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[[Navigation(children)]]
'''Index'''
[[TableOfContents]]
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mri_watershed - strips skull and other outer non-brain voxels from an acquired volume (usually T1). mri_watershed - strip skull and other outer non-brain tissue
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= Synopsis =
mri_watershed [<options>] invol outvol
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= Synopsis =
mri_watershed [<options>] [input volume] [brain volume]
= Arguments =
== Positional Arguments ==
|| invol || input volume ||
|| outvol || output volume ||
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= Positional Arguments =
||[input volume]|| ||
||[output volume]|| ||

= Required Flagged Arguments =
== Required Flagged Arguments ==
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= Optional Flagged Arguments = == Optional Flagged Arguments ==
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|| [brain volume] || skull stripped brain volume ||
|| [BEM surfaces] || when you specify the option -brainsurf surfname ||
|| brainvol || skull stripped brain volume ||
|| BEMsurfaces || when you specify the option -brainsurf surfname ||
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= Example 1 = = Examples =
=
= Example 1 ==
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= Example 2 = == Example 2 ==

Navigation(children) Index TableOfContents

Name

mri_watershed - strip skull and other outer non-brain tissue

Synopsis

mri_watershed [<options>] invol outvol

Arguments

Positional Arguments

invol

input volume

outvol

output volume

Required Flagged Arguments

None

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 usage message

--version

show the current version

Outputs

brainvol

skull stripped brain volume

BEMsurfaces

when you specify the option -brainsurf surfname

Description

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

Examples

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.

Bugs

None

See Also

["mri_normalize"]

Links

FreeSurfer, FsFast

Methods Description

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.

(Segonne 2004) 

References

["References/Segonne2004"]

Reporting Bugs

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

Author/s

YasunariTosa

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