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


= Name =
mri_seghead - binarizes volume so that all voxels in head are set to 255

= Synopsis =
mri_seghead --invol <invol> --outvol <outvol> --thresh1 <thr1> --thresh2 <thr2> [options]

= Arguments =
== Positional Arguments ==
none

== Required Flagged Arguments ==
|| --invol <invol>   || input volume ||
|| --outvol <outvol> || output volume ||
|| --thresh1 <thr1>  || ?? || 
|| --thresh2 <thr2>  || ?? ||

== Optional Flagged Arguments ==
|| --fill ||    || fill value  (default = 255) ||
||   --thresh   || single threshold value for 1 and 2. sets thresh1 and thresh2 to threshold. typical value = 20 || 
||   --nhitsmin || min number of consecutive hits (2). typical value = 2||

= Outputs =
|| <outvol> || output volume ||

= Description =
[[mri_seghead]] binarizes the input volume such that all the voxels in the 
head are set to 255 (or whatever is passed with --fill). The result is 
stored in the output volume passed by --outvol. 
 
The program first creates a binarized mass just a few mm below the skin.
This mass is then grown out using a connected components algorithm so 
that most of the skin details are retained. 
 
The initial mass is created in the following way. First, for every row 
and slice, the column is searched from both ends for the 'skin'. The 
skin is defined as the first consecutive nhitsmin voxels over thresh1.
Once the skin is found coming from both directions, everything in between
is binarized to the fill value. This process is repeated for the rows 
and slices. The initial mass is created by ANDing all three voxels.
 
After the initial mass is defined, the original volume is modified so
that all the voxels in the mass are set to 255. This has the effect of 
filling in all of the subepidermal features that would normally be below 
threshold. A seed point is chosen at the center of the volume. The final 
binarized volume is computed as all the voxels above thresh2 connected to  
the seed point. 

= Examples =
== Example 1 ==
??

== Example 2 ==
??

= Bugs =
none

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

= Links =
FreeSurfer

= Methods Description =
{{{
??
}}}

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

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

= Author/s =
BruceFischl