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


= Name =
sliceview-sess - the results are viewed on 2D slices of the brain

= Synopsis =
sliceview-sess -slice <slicenumber> -analysis <analysis name> -contrast <contrast name> -map <map name> -sf <sessidfile> -sf <sesssirfile>

= Arguments =
== Positional Arguments ==

== Required Flagged Arguments ==
|| -slice    || slicenumber  || number of the slice to view ||
|| -analysis || analysisname || name of analysis (from mkanalysis-sess)||
|| -contrast || contrastname || name of contrast  (from mkcontrast-sess)||
|| -map      || mapname      || name of map produced by stxgrinder-sess (sig, t, minsig, iminsig)||
|| -sf       || sessidfile   || see above ||
|| -df       || sessdirfile  || see above ||

== Optional Flagged Arguments ==
||-mapanalysis|| ||analysisname|| ||get map/contrast from this analysis||
||-thmin||       ||thresh      || ||minimum threshold for display (2)||
||-thmax||       ||thresh      || ||maximum threshold for display (7)||
||-thmask||      ||            || ||set thmin = .5 and thmax = 1 (good for masks)||
||-nohdr||       ||            || ||do not load/show hemodynamic response||
||-nosig||       ||            || ||do not load/show significance map||
||-raw||         ||run         || ||display raw MR from run||
||-rawstem||     ||stem        || ||display raw MR from run/stem||
||-motioncor||   ||            || ||display motion corrected raw data (with -raw)||
||-base||        ||volume      || ||t2epi, t1epi, t2conv||
||-mask||        ||maskid      || ||mask using FSD/masks/maskid||
||-subject||     ||subjectname || ||display on subject's talairached anatomical.only with -space tal; spec -base bshortBI where B = tal res, and I is 1, 2, or 4 ||
||-s||           ||sessid||       ||     ||
||-d||           ||srchdir||      || ||
||-fsd||         ||dir||          ||functional subdirectory (bold)||
||-scriptonly||  ||     ||        ||don't run, just generate a script||
||-umask||       ||umask||        ||set unix file permission mask||
||-version||     ||     ||        ||print version and exit||

= Outputs =

No output files are created.  When you run sliceview, the functional results are displayed on 2D slices of the brain.  You can scroll through different timepoints by using the -/+ keys.  To view the hemodynamic response for a particular voxel, click on that voxel and type “g”.     

= Description =

In Slice-based visualization, the results are viewed on 2D slices of the brain (either individual slices or mosaics of slices).  No information about the volume is available.  The slices are defined as those in the native functional space.  Typically, a significance map from a particular contrast is thresholded and laid over a structural slice.  Additionally, for event-related studies the hemodynamic response for each condition can be viewed by clicking on a particular voxel in the slice.  To see the individual results for all subjects for a single slice, run sliceview-sess from the Study Directory with the following options.

The results for each subject will be displayed sequentially (ie, you must close the window for one subject before you can see the next). The T1 EPI image as the underlay.  If the T1 does not exist, it will use mean functional image as the underlay.  For event-related studies, the hemodynamic responses will  be automatically loaded.  See Appendix A for more details on how to operate the viewer.

== Variation 1 ==

Viewing raw/motion-corrected time courses.  To view a raw or motion corrected time course, cd into the Study Directory and run sliceview with the following options:
||-raw  || ||runnumber||
||-slice|| ||slicenumber|| ||number of the slice to view||
||-sf 	|| ||sessidfile||  ||see above||
||-df	|| ||sessdirfile|| ||see above||

where runnumber is the number of the run whose raw data you want to view.  To view motion corrected data, add the flag "-motioncor".  If the functional subdirectory is not named "bold" then use the –fsd flag to specify the name.  The –raw and –fsd flags can be use at the same time with –analysis, -contrast, and –map flags to simultaneously view raw time courses, hemodynamic responses, and statistical maps.

== Variation 2 ==

Viewing Individual Talairach-Resampled Results. Add –space tal (cannot view raw data with tal).

= Examples =
== Example 1 ==
sliceview-sess  -slice mos -s 020710JG -df dir -analysis tau_sm6 -contrast all_fix_6-10 -map sig

= Bugs =
None

= See Also =

= Links =
FreeSurfer, FsFast

= Methods Description =
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= References =


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

= Author/s =
DougGreve