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| ## 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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mri_watershed - strips skull and other outer non-brain tissue voxels from a normalized T1 volume |
mri_watershed - strips skull and other outer non-brain voxels from an acquired volume (usually T1). |
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| command argA argB -flag1 <arg1> -flag2 <arg2> -flag3 <arg3> | mri_watershed [<options>] <input volume> <brain volume> |
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| argA Description argB Description |
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| -flag1 <arg1> Description - flag2 <arg2> Description |
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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. = Outputs = || volume1 || description || || volume2 || description || |
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| -flag3 <arg3> Description. = Outputs = file1 Description file2 Description |
= Description = description |
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| command argA argB -flag1 foo -flag2 goo | mri-watershed foo -i f -o out |
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| Description | description |
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| command argA argB -flag1 foo -flag2 goo -flag3 hoo | mri-watershed foo -i f -o out -f fvalue |
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| Description | description |
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| ["command2"] ["command3"] = Author = JaneSmith |
["othercommand1"], ["othercommand2"] |
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| CommandGuide | FreeSurfer, FsFast |
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| SkullStripping | = Methods Description = {{{ description description }}} |
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| [wiki:Self:References#NameYear NameYear] | ["References/Lastname###"] |
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| = Category = CategoryFreeSurferCommandSkullStripping |
= Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = Author/s = JaneSmith |
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.
Outputs
volume1 |
description |
volume2 |
description |
Description
description
Example 1
mri-watershed foo -i f -o out
description
Example 2
mri-watershed foo -i f -o out -f fvalue
description
See Also
["othercommand1"], ["othercommand2"]
Links
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>