Provided by: ants_2.2.0-1ubuntu1_amd64 bug


       CreateTiledMosaic - part of ANTS registration suite



              Render a 3-D image volume with optional Rgb overlay.

       -i, --input-image inputImageFilename

              Main input is a 3-D grayscale image.

       -r, --rgb-image rgbImageFilename

              An  optional  Rgb  image  can  be  added as an overlay. It must have the same image
              geometry as the input grayscale image.

       -x, --mask-image maskImageFilename

              Specifies the ROI of the RGB voxels used.

       -a, --alpha value

              If an Rgb  image  is  provided,  render  the  overlay  using  the  specified  alpha

       -e, --functional-overlay [rgbImageFileName,maskImageFileName,<alpha=1>]

              A  functional  overlay  can  be  specified  using  both  and  rgb  image and a mask
              specifying where that rgb image should be applied. Both images must have  the  same
              image  geometry  as  the  input  image.  Optionally,  an  alpha  parameter  can  be
              specified.Note that more than one functional overlays can be rendered, the order in
              which they are specified on the command line matters, and rgb images are assumed to
              be unsigned char [0,255].

       -o, --output tiledMosaicImage

              The output is the tiled mosaic image. Without an RGB overlaywe  do  not  alter  the
              intensity  values  of  the  input  image.  Therefore, the output suffix needs to be
              associated with a format that supports float images (not .jpg or .png). If  one  or
              more RGB overlays are supported then we rescale the input image intensities to also
              be in the range of [0,255] which permits a .png or .jpg output.

       -t, --tile-geometry RxC

              The tile geometry specifies the number of rows and columns  in  the  output  image.
              For  example, if the user specifies '5x10', then 5 rows by 10 columns of slices are
              rendered. If R < 0 and C > 0 (or vice versa), the negative value is selected  based
              on direction.

       -d, --direction 0/1/2/x/y/(z)

              Specifies  the  direction  of the slices. This can be based on the how the image is
              stored in memory or can be based on how the image is aligned in physical space.  If
              no direction is specified, the z-direction (axial?) is chosen.

       -p, --pad-or-crop padVoxelWidth

              The user can specify whether to pad or crop a  specified  voxel-width  boundary  of
              each  individual  slice. For this program, cropping is simply padding with negative
              voxel-widths. If one pads (+), the user can  also  specify  a  constant  pad  value
              (default  =  0).  If  a  mask is specified, the user can use the mask to define the
              region, by using the keyword "mask" plus an offset, e.g. "-p mask+3".

       -s, --slices Slice1xSlice2xSlice3...


              This option gives the user more control over what slices to use for rendering.  The
              user can specify specific slices for a particular order. Alternatively the user can
              specify  the  number  slices  to increment with the optional specification of which
              slices  to   start   and   end   the   sequence.   A   negative   value   for   the
              numberOfSlicesToIncrement  causes  rendering  in  the  reverse order. For the third
              option, minSlice < maxSlice. If a mask is specified, the user can use the  mask  to
              define  the  region,  by  using  the  keyword  "mask"  plus  an  offset,  e.g.  "-s
              [1,mask-3,200]".For the third option, minSlice < maxSlice.

       -f, --flip-slice flipXxflipY

              Flip individual slice images horizontally  and/or  vertically,  specified  e.g.  as
              '0x1' or '1x1'.

       -g, --permute-axes doPermute

              Permute (or swap) the axes of the individual slice images.


              Print the help menu (short version).


              Print the help menu.  <VALUES>: 1