This document outlines BRAINSDemonsWarp usage.

This program provides three different demons filters for image registration.

For ThirionDemons and FastSymmetricDemonsforce filter, one fixed and moving image are allowed as input images. For diffeomorphic filter, it supports multi-inputs fixed and moving images.

USAGE:
BRAINSDemonWarpCLP <Arguments>  or VBRAINSDemonWarpCLP <Arguments>

Arguments:
Required Arguments are
The Input fixed image file name is given  with -f option, if multi-images(only VBRAINSDemonWarpCLP), use ',' between names.
The Input moving image file name is given with -m option, if multi-images(only VBRAINSDemonWarpCLP), use ',' between names.
The ouput image is set by -o option.

The other optional arguments are

 --registrationFilterType: The registration filter type(Demons—FastSymmetricForces—Diffeomorphic)
is given with –registrationFilterType option. Default Demons
 --medianFilterSize: X Neighborhood to be included for BOBF. Default 0,0,0
 --maxStepLenght: Maximum length of an update vector(0: no restriction) with -l option. Default 2
 --numberOfLevels: Number of multiresolution levels with -n option. Default 3
 --numberOfIterations: Number of demons iterations per level with -i option. Default 10,10,10
 --smoothDefomationFieldSigma: Smoothing sigma for the deformation field at each iteration with -s
option. Default 0.0001
 --smoothingUp: Smoothing sigma for the update field at each iteration with -g option. Default 0
 --histogramMatch: Use histogram matching with -e option.
 --numberOfHistogramLevels: Number of histogram bins to use in the histogram equalization. Default
256
 --numberOfMatchPoints: Number of match points to use in the histogram matching algorithm. Default
2
 --minimumFixedPyramid: The shrink factor for the first level of the fixed image pyramid. Default
4,4,4
 --minimumMovingPyramid: The shrink factor for the first level of the moving image pyramid. Default
4,4,4
 --inputPixelType: The input image pixel type is given with –inputPixelType option. Th input image
is read using this option. Valid Input data types are: UCHAR SHORT USHORT INT UINT FLOAT
DOUBLE. Default float
 --outputPixelType: Output image type. Image is written to the file in this type. Default is float.
 --outputCheckerboardVolume: If this option is set the checker board image comparing the deformed
image with the target image is written
 --checkerboardPatternSubdivisions: This option sets the checker board image pattern. Enter a non
zero number for each dimension. Default is 4 in all dimensions.
 --outputDisplacementFieldPrefix: You can write the displacement fields by giving the prefix of the
displacement fields, (suffix of xdisp.hdr, ydisp.hdr, zdisp.hdr will be added).
 --outputDeformationFieldVolume: Write the deformation fields with -O option
 --outputDebug: This option is to write all the intermediate images, debug information and metric value
file for debugging purposes with -v option.
 --maskProcessingMode- What mode to use for using the masks: NOMASK|ROI AU T O|ROI |BOBF . 
If ROIAUTO is choosen, then the mask is implicitly deﬁned using a otsu forground and hole ﬁlling 
algorithm. Where the Region Of Interest mode uses the masks to deﬁne what parts of the image 
should be used for computing the deformation ﬁeld. Brain Only Background Fill uses the masks to 
pre-process the input images by clipping and ﬁlling in the background with a predeﬁned value. The 
option of BOBF is to make Brain Only Background Filled(BOBF) images.(default: NOMASK) 
 --movingBinaryVolume- Mask ﬁlename for desired region of interest in the Moving image. 
 --ﬁxedBinaryVolume- Mask ﬁlename for desired region of interest in the Fixed image.
 --lowerThreasholdForBOBF: Lower Threshold for performing BOBF. Default 0
 --upperThresholdForBOBF: Upper Threshold for performing BOBF. Default 70
 --backgroundFilleValue: Backgond fill with this value Default 70
 --seedForBOBF: Seed (X,Y,Z) for BOBF. Default 0,0,0
 --neighborhoodForBOBF: Neighborhood in all 3 directions to be included when performing BOBF.
Default 1,1,1
 --movingLandmarks: Landmarks filename for moving image to initialize deformation field.
 --fixedLandmarks: Landmarks filename for fixed image to initialize deformation field.
 --initialDeformationFieldVolume: Initial deformation field vector image file name.
 --initializeWithFourier: Initial Coefficient filename.
 --initializeWithTransform: Initial Transform filename
 --forceCoronalZeroOrigin: Flag to indicate that all images being read inmust have their spatial centers
matched.
 --weightFactors: Weight factors for different modal images(only for VBRAINSDemonWarpCLP) with -w option. Default 1.0,1.0 

For example:
1.BRAINSDemonWarpCLP -f fixedimage.nii.gz -m movingimage.nii.gz -o outputimage.nii.gz -O outputdeformationfield.nii.gz -n 5 -s 3.0 -e –numberOfHistogramBins 1024 –numberOfMatchPoints 7 -i 1000, 400,300,200,100 -v 

2.VBRAINSDemonWarpCLP -f fixedimage1.nii.gz,fixedimage2.nii.gz -m movingimage1.nii.gz,movingimage2.nii.gz -o outputimage.nii.gz -O outputdeformationfield.nii.gz -n 5 -s 3.0 -w 0.5,0.5  -e –numberOfHistogramBins 1024 –numberOfMatchPoints 7 -i 1000, 400,300,200,100 -v –registrationFilterType Diffeomorphic


