## Note: This page was created with the CommandTemplate
##
## If you're modifying this page please take a look at the
## latest version of CommandTemplate to ensure that you're
## using the latest version of the CommandTemplate
##
## See HelpOnCommandTemplate for description of formatting

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


= Name =
mri_fill 

= Synopsis =
mri_fill [options] <input MR directory> <output MR directory>

= Arguments =
== Positional Arguments ==

|| <input MR directory> || input directory ||
|| <output MR directory> || output directory ||


== Required Flagged Arguments ==
none

== Optional Flagged Arguments ==
=== General ===
|| -T <threshold> || specify fill_holes threshold (default=1)||
|| -xform <xformname> ||use xform dst offset to get an accurate Talairach volume||
|| -segmentation <filename> || aseg volume used to perform fill ||
|| -atlas <filename> || specify atlas to use for auto-filling ||
|| -fillven || fill ventricles ||

=== Seed point options in Talairach coordinates ===
||-C <x> <y> <z> || Talairach coords of the seed for the corpus callosum||
||-P <x> <y> <z> || Talairach coords of the seed for the pons||
||-lh <x> <y> <z>  || Talairach coords of the white matter seed for the left hemisphere||
||-rh <x> <y> <z>  || Talairach coords of the white matter seed for the right hemisphere||

=== Alternative seed point options in voxel coordinates ===
|| -CV <x> <y> <z> || voxel coords of the seed for the corpus callosum||
|| -PV <x> <y> <z> || voxel coords of the seed for the pons||

= Outputs =
|| filled || The filled volume for the cortical reconstruction- used for subsequent surface tesselation. ||

= Description =
This program creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation. 

= Examples =
== Example 1 ==
{{{
mri_fill SUBJECT/mri/wm/. SUBJECT/mri/filled
}}}
Takes a subjects wm volume as input and uses this to find cutting planes to seperate the hemispheres and remove the brainstem, and fills hemispheres with specific values as filled volume output.

= Bugs =


= See Also =
[[mri_segment]]

= Links =
FreeSurfer, FsFast

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

= Author/s =
BruceFischl