NAME

mri_watershed

SYNOPSIS

mri_watershed [<options>] invol outvol

DESCRIPTION

This program strips skull and other outer non-brain tissue and produces the brain volume from T1 volume or the scanned volume.

The \"watershed\" segmentation algorithm was used to dertermine the intensity values for white matter, grey matter, and CSF.
A force field was then used to fit a spherical surface to the brain. The shape of the surface fit was then evaluated against a previously derived template.

If you used -atlas option, then { The template was used to correct the surface. }

The finely grained sphere was fit to the brain.

The default parameters are: -w 0.82 -b 0.32 -h 10 -seedpt -ta -wta
You can use one of the first five flags to change these default parms.

(Segonne 2004)

POSITIONAL ARGUMENTS

ArgumentExplanation
involinput volume
outvoloutput volume

REQUIRED-FLAGGED ARGUMENTS

None

OPTIONAL-FLAGGED ARGUMENTS

ArgumentExplanation
-w weightpreweight the input image using atlas information (no_w -> 1)
-no_wtadont use the preweighting fot the template deformation
-b proba_merginguse the basins merging using atlas information (no_b -> 1)
-h int_hpfpresize the preflooding height (in percent)
-no_seedptdont use (seedpoints using atlas information)
-no-tadont use (template deformation using atlas information)
-atlasuse the atlas information to correct the segmentation. When the segmented brain is not correct, this option might help you.
-surf [surfname]save the BEM surfaces.In order to get the surfaces consistent with tkmedit, you have to use the option -useSRAS.
-useSRASuse the surface RAS coordinates (not the scanner RAS) for surfaces.
-noT1don't do T1 analysis. (Useful when running out of memory)
-lessshrink the surface
-moreexpand the surface
-watuse only the watershed algorithm
-T1specify T1 input volume (T1 grey value = 110)
-wat+tempwatershed algo and first template smoothing
-first_tempuse only the first template smoothing + local matching
-surf_debugvisualize the surfaces onto the output volume
-brainsurf [surfname]save the brain surface
-shk_br_surf [int_h surfname]to save the brain surface shrank inward of int_h mm
-s [int_i int_j int_k]add a seed point
-c [int_i int_j int_k]specify the center of the brain (in voxel unit)
-r int_rspecify the radius of the brain (in voxel unit)
-t int_thresholdchange the threshold in the watershed analyze process
-h int_hpfprecize the preflooding height (in percent)
-nnot use the watershed analyze process
-LABELlabelize the output volume into scalp, skull, csf, gray and white
-man [int_csf int_trn int_gray]to change the different parameters csf_max, transition_intensity and GM_intensity
-maskmask a volume with the brain mask
--helpshow usage message
--versionshow the current version

OUTPUTS

OutputExplanation
brainvolskull stripped brain volume
BEMsurfaceswhen you specify the option -brainsurf surfname

EXAMPLE 1

mri-watershed -atlas T1 brain

where T1 is the T1 volume and brain is the output brain volume. When the cerebellum is cut-off from the brain or getting the left/right asymmetric brain, you should first try this -atlas option.

EXAMPLE 2

mri-watershed T1 brain

The same as the first example, but no correction is applied to the intermediate result.

REPORTING

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

SEE-ALSO

mri_normalize