Differences between revisions 1 and 16 (spanning 15 versions)

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.

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

-  ⇤ ← Revision 1 as of 2004-08-03 20:51:31 → 
  Size: 854
  Editor: EvelinaBusa
  Comment:
+   ← Revision 16 as of 2004-08-18 18:15:34 → ⇥
  Size: 3710
  Editor: YasunariTosa
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= mri_watershed =
+## See HelpOnCommandTemplate for description of formatting
##
## 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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+Line 7:
-This command is used to automatically strip the skull and other non-brain tissue voxels from an individual's normalized T1 volume to create a brain volume.
+= Name =
mri_watershed - strips skull and other outer non-brain voxels from an acquired volume (usually T1).
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+Line 12:
- command argA argB -flag1 <arg1> -flag2 <arg2> -flag3 <arg3>
+mri_watershed  [<options>] <input volume> <brain volume>
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+Line 15:
- argA

 Description

 argB 

 Description
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+Line 17:
- -flag1 <arg1>

 Description

 - flag2 <arg2>

 Description
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+Line 19:
- -flag3 <arg3>

 Description.
+|| -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 ||
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- file1
+|| <brain volume> || skull stripped brain volume ||
|| [BEM surfaces] || when you specify the option -brainsurf surfname ||
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+Line 48:
- Description

 file2 

 Description
+= Description =
Produce the brain volume from T1 volume or the scanned volume.
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+Line 52:
- command argA argB -flag1 foo -flag2 goo
+mri-watershed -atlas T1 brain
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+Line 54:
- Description
+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.
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+Line 59:
- command argA argB -flag1 foo -flag2 goo -flag3 hoo
+mri-watershed T1 brain
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+Line 61:
- Description
+The same as the first example, but no correction is applied to the intermediate result.
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+Line 63:
-= Version =
 $ CVS ID $

= Author =
 JaneSmith
+= See Also =
["mri_normalize"]
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+Line 67:
- CommandGuide
+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###"]
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+Line 84:
- Report bugs to <>
+Report bugs to <freesurfer@nmr.mgh.harvard.edu>

= Author/s =
Yasunari Tosa