Name

mri_diff - test for differences between two volumes

Synopsis

mri_diff [options] vol1file vol2file [options]

Arguments

Positional Arguments

vol1file, vol2file

volumes to be compared

Optional Flagged Arguments

--allow-res	do not check for resolution diffs
--allow-acq	do not check for acq param diffs
--allow-geo	do not check for geometry diffs
--allow-prec	do not check for precision diffs
--allow-pix	do not check for pixel diffs
--allow-ori	do not check for orientation diffs
--qa	check res, acq, precision, and orientation only
--thresh thresh	pix diffs must be greater than this
--log DiffFile	store diff info in this file
--debug	turn on debugging
--checkopts	don't run anything, just check options and exit
--help	print out information on how to use this program
--version	print out version and exit

Outputs

0	Volumes are not different and there were no errors
1	Errors encounted. Volumes may or may not be different
101	Volumes differ in dimension
102	Volumes differ in resolution
103	Volumes differ in acquisition parameters
104	Volumes differ in geometry
105	Volumes differ in precision
106	Volumes differ in pixel data
107	Volumes differ in orientation

Description

Determines whether two volumes differ. See below for what 'differ' means.

The basic usage is something like:

mri_diff vol1 vol2

It then prints to the terminal whether they differ or not.

NOTE: stuff might get printed to the terminal regardless of whether the volumes are different or not, so you cannot just use the presence or absence of terminal output to determine whether they are different as you can with unix diff.

There are three ways to determine whether they are different: 1. Look for 'volumes differ' in the terminal output 2. Program exits with status > 100 3. Create a log file

To create a log file, add --log yourlogfile any where in the command line, eg:

mri_diff vol1 vol2 --log yourlogfile

If youlogfile exists, it will be immediately deleted when the program starts. If a difference is detected, yourlogfile will be created, and information about the difference will be printed to it. If there is no difference, yourlogfile will not exist when the program finishes.

Volumes can differ in six ways:

Dimension, return status = 101
Resolutions, return status = 102
Acquisition Parameters, return status = 103
Geometry, return status = 104
Precision, return status = 105
Pixel Data, return status = 106

Dimension is number of rows, cols, slices, and frames. Resolution is voxel size. Acqusition parameters are: flip angle, TR, TE, and TI. Geometry checks the vox2ras matrices for equality. Precision is int, float, short, etc.

By default, all of these are checked, but some can be turned off with certain command-line flags:

--allow-res	turns of resolution checking
--allow-acq	turns of acquistion parameter checking
--allow-geo	turns of geometry checking
--allow-prec	turns of precision checking
--allow-pix	turns of pixel checking

In addition, the minimum difference in pixel value required to be considered different can be controlled with --thresh. Eg, if two volumes differ by .00001, and you do not consider this to be significant, then --thresh .00002 will prevent that difference from being considered different. The default threshold is 0.

mri_diff can be used to check that two volumes where acquired in the same way with the --qa flag. This turns on Res, Acq, and Prec, and turns of Geo and Pix. Instead of checking geometry, it checks for the basic orientation of the volumes (eg, RAS, LPI, etc). The idea here is that the pixel data and exact geometry may be different, but other things should be the same.

Bugs

None

Links

FreeSurfer, FsFast

Methods Description

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References

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

DougGreve