vbim(1) manipulate 3D and 4D volumes


vbim <flag> ...


vbim is part of the VoxBo suite of tools for brain image analysis.

vbim is a multi-purpose program that applies various simple manipulations to 3D and 4D images.


vbim performs a set of operations, specified by option flags, in sequence. To get a complete list of available flags, run the program with no arguments.


To get very basic info about a file:
vbim foo.nii -info

To get more detailed information about the data within a mask:

vbim foo.nii -regioninfo mask.nii

To apply a mask to a 3D image and write out the result:

vbim image.nii -mask mask.nii -write maskedimage.nii

To mask a 4D image:

vbim image.nii -mask mask.nii -write4D maskedimage.nii

To average a bunch of 3D volumes:

vbim *.nii.gz -average -write mean.nii.gz

To create a lesion count map from a set of lesion masks:

vbim *.nii -count -write count.nii.gz

To create a 4D volume (20x20x20 voxels, 32-bit int, 10 time points) of random data with a mean of 100 and sd of 10:

vbim -newvol 20 20 20 10 int32 -addnoise 100 10 -write3d myvol.nii



Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and via the NeuroDebian project (neuro.debian.net) for Debian derivatives.


VoxBo is provided with no warranty whatsoever.


For an historical roster of the VoxBo development team, visit www.voxbo.org.