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'''Index'''
[[TableOfContents]]


= Name =
stxgrinder-sess - compute contrasts based on GeneralLinearModel

= Synopsis =
stxgrinder-sess - ??

= Arguments =
== Required Flagged Arguments ==
??

== Optional Flagged Arguments ==
||-a <analysisname> || session-level functional analysis name||
||-c <contrast> [<-c contrast>] || contrasts||
||-all || compute all contrasts for given analysis||
||-space <spacename> || space in which to average (native, tal, sph)||
||-spacedir <spacedir> || space directory (default spacename)||
||-hemi <hemisphere> || with sph space <lh rh>||
||-fdofmax <dofmax> || max dof for F-test||
||-sf <sessidfile> || ...||
||-df <srchdirfile>|| ...||
||-s <sessid> ||...||
||-d <srchdir> ||...||
||-help|| ||
||-umask <umask> || set unix file permission mask||
||-version || print version and exit||

 
= Outputs =
||ces || Contrast Effect Size = C*bhat||
||cespct || ces expressed as a percentage of mean baseline||
||cesvar || variance of ces||
||t || t-ratio||
||sig || significance based on t-test||
||f || f-ratio (when J>1)||
||fsig || significance based on F-test (when J>1)||
||minsig || best significance, boferroni corrected (when J>1)||
||iminsig || index of best significance (when J>1)||

= Description =
== Notes ==

The significances are stored as -log10(p).

For t-tests, the signifiance is given the same sign as the t-value.

For F-tests, the signifiance is not given a sign. This is the only
difference with stxgrinder-sess.

t-test is not saved when contrast is omnibus or zomnibus

An "old" version of stxgrinder-sess is available as ["stxgrinder0-sess"].

= Examples =
== Example 1 ==
??

== Example 2 ==
??

= Bugs =
The program occasionally hangs when performing the F-test. This is
caused when the DOF is very large (eg, > 1000). This ofen happens
when analyzing group fixed effects. If the program appears to hang,
reduce FtestDOFMax with -fdofmax until it seems to run ok. You can
also just skip the F-test with -noftest.


= See Also =
["othercommand1"], ["othercommand2"]

= Links =
FreeSurfer, FsFast

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

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

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

= Author/s =
JaneSmith