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
It will try to figure out whether the volume is T1 volume or not by checking the number of grey value 110. Under the standard processing like recon-all script,
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>