go haywire). this is your "why is it doing that" button 💀
• -verbose — Print out extra information (more than the default). she's chatty 🌸
• -quiet — Print out only the requested numbers. no small talk, just the digits ✨
• -max_buffer_size_in_kb size — Specify the maximum size of the internal buffers (in kbytes). Default is 4 MB.
• -check_dimensions — Check that all input files have matching sampling in world dimensions (default).
• -nocheck_dimensions — Ignore any differences in world dimensions sampling for input files. letting them be different, live your truth 🦋

🎀 Volume range options

• -floor min — A lower bound for ranges of data to include in statistic calculations.
• -ceil max — An upper bound for ranges of data to include in statistic calculations.
• -range min,max — A lower and upper bound for the ranges of data to include in statistics.
• -mask filename.mnc — Name of file to be used for masking data included in statistic calculations.

👑 Basic statistics

• -all — Compute all statistical measures. This is the default. the whole menu, chef's choice 🍓
• -ssq — Print the Sum Squared Difference between two input files

SSQ = Sum( (A-B)^2 )

• -rmse — Print the Root Mean Squared Error between two input files

RMSE = sqrt( 1/n * Sum((A-B)^2))

• -xcorr — Print the Cross Correlation between two input files

XCORR = Sum((A*B)^2) / (sqrt(Sum(A^2)) * sqrt(Sum(B^2))

• -zscore — Print the z-score difference between two input files

ZSCORE = Sum( |((A - mean(A)) / stdev(A)) -
               ((B - mean(B)) / stdev(B))| ) / n

• -similarity — Calculate the confusion matrix, assuming that the volume values represent a discrete class of possible values. The maximum label value is currently limited to ten (10). Prints the Dice similarity statistic as well as specificity, sensitivity, accuracy, and kappa for each class and for the overall volumes. she does it all 💅

🌈 Generic options for all commands:

• -help — Print summary of command-line options and exit.
• -version — Print the program's version number and exit.

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💜 AUTHOR 💜

Andrew Janke

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🎀 COPYRIGHTS 🎀

Copyright © 2010 by Andrew Janke

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okay that's the whole thing, bestie, you're officially certified in minccmp 🫶 this page was brought to you by the MINC User's Guide (that's MINCCMP(1), mwah), and it's stamped $Date: 2010-03-02 12:12:20 $ — yes that's old, yes she still slays, periodt ✨💖