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Index
Contents
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
See Also
Links
Methods Description
description description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>