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

= Name =
preproc-sess - pre-process fMRI data (motion correction, smoothing, intensity normalization (optional), and brain-mask creation)

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

= Arguments =
== Positional Arguments ==
none

== Required Flagged Arguments ==
||-sf ||sessidfile ||
||-df ||srchdirfile ||
||-s ||sessid ||
||-d ||srchdir ||


== Optional Flagged Arguments ==
||-surface||'''self''' or '''fsaverage''' followed by hemi '''lh rh lhrh''' (for both, the default)||
||-mcin   mcinstem ||stem to used as input to MC ||
||-mcout  mcoutstem ||stem to use as output of MC ||
||-smin   sminstem ||'''Expected "=" to follow "mcoutstem"''' ||
||-smout  smoutstem ||'''Expected "=" to follow "sminstemsm"''' ||
||-inorm  inormstem ||||<style="text-align:center">'''Expected "=" to follow "smoutstem"''' ||
||-mask   maskstem ||'''Expected "=" to follow "brain"''' ||
||-fwhm   fwhm ||fwhm in mm (volume and surface separately) ||
||-fsd    fsd ||'''Expected "=" to follow "bold"''' ||
||-rlf    rlf ||run list file (default all runs) ||
||-sliceorder so ||turn on slice timing correction with the given slice order ||
||-inorm ||perform intensity normalization (off by default) ||
||-update ||only run a stage if input is newer than output (default) ||
||-force ||force reprocessing of all stages (turns off -update) ||


= Outputs =
'''Expected "=" to follow "fmcsm"'''
||'''Expected "=" to follow "fmcsm"''' ||output volume ||




= Description =
[[preproc-sess]] runs the following preprocessing steps: motion correction ([[mc-sess]]), smoothing ([[spatialsmooth-sess]]), and brain-mask creation ([[mkbrainmask-sess]]). This will run preprocessing steps: motion correction (MC), slice-timing correction (STC), smoothing, intensity normalization (INorm), and brain mask creation. By default, it will perform MC, smoothing, and masking, but not STC or INorm. All stages producde a new volume that can be used as input to mkanalysis-sess. Note: MC and INorm require matlab but none of the other stages does.  By default, motion correction uses the first volume of the first run as the reference for all runs.

= Examples =
== Example 1 ==
To perform MC, smoothing by fwhm of 5mm, and brain mask, run

 . preproc-sess -sf sessidlist -df sessdirlist -vol-fwhm 5

For MC the input will be f and the output will be fmc For Smoothiing the input will be fmc and the output will be fmcsm5 Use this name (i,e fmcsm5) as the -funcstem argument in [[mkanalysis-sess.new]]

== Example 2 ==
To perform MC, STC, smoothing by fwhm of 7.1 mm, and brain mask, run

 . preproc-sess -sf sessidlist -df sessdirlist -vol-fwhm 7.1 -stc

For MC  the input will be f and the output will be fmc For STC the input will be fmc and the output will be fmcstc For Smoothiing the input will be fmcstc and the output will be fmcstcsm7.1

= Bugs =
??

= See Also =
[[mc-sess]], [[spatialsmooth-sess]], [[inorm-sess]],[[mkbrainmask-sess]], [[mkanalysis-sess.new]]

= Links =
FreeSurfer, FsFast

= Methods Description =
{{{
??
}}}
= References =
[[References/Lastname|References/Lastname###]]

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

= Author/s =
DougGreve