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| ## 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]] |
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| mri_watershed - strip skull and other outer non-brain tissue = Synopsis = mri_watershed [<options>] invol outvol = Arguments = == Positional Arguments == || invol || input volume || || outvol || output volume || == Required Flagged Arguments == None == 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 usage message || || || --version || show the current version || || = Outputs = || brainvol || skull stripped brain volume || || BEMsurfaces || when you specify the option -brainsurf surfname || = Description = 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 = See Also = ["mri_normalize"] = Links = FreeSurfer, FsFast = Methods Description = |
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| mri_watershed - strips skull and other outer non-brain voxels from a normalized T1 volume }}} = Synopsis = {{{ mri_watershed arg1 -i <arg2> -o <arg3> [<options>] |
The "watershed" segmentation algorithm was used to dertermine 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. If you used -atlas option, then { The template was used to correct the surface. } The finely grained sphere was fit to the brain. (Segonne 2004) |
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| = Positional Arguments = {{{ arg1 description description }}} = Required Flagged Arguments = {{{ -i <arg2> description description -o <arg3> description description }}} = Optional Flagged Arguments = {{{ -f <fvalue> description description -g <gvalue> description description }}} = Outputs = {{{ volume1 - description volume2 - description }}} = Example 1 = {{{ mri_watershed foo -i f -o out }}} = Example 2 = {{{ mri_watershed foo -i f -o out -f fvalue }}} = See Also = ["othercommand1"], ["othercommand2"] = Author = JaneSmith = Links = FreeSurfer |
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| ## For example: ["Belliveau1991"] ["References/NameYear"] |
["References/Segonne2004"] |
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| Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> | Report bugs to <freesurfer@nmr.mgh.harvard.edu> |
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| = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFreeSurferCommandSkullStripping |
= Author/s = YasunariTosa |
Navigation(children) Index TableOfContents
Name
mri_watershed - strip skull and other outer non-brain tissue
Synopsis
mri_watershed [<options>] invol outvol
Arguments
Positional Arguments
invol |
input volume |
outvol |
output volume |
Required Flagged Arguments
None
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 usage message |
|
--version |
show the current version |
|
Outputs
brainvol |
skull stripped brain volume |
BEMsurfaces |
when you specify the option -brainsurf surfname |
Description
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
See Also
["mri_normalize"]
Links
Methods Description
The "watershed" segmentation algorithm was used to dertermine 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.
If you used -atlas option, then { The template was used to correct the surface. }
The finely grained sphere was fit to the brain.
(Segonne 2004)
References
["References/Segonne2004"]
Reporting Bugs
Report bugs to <freesurfer@nmr.mgh.harvard.edu>