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


= Name =
mergecontrasts-sess - mergedcontrast name of new contrast

= Synopsis =
mergecontrasts-sess ??

= Arguments =
== Positional Arguments ==
None

== Required Flagged Arguments ==
None

== Optional Flagged Arguments ==
|| -conjunction name || and, or, andor ||
|| -analysis analysisname || name of session-level functional analysis ||
|| -contrast || name thresch tail complement ||
|| -map || mapname ||
|| -space spacename || tal or sph ||
|| -spacedir spacedir || if not tal or sph ||
|| -sf sessidfile || ... ||
|| -df srchdirfile || ... ||
|| -s sessid || ... ||
|| -d srchdir || ... ||
|| -version || print version and exit ||
|| -help || print help and exit ||
|| -umask umask || set unix file expression mask ||

= Outputs =
|| <??> || ?? ||

= Description =

[[mergecontrasts-sess]] will merge two or more contrasts. The merging is done by
comparing each thresholded contrast on a voxel-by-voxel basis. The
result depends upon the conjunction chosen. For the 'and' conjunction,
each contrast must meet the threshold criteria at a voxel for the
voxel to be set to 1.  For the 'or' conjunction, the voxel is set to 1
if any contrast meets the threshold criteria. Otherwise, the voxel is
set to zero. For the 'andor' conjunction, a voxel is set to 2 if both
of the inputs meet the criteria. If the first input meets the criteria,
then the voxel is set to 1. If the second input meets the criteria,
then the voxel is set to 2. Otherwise, the voxel is zero. The andor
only makes sense with two input. The andor conjunction allows four
distinct areas to be visualized.

The output is a map with the same name as the input map which will be
placed in a new contrast directory. The merged contrast can be
accessed in the same was as any other contrast.  However, remember
that the voxel values of the merged contrast will be either 0 or 1, so
set thresholds appropriately.

The contrast and threshold criteria are set with the -contrast flag.
The first argument is the name of the contrast. The second is the
threshold to apply. If the map is a significance map, then set the
threshold based on log10(p) (eg, 2 = .01). The third argument is the
tail, which can be either pos, neg, or abs for positive, negative, or
ignore sign. The final arugment allows the user to use a
complement. Ie, if the fourth argument is non-zero and the threshold
criteria is met, then a 0 is input to the conjunction.

There is a .ovlp file created with the following three numbers:
 a. number of voxels in contrast 1 that met threshold criteria
 a. number of voxels in contrast 2 that met threshold criteria
 a. number of voxels that overlapped


= Examples =
== Example 1 ==
??


= Bugs =
??

= See Also =
[[othercommand1]]

= Links =
FsFast

= Methods Description =
{{{
??
}}}

= References =
[[References/Lastname###]]

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

= Author/s =
DougGreve