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description

Name

mri_watershed - strips skull and other outer non-brain voxels from an acquired volume (usually T1).

Synopsis

mri_watershed [<options>] <input volume> <brain volume>

Positional Arguments

Required Flagged Arguments

Optional Flagged Arguments

-atlas

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.

-useSRAS

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

-noT1

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

-less

shrink the surface

-more

expand the surface

-wat

use only the watershed algorithm

-T1

specify T1 input volume (T1 grey value = 110)

-wat+temp

watershed algo and first template smoothing

-first_temp

use only the first template smoothing + local matching

-surf_debug

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)

-n

not use the watershed analyze process

-LABEL

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

mask a volume with the brain mask

--help

show this usage message

--version

show the current version

Outputs

<brain volume>

skull stripped brain volume

[BEM surfaces]

when you specify the option -brainsurf surfname

Description

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

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

["mri_normalize"]

Links

FreeSurfer, FsFast

Methods Description

See Florent Segonne et al. paper for details.

First uses "watershed" process to figure out the grey scale values for white matter, grey matter, and CSF.
Second uses the force fields to shrink the rough sphere onto the brain.
Third evaluate the shape using the template ($FREESURFER_HOME/average/rigidly_aligned_brain_template.tiff)
for correctness.  If you used -atlas option, then use the template to correct the shape.   
Fourth use the finely grained sphere to fit onto the brain.

References

["References/Segonne, F###"]

Reporting Bugs

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

Author/s

Yasunari Tosa

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