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minccmp - Online in the Cloud

Run minccmp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command minccmp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


minccmp - compare one or more minc file using comparator operators

SYNOPSIS


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

DESCRIPTION


minccmp will calculate simple statistical measures between two minc files or more by
comparing all subsequent files to the first. The results for each subseqent file are then
returned in order. By default all statistics are calculated. If specifitc statistics are
requested via a command-line option, then only the requested statistics are printed.

A very useful feature of this program is the ability to restrict the set of voxels
included in the statistic calculation, either by restricting the range of included values
(-floor, -ceil or -range), or by 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.

OPTIONS


Note that options can be specified in abbreviated form (as long as they are unique) and
can be given anywhere on the command line.

General options


-clobber
Overwrite an existing file.

-noclobber
Don't overwrite an existing file (default).

-debug Dump a lot of extra information (for when things go haywire).

-verbose
Print out extra information (more than the default).

-quiet Print out only the requested numbers

-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 .

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.

-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.

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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