NAME

mri_fill

SYNOPSIS

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

DESCRIPTION

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

POSITIONAL ARGUMENTS

Argument	Explanation
<input MR directory>	input directory
<output MR directory>	output directory

REQUIRED-FLAGGED ARGUMENTS

None

OPTIONAL-FLAGGED ARGUMENTS

Where options

Argument	Explanation
-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

Argument	Explanation
-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

Argument	Explanation
-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

Output	Explanation
filled	The filled volume for the cortical reconstruction- used for subsequent surface tesselation.

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

None

REPORTING

Report bugs to <freesurfer@nmr.mgh.harvard.edu>

SEE-ALSO

mri_segment