mri_watershed - strip skull and other outer non-brain tissue


Positional Arguments


input volume


output volume

Optional Flagged Arguments

-w weight

preweight the input image using atlas information (no_w -> 1)


don't use the preweighting for the template deformation

-b proba_merging

use the basins merging using atlas information (no_b -> 1)


just copy input to output, ignore other options


use 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.


use the surface RAS coordinates (not the scanner RAS) for surfaces.


don't do T1 analysis. (Useful when running out of memory)


shrink the surface


expand the surface


use only the watershed algorithm


specify T1 input volume (T1 grey value = 110)


watershed algo and first template smoothing


use only the first template smoothing + local matching


visualize 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_r

specify the radius of the brain (in voxel unit)

-t int_threshold

change the threshold in the watershed analyze process

-h int_hpf

precize the preflooding height (in percent)


not use the watershed analyze process


labelize 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


mask a volume with the brain mask


show usage message


show the current version



skull stripped brain volume


when you specify the option -brainsurf surfname

Produce the brain volume from T1 volume or the scanned volume.


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

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

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 parameters.


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.



See Also



FreeSurfer, FsFast

Methods Description

The "watershed" segmentation algorithm was used to determine 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.

The finely grained sphere was fit to the brain.

(Segonne 2004)

"-surf" Description:
The BEM surfaces are generated after the initial mri_watershed procedure has run and produced a "brain" surface file. This brain surface file is then grown by 3mm outward to generate the "inner skull" surface. This growth is meant to account for the CSF located between the pial matter and the inner skull (see Figure 17 in Segonne et al. 2004 for a description). Next a fifth order icosahedral surface is fit arround the outer edge of the Volume and smoothed making the "outer skin" surface. Finally, this surface is shrunk by 3mm to attempt to account for the SCALP (Skin, Connective tissue, Aponeurosis, Loose areolar connective tissue, and the Pericranium). This surface is saved as the "outer skull" surface. 

The -surf tool is intended as an added convenience and not as a high quality estimation of these tissue boundaries (one would not use an MPRAGE type volume for defining these tissue boundaries). For a tool designed to do that please see mri_make_bem_surfaces.

Reporting Bugs

Report bugs to < > YasunariTosa

mri_watershed (last edited 2018-01-04 10:17:45 by MorganFogarty)