--i <invol>

input volume to be binarized

--o <outvol>

path to output volume

--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)

Set min threshold so that the top P percent of the voxels are captured in the output mask. The percent will be computed based on the number of voxels in the volume (if not input mask is specified) or within the input mask.

--rimin rmin

Compute minimum based on rmin*globalmean

--rmax rmax

Compute maximum based on rmax*globalmean

--fdr fdrthres

Compute min based on FDR assuming -log10(p) input. --fdr-pos, -fdr-neg, fdr-abs (use only pos, neg, or abs). Abs is the default.

Set min threshold to achieve a given FDR. By default, it uses the absolute value but this can be changed with --fdr-pos and --fdr-neg. If a mask is passed, it will compute the voxel-wise threshold only with in the places where mask > 0.5. The mask threshold will be ignored.

--match matchval <matchval2 ...>

Use match instead of threshold

Binarize based on matching volumes. Any number of match values can be specified. Cannot be used with --min/--max.

--replaceonly V1 V2

Replace voxels equal to V1 with V2 and propagate other src voxels instead of binarizing

--replace V1 V2

Replace voxels equal to V1 with V2

Replace every occurrence of (int) value V1 with value V2. Multiple --replace args are possible.

--ctx-wm

Set match vals to 2, 41, 77, 251-255 (aseg for cerebral WM)

--all-wm

Set match vals to 2, 41, 77, 251-255, 7, and 46 (aseg for all WM)

--ventricles

Set match vals those for aseg ventricles+choroid (not 4th)

--wm+vcsf

WM and ventricular CSF, including choroid (not 4th)

--gm

Match for all Wm and VCSF and background, then invert

--subcort-gm

Subcortical gray matter

--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).

-no-count

Turn off counting number of voxels in the first frame (good for large volumes)

--binval val

Set voxels within threshold to val (default is 1)

Value to use for those voxels that are in the threshold/match (--binval) or out of the range (--binvalnot). These must be integer values.

--binvalnot notval

Set voxels outside range to notval (default is 0)

Value to use for those voxels that are in the threshold/match (--binval) or out of the range (--binvalnot). These must be integer values. Only applies when a merge volume is NOT specified.

--inv

set binval=0, binvalnot=1

--frame frame#

Use 0-based frame of input (default is 0)

--frame-sum

Sum frames together before binarizing

Sum the frames together before applying threshold

--frame-and

Take intersection (AND) of frames

You do not need to specify a --min (the min will be set to nframes-0.5). Treat the multi-frame volume as binary 'AND' the frames together. This takes an intersection of the individual frames

--frameno

Use give frame of the input, 0-based, default is 0.

--merge mergevol

Merge with mergevolume

mergevol must be the same dimension as the input volume. Merge binarization with the mergevol. If the voxel is within the threshold range (or matches), then its value will be binval. If not, then it will inherit its value from the value at that voxel in mergevol. 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

Mask input with mask. The mask volume is itself binarized at thresh (default is 0.5). If a voxel is not in the mask, then it will be assigned binvalnot or the value from the merge volume.

--mask-thresh thresh

Set threshold for mask (default is 0.5)

Mask input with mask. The mask volume is itself binarized at thresh (default is 0.5). If a voxel is not in the mask, then it will be assigned binvalnot or the value from the merge volume.

--abs

Take abs of invol first (ie, make unsigned)

--bincol

Set binarized voxel value to its column number

--zero-edges

Set edge voxels to zero

Set the first and last planes in all dimensions to zero (or --binvalnot_. This makes sure that all the voxels on the edge of the imaging volume are zero.

--zero-slice-edges

Set edge slice voxels to zero

Same as --zero-edge, but only for slices

--dilate ndilate

Dilate binarization in 3D

--erode nerode

Erode binarization in 3D (after any dilation)

--erode2d nerode2d

Erode binarization in 2D (after any 3D erosion)

--erode-face nerode

Erode binarization using 'face' nearest neighbor

--erode-edge nerode

Erode binarizaiton using 'edge' nearest neighbor

--erode-corner nerode

Erode binarization using 'corner' nearest neighbor, same as --erode

--bb npad

Reduce dim of output to the minimum volume of non-zero voxels with npad boundary

--surf surfname

Create a surface mesh from the binarization

--surf-smooth niteration

Iteratively smooth the surface mesh

--noverbose

Default is verbose

--uchar

Save output file in 'uchar' format

--checkopts

Don't run anything, just check options and exit

--help

Print out information on how to use this program

--version

Print out version and exit

--debug

Turns on debugging