Name

mri_watershed - strip skull and other outer non-brain tissue

Arguments

Positional Arguments

invol	input volume
outvol	output volume

Optional Flagged Arguments

-w weight	preweight the input image using atlas information (no_w -> 1)
-no_wta	don't use the preweighting for the template deformation
-b proba_merging	use the basins merging using atlas information (no_b -> 1)
-copy	just copy input to output, ignore other options
-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

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

Links

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 < freesurfer@nmr.mgh.harvard.edu > YasunariTosa

-  ⇤ ← Revision 10 as of 2004-08-05 03:18:14 → 
  Size: 1126
  Editor: DavidTuch
  Comment: Removed indentation.
+   ← Revision 28 as of 2018-01-03 17:50:01 → ⇥
  Size: 4792
  Editor: MorganFogarty
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-## see dtrecon as an exmaple
+## 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
##
## See HelpOnCommandTemplate for description of formatting
<<Navigation(children)>> '''Index''' <<TableOfContents>>
-Line 3:
+Line 11:
-{{{
mri_watershed - strips skull and other outer non-brain voxels from a normalized T1 volume
}}}
= Synopsis =
{{{
mri_watershed arg1 -i <arg2> -o <arg3> [<options>]
}}}
+mri_watershed - strip skull and other outer non-brain tissue
-Line 11:
+Line 13:
-= Positional Arguments =
{{{
arg1
  description
  description
}}}
+= Arguments =
== Positional Arguments ==
||invol ||input volume ||
||outvol ||output volume ||
 Line 18:
-= Required Flagged Arguments =
{{{
-i <arg2> 
  description
  description
-Line 24:
+Line 19:
--o <arg3>
  description
  description
}}}
+== Optional Flagged Arguments ==
||-w weight || preweight the input image using atlas information (no_w -> 1) || ||
||-no_wta || don't use the preweighting for the template deformation || ||
||-b proba_merging || use the basins merging using atlas information (no_b -> 1) || ||
||-copy || just copy input to output, ignore other options || ||
||-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 || ||
-Line 29:
+Line 49:
-= Optional Flagged Arguments =
{{{
-f <fvalue>
  description
  description

-g <gvalue>
  description
  description
}}}
-Line 41:
+Line 51:
-{{{     
volume1 - description
volume2 - description
+||brainvol ||skull stripped brain volume ||
||BEMsurfaces ||when you specify the option -brainsurf surfname ||


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

= Examples =
== Example 1 ==
{{{
mri-watershed -atlas T1 brain
-Line 45:
+Line 62:
+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.
-Line 46:
+Line 64:
-= Example 1 =
+== Example 2 ==
-Line 48:
+Line 66:
-mri_watershed foo -i f -o out
+mri-watershed T1 brain
-Line 50:
+Line 68:
+The same as the first example, but no correction is applied to the intermediate result.
-Line 51:
+Line 70:
-= Example 2 =
{{{
mri_watershed foo -i f -o out -f fvalue
}}}
+= Bugs =
None
-Line 57:
+Line 74:
-["othercommand1"], ["othercommand2"]

= Author =
JaneSmith
+[[mri_normalize]]
-Line 63:
+Line 77:
-FreeSurfer
+FreeSurfer, FsFast
-Line 65:
+Line 79:
-= References =
## For example: ["Belliveau1991"]
["References/NameYear"]
+= 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]].
-Line 70:
+Line 94:
-Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Category =
## For example: CategoryFreeSurferCommandVolumeConversion
CategoryFreeSurferCommandSkullStripping
+Report bugs to < freesurfer@nmr.mgh.harvard.edu > YasunariTosa