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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

[input volume]
[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

[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.

Bugs

None

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

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+## Note: This page was created with the CommandTemplate

##

## If you're modifying this page please take a look at the

## latest version of CommandTemplate to ensure that you're

## using the latest version of the CommandTemplate

##
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-##

## Note: If you are modifying this page please refer to the

## CommandTemplate page and confirm that this page has the latest

## CommandTemplate formatting
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-mri_watershed  [<options>] <input volume> <brain volume>
+mri_watershed  [<options>] [input volume] [brain volume]
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+||[input volume]|| ||

||[output volume]|| ||
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+None
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-|| -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 ||
+|| -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 || ||
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-|| <brain volume> || skull stripped brain volume ||
+|| [brain volume] || skull stripped brain volume ||
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+= Bugs =

None
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-See Florent Segonne et al. paper for details.
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-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.
+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)
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-["References/Segonne, F et al., paper"]
+["References/Segonne2004"]
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-Yasunari Tosa
+YasunariTosa