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| ## see dtrecon as an exmaple | ## 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 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. description = Example 2 = mri-watershed T1 brain The same as the first example, but no correction is applied to the intermediate result. description = 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>] |
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. |
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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/Segonne, F###"] |
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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 = Yasunari Tosa |
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.
description
Example 2
mri-watershed T1 brain
The same as the first example, but no correction is applied to the intermediate result.
description
See Also
["mri_normalize"]
Links
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