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'''Index'''
<<TableOfContents>>


= 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:
  1. Dimension,               return status = 101
  2. Resolutions,             return status = 102
  3. Acquisition Parameters,  return status = 103
  4. Geometry,                return status = 104
  5. Precision,               return status = 105
  6. 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 =
FreeSurfer, FsFast

= Methods Description =
{{{
description
description
}}}

= References =

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

= Author/s =
DougGreve