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| mri_binarize - Binarize a volume (or volume-encoded surface file) |
mri_binarize = Description = Program to binarize a volume (or volume-encoded surface file). Can also be used to merge with other binarizations. Binarization can be done based on threshold or on matched values. |
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| ||-flag3 arg3 ||brief description || Cannot be used with --match || | |
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| ||--max || Maximum voxel threshold (default is infinity) || || | ||--max || Maximum voxel threshold (default is infinity) || Cannot be used with --match || |
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= Description = Program to binarize a volume (or volume-encoded surface file). Can also be used to merge with other binarizations. Binarization can be done based on threshold or on matched values. |
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== Example 2 == command foo -i f -o out -f fvalue |
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= Methods Description = {{{ description description }}} = References = [[References/Lastname##|References/Lastname###]] |
Index
Contents
Name
mri_binarize
Description
Program to binarize a volume (or volume-encoded surface file). Can also be used to merge with other binarizations. Binarization can be done based on threshold or on matched values.
Synopsis
mri_binarize --i aseg.mgz --o left_hippocampus.mgz --match 17
Arguments
Required Flagged Arguments
--i <invol> |
input volume to be binarized |
--o <outvol> |
path to output volume |
Optional Flagged Arguments
--min |
Minimum voxel threshold (default is -infinity) |
Cannot be used with --match |
--max |
Maximum voxel threshold (default is infinity) |
Cannot be used with --match |
--pct P |
Set threshold to capture top P% (in mask or total volume) |
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--rimin rmin |
Compute minimum based on rmin*globalmean |
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--rmax rmax |
Compute maximum based on rmax*globalmean |
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--match matchval <matchval2 ...> |
Use match instead of threshold |
Any number of match values can be specified. Cannot be used with --min/--max. |
--wm |
Set match vals to 2, 41, 77, 251-255 (aseg for cerebral WM) |
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--ventricles |
Set match vals those for aseg ventricles+choroid (not 4th) |
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--wm+vcsf |
WM and ventricular CSF, including choroid (not 4th) |
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--subcort-gm |
Subcortical gray matter |
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--count countfile |
Save number of hits in ascii file |
Four numbers are saved: the number of voxels that match(nhits), the volume of the voxels that match, the total number of voxels in the volume (nvoxtot), and the percent matching (100*nhits/nvoxtot). |
--binval val |
Set voxels within threshold to val (default is 1) |
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--binvalnot notval |
Set voxels outside range to notval (default is 0) |
Only applies when a merge volume is NOT specified. |
--inv |
set binval=0, binvalnot=1 |
detailed description (eg, help file information) |
--frame frame# |
Use 0-based frame of input (default is 0) |
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--frame-sum |
Sum frames together before binarizing |
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--frame-and |
Take intersection (AND) of frames |
You do not need to specify a --min (the min will be set to nframes-0.5). |
--merge mergevol |
Merge with mergevolume |
mergevol must be the same dimension as the input volume. Combining this with --binval allows you to construct crude segmentations. |
--mask maskvol |
Mask input with maskvol |
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--mask-thresh thresh |
Set threshold for mask (default is 0.5) |
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--abs |
Take abs of invol first (ie, make unsigned) |
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--bincol |
Set binarized voxel value to its column number |
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--zero-edges |
Set edge voxels to zero |
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--zero-slice-edges |
Set edge slice voxels to zero |
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--dilate ndilate |
Dilate binarization in 3D |
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--erode nerode |
Erode binarization in 3D (after any dilation) |
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--erode2d nerode2d |
Erode binarization in 2D (after any 3D erosion) |
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--checkopts |
Don't run anything, just check options and exit |
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--help |
Print out information on how to use this program |
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--version |
Print out version and exit |
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--uchar |
Save output file in 'uchar' format |
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Outputs
volume1 |
description |
volume2 |
description |
Examples
Example 1
mri_binarize --i yoursubjectname/mri/aseg.mgz --match 17 --o left_hip.nii
Creates a binary mask (.nii) of the left hippocampus from the subject aseg.mgz.
description
Bugs
None
See Also
Links
Reporting Bugs
Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >