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

= Name =
mc-sess - MotionCorrection using [[AFNI]]

= Synopsis =
mc-sess -s <sessid> -d <srchdir> [options] <<BR>>
mc-sess -sf <sessidfile> -df <srchdirfile>  [options]

= Arguments =
== Positional Arguments ==
none

== Required Flagged Arguments ==
|| -s <sessid> or -sf <sessidfile>   || description ||
|| -d <srchdir> or -df <srchdirfile> || description ||

== Optional Flagged Arguments ==
|| -method <mcmethod> || afni ||
|| -targnthrun <n>    || uses nth run as target. default: n=1 ||
|| -toff <m>      || m is target image offset ||
|| -fstem <outstem>   || stem of output motion-corrected volume (fmc) ||
|| -fmcstem <outstem> || stem of output motion-corrected volume (fmc) ||
|| -umask <umask>     || set unix file permission mask to umask ||
|| -version           || print version and exit ||
|| -rlf <runlistfile> || only process those in the runlist file ||

= Outputs =
|| outstem || motion-corrected volume ||

= Description =
mc-sess performs MotionCorrection using the [[AFNI]] MotionCorrection tool. By default, the MotionCorrection is performed to the first run, although you can motion correct to a different run using the -targnthrun flag.

= Examples =
== Example 1 ==
mc-sess -s grp1id -d grp1dir

mc-sess using sess id and a search directory

== Example 2 ==
mc-sess -sf grp1sessfile -df grp1dirfile

mc-sess using sess id file and search directory file

= Bugs =
none

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

= Links =
FsFast, FsFastMotionCorrect, [[AFNI]]

= Methods Description =
{{{
The images were then motion corrected using the AFNI motion correction tool (http://afni.nimh.nih.gov/afni/).
}}}

= References =
[[References/Cox1999]]

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

= Author =
DougGreve