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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
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>