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


= Name =
[[intergroupavg-sess]] - computes random effects analysis between 2 groups or subject populations (i.e. controls vs. patients)

= Synopsis =
[[intergroupavg-sess]] -analysis <analysisname> -contrast <contrastname> -group1 <group1name> -group2 <group2name> -intergroup <intergroupname>-space <spacename>

= Arguments =
== Positional Arguments ==
|| none ||

== Required Flagged Arguments ==
||  -analysis analysisname  || session-level functional analysis name || analysis created by [[mkanalysis-sess.new]] and used with [[selxavg-sess]] on each individual session ||
||   -contrast contrastname || contrast used in the random effects avg || contrast created by [[mkanalysis-sess.new]]  and used when running [[isxavg-re-sess]] If the contrast is multivariate, then sig and minsig maps will be produced ||
||   -group1    groupname    || name of group1 (positive) || group name given when calling [[isxavg-re-sess]]. This refers to the group that will be "positive'' ||
||   -group2    groupname    || name of group2 (negative) ||  group name given when calling [[isxavg-re-sess]]. This refers to the group that will be "negative'' ||
||   -intergroup intergroupname || name of intergroup average || name given to the intergroup average. This name is used in subsequent commands just as one would use the session id or the group name ||
||   -space    spacename  || space in which to average (tal, sph) ||  Space in which {\em isxavg-re-sess} was run. This is the space that each individual was transformed to so that all individuals across all groups are registered. Options are: tal (for talairach), sph (for spherical surface-based), or the name of a region-of-interest (created with [[func2roi-sess]] ||

== Optional Flagged Arguments ==
||   -polarity   +1 or -1 || only consider voxels with avg > 0 (or < 0) ||
||   -spacedir  dir || default is spacename ||
||   -hemi     hemisphere   || with sph space <lh rh> ||
||   -umask umask   || set unix file permission mask ||
||   -scriptonly    || don't run, just generate a script ||
||   -version       || print version and exit ||
 
= Outputs =


= Description =
[[intergroupavg-sess]] is a program for intergroup averaging. The
individual groups are assumed to have been averaged using a random
effects model (see [[isxavg-re-sess]]).  Inter-group statistics are
computed based on a t-statistic.  The average and
variance for each group are computed according to a random effects
model.  To run the random effects averaging, the user chooses a
contrast which is used to collapse the hemodynamic responses across
time and condition to yield a single number for each subject.  The
group average will be the average of this number over all the
subjects. The group variance will be the variance of this number
across all the subjects in the group.

= Examples =
== Example 1: Whole Processing Stream ==

Say you have 10 subjects in 2 groups (A and B) with sessids: subject1a, ..., subject5a, subject1b, ..., subject5b. 

Create sessid files called a.sid and b.sid and sessdir file sess.dir. Let the analysis name be "main''. The contrast you are interested in is "up-vs-down''.

Run [[selxavg-sess]] on all subjects:
 [[selxavg-sess]] -sf a.sid -sf b.sid -df sess.dir -analysis main

Resample them into talairach space:
 [[func2tal-sess]] -res 4 -sf a.sid -sf b.sid -df sess.dir -analysis main

Run random effects group averaging for each group:
 [[isxavg-re-sess]] -group GroupA -sf a.sid -df sess.dir -analysis main-contrast up-vs-down -space tal
 [[isxavg-re-sess]] -group GroupB -sf b.sid -df sess.dir -analysis main-contrast up-vs-down -space tal

Run intergroup averaging
 [[intergroupavg-sess]] -analysis main -contrast up-vs-down -group1 GroupA -group2 GroupB -intergroup AMinusB -space tal

View the results on the talairach volume:
 [[tkmedit-sess]] -analysis main -s AMinusB -isxavg random -contrast up-vs-down  -space tal -d .

== Example 2: Spherical ==
[[intergroupavg-sess]] -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space sph -spacedir <outdir from [[sphsmooth-sess]]

== Example 3: Volume/Talairach ==
[[intergroupavg-sess]] -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space tal -polarity 1

performs a between-group average but only considers voxels that are <1 for the given contrast for each of the two groups (i.e. only considers voxels that were "red" in the given contrast for controls and for patients, and only uses these voxels in the between-group contrast

= Bugs =
None

= See Also =
[[isxavg-re-sess]]

= Links =
FreeSurfer, FsFast

= Methods Description =

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

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

= Author/s =
DougGreve PhD