|
Size: 854
Comment:
|
Size: 1435
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | 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 |
| Line 3: | 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). |
| Line 6: | Line 12: |
| command argA argB -flag1 <arg1> -flag2 <arg2> -flag3 <arg3> | mri_watershed [<options>] <input volume> <brain volume> |
| Line 9: | Line 15: |
| argA Description argB Description |
|
| Line 18: | Line 17: |
| -flag1 <arg1> Description - flag2 <arg2> Description |
|
| Line 27: | Line 19: |
| || -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 || |
|
| Line 28: | Line 27: |
| -flag3 <arg3> Description. = Outputs = file1 Description file2 Description |
= Description = description |
| Line 42: | Line 31: |
| command argA argB -flag1 foo -flag2 goo | mri-watershed foo -i f -o out |
| Line 44: | Line 33: |
| Description | description |
| Line 47: | Line 36: |
| command argA argB -flag1 foo -flag2 goo -flag3 hoo | mri-watershed foo -i f -o out -f fvalue |
| Line 49: | Line 38: |
| Description | description |
| Line 51: | Line 40: |
| = Version = $ CVS ID $ = Author = JaneSmith |
= See Also = ["othercommand1"], ["othercommand2"] |
| Line 58: | Line 44: |
| CommandGuide | FreeSurfer, FsFast = Methods Description = {{{ description description }}} = References = ["References/Lastname###"] |
| Line 61: | Line 56: |
| Report bugs to <> | 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>