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warpimagemultitransform(1) [debian man page]


WarpImageMultiTransform - part of ANTS registration suite DESCRIPTION
Usage: ./WarpImageMultiTransform ImageDimension moving_image output_image -R reference_image --use-NN SeriesOfTransformations--(See Below) SeriesOfTransformations --- ./WarpImageMultiTransform can apply, via concatenation, an unlimited number of transformations to your data . Thus, SeriesOfTransformations may be an Affine transform followed by a warp another affine and then another warp. Inverse affine transformations are invoked by calling -i MyAffine.txt InverseWarps are invoked by passing the InverseWarp.nii.gz filename (see below for a note about this). Example 1: Mapping a warped image into the reference_image domain by applying abcdWarpxvec.nii.gz/abcdWarpyvec.nii.gz/abcd- Warpzvec.nii.gz and then abcdAffine.txt ./WarpImageMultiTransform 3 moving_image output_image -R reference_image abcdWarp.nii.gz abcdAffine.txt Example 2: To map the fixed/reference_image warped into the moving_image domain by applying the inversion of abcdAffine.txt and then abcdInverseWarpxvec.nii.gz/abcdInverseWarpyvec.nii.gz/abcdInverseWarpzvec.nii.gz . ./WarpImageMultiTransform 3 reference_image output_image -R moving_image -i abcdAffine.txt abcdInverseWarp.nii.gz Note that the inverse maps (Ex. 2) are passed to this program in the reverse order of the forward maps (Ex. 1). This makes sense, geometrically ... see ANTS.pdf for visualization of this syntax. Compulsory arguments: ImageDimension: 2 or 3 (for 2 or 3 Dimensional registration) moving_image: the image to apply the transformation to output_image: the resulting image Optional arguments: -R: reference_image space that you wish to warp INTO. --tightest-bounding-box: Computes the tightest bounding box using all the affine transformations. It will be overrided by -R refer- ence_image if given. --reslice-by-header: equivalient to -i -mh, or -fh -i -mh if used together with -R. It uses the orientation matrix and origin encoded in the image file header. It can be used together with -R. This is typically not used together with any other transforms. --use-NN: Use Nearest Neighbor Interpolation. --use-BSpline: Use 3rd order B-Spline Interpolation. -i: will use the inversion of the following affine transform. Other Example Usages: Reslice the image: WarpImageMultiTransform 3 Imov.nii.gz Iout.nii.gz --tightest-bounding-box --reslice-by-header Reslice the image to a reference image: WarpImageMultiTransform 3 Imov.nii.gz Iout.nii.gz -R Iref.nii.gz --tightest-bounding-box --reslice-by-header Important Notes: Prefixname "abcd" without any extension will use ".nii.gz" by default The abcdWarp and abcdInverseWarp do not exist. They are formed on the basis of abcd(Inverse)Warpxvec/yvec/zvec.nii.gz when calling ./WarpImageMultiTransform, yet you have to use them as if they exist. WarpImageMultiTransform 1.9 May 2012 WARPIMAGEMULTITRANSFORM(1)

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vbim(1) 							 The VoxBo Manual							   vbim(1)

vbim - manipulate 3D and 4D volumes SYNOPSIS
vbim <flag> ... DESCRIPTION
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. OPTIONS
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. EXAMPLES
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 NOTES
Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and via the NeuroDebian project ( for Debian deriva- tives. CAVEATS
VoxBo is provided with no warranty whatsoever. AUTHOR
For an historical roster of the VoxBo development team, visit SEE ALSO
For detailed help on any VoxBo command-line program, run it with no arguments. For graphical programs, use the -h flag. For more help with VoxBo, for information about the mailing list, or to report bugs, visit the web site at For information about file format support in VoxBo, see voxbo-fileformats(7). For general information about VoxBo, see voxbo(7). VoxBo January, 2011 (v1.8.5) vbim(1)
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