Provided by: plastimatch_1.8.0+dfsg.1-2build1_amd64 bug

NAME

       plastimatch - register, convert, warp, and manipulate 3D images

SYNOPSIS

          plastimatch command [options]

DESCRIPTION

       The plastimatch executable is used for a variety of operations on either 2D or 3D images, including image
       registration, warping, resampling, and file format conversion.  The form of the options depends upon  the
       command  given.   The  list  of  possible commands can be seen by simply typing "plastimatch" without any
       additional command line arguments:

          $ plastimatch
          plastimatch version 1.8.0
          Usage: plastimatch command [options]
          Commands:
           add           adjust        average       bbox          boundary
           crop          compare       compose       convert       dice
           diff          dmap          dose          drr           dvh
           fdk           fill          filter        gamma         header
           jacobian      lm-warp       mabs          mask          maximum
           ml-convert    multiply      probe         register      resample
           scale         segment       sift          stats         synth
           synth-vf      threshold     thumbnail     union         warp
           xf-convert    xf-invert

          For detailed usage of a specific command, type:
            plastimatch command

PLASTIMATCH ADD

       The add command is used to add one or more images together and create an output image.  The contributions
       of the input images can be weighted with a weight vector.

       The command line usage is given as follows:

          Usage: plastimatch add [options] input_file [input_file ...]
          Options:
            --average        produce an output file which is the average of the
                              input files (if no weights are specified), or
                              multiply the weights by 1/n
            --output <arg>   output image
            --weight <arg>   specify a vector of weights; the images are
                              multiplied by the weight prior to adding their
                              values

   Examples
       To  add together files 01.mha, 02.mha and 03.mha, and save the result in the file output.mha, you can run
       the following command:

          plastimatch add --output output.mha 01.mha 02.mha 03.mha

       If you wanted output.mha to be 2 * 01.mha + 0.5 * 02.mha + 0.1 * 03.mha, then you should do this:

          plastimatch add \
            --output output.mha \
            --weight "2 0.5 0.1" \
            01.mha 02.mha 03.mha

PLASTIMATCH ADJUST

       The adjust command is used to adjust the intensity values within an  image.   The  adjustment  operations
       available are truncation, linear scaling, histogram matching as well as global and local linear matching.

       The command line usage is given as follows:

          Usage: plastimatch adjust [options]
          Options:
            -h, --help                    display this help message
                --hist-levels <arg>       number of histogram bins for histogram
                                           matching, default is 1024
                --hist-match <arg>        reference image for histogram matching
                --hist-points <arg>       number of match points for histogram matching,
                                           default is 10
                --hist-threshold          threshold at mean intensity (simple background
                                           exclusion) for histogram matching
                --input <arg>             input directory or filename
                --input-mask <arg>        input image mask, only affects --linear-match
                                           and --local-match
                --linear <arg>            shift and scale image intensities, provide a
                                           string with "<shift> <scale>"
                --linear-match <arg>      reference image for linear matching with mean
                                           and std
                --local-match <arg>       reference image for patch-wise shift and
                                           scale. You must specify the --patch-size
                --local-blending-off      no trilinear interpolation of shifts and
                                           scales
                --local-scale-out <arg>   filename to store pixel-wise scales
                --local-shift-out <arg>   filename to store pixel-wise shifts
                --output <arg>            output image
                --patch-size <arg>        patch size for local matching; provide 1 "n"
                                           or 3 values "nx ny nz"
                --pw-linear <arg>         a string that forms a piecewise linear map
                                           from input values to output values, of the
                                           form "in1,out1,in2,out2,..."
                --ref-mask <arg>          reference image mask, only affects
                                           --linear-match and --local-match
                --version                 display the program version

       The  adjust  command  can  be  used  to make a piecewise linear adjustment of the image intensities.  The
       --pw-linear option is used to create the mapping from input intensities to output intensities.  The input
       intensities  in  the  curve  must  increase  from left to right in the string, but output intensities are
       arbitrary.  Input  intensities  below  the  first  pair  or  after  the  last  pair  are  transformed  by
       extrapolating  the  curve  out to infinity with a slope of +1.  A different slope may be specified out to
       positive or negative infinity by specifying the special input values of -inf and +inf.  In this case, the
       second  number  in the pair is the slope of the curve, not the output intensity.  You can do a simplified
       linear transformation of gray levels with the --linear option.  For this, you need to  provide  a  string
       with "<shift> <scale>".

       In  addition,  you  can  adjust  the image intensities based on a reference image. With --linear-match, a
       linear transformation (shift and scale) is determined from mean and standard deviation of pixel values in
       reference  and  input image. If the input image feaures local intensity inconsistencies, you can choose a
       patch-based intensity correction using the --local-match option.  Similar to  --linear-match,  shift  and
       scale  are computed patch-wise from mean and standard deviation.  For both options, you can provide masks
       that specify the regions taken into account.  Finally, choose --hist-match to perform histogram matching.

       You can only choose one of --linear, --pw-linear, --linear-match, --local-match and --hist-match.  Beware
       that a reference filename has to be added for matching options.

   Examples
       The following command will add 100 to all voxels in the image:

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --pw-linear "0,100"

       The  following  command  does  the  same  thing,  but  with  explicit  specification  of the slope in the
       extrapolation area:

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --pw-linear "-inf,1,0,100,inf,1"

       The following command truncates the inputs to the range of [-1000,+1000]:

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --pw-linear "-inf,0,-1000,-1000,+1000,+1000,inf,0"

       The following command scales and then shifts all voxel values by 2.5 and +1000, respectively. (Use either
       comma or space to separate the values):

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --linear "1000,2.5"

       The following command matches the histogram of infile.nrrd to be similar to that of reference.nrrd:

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --hist-match reference.nrrd \
            --hist-levels 1000 --hist-points 12

       The  following  command  matches  mean  and standard deviation of intensities in the input image to equal
       those of the reference image:

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --linear-match reference.nrrd

       The following command also matches mean and standard  deviation,  but  calculates  statistics  only  from
       inside  the mask regions (note that masks are only used for statistic calculations, you would need to use
       plastimatch mask to reset outside values):

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --linear-match reference.nrrd \
            --input-mask inmask.nrrd --ref-mask refmask.nrrd

       Finally, you can apply patch-wise local intensity adjustment using the following command:

          plastimatch adjust \
            --input infile.nrrd \
            --output outfile.nrrd \
            --local-match reference.nrrd \
            --patch-size "20 20 10"

       The --local-match option requires the input and reference to be spatially aligned.  In  order  to  reduce
       the  influence  of  background pixels at the border, you can provide foreground masks for both images (if
       only one mask is given, it as also used for the second image):

          plastimatch adjust \
            --input infile.nrrd
            --output outfile.nrrd \
            --local-match reference.nrrd \
            --patch-size "20 20 10" \
            --input-mask inmask.nrrd \
            --ref-mask refmask.nrrd

PLASTIMATCH AVERAGE

       The average command is used to compute the (weighted) average of multiple input images.  It is  the  same
       as the plastimatch add command, with the --average option specified.  Please refer to plastimatch add for
       the list of command line arguments.

   Example
       The following command will compute the average of three input images:

          plastimatch average \
            --output outfile.nrrd \
            01.mha 02.mha 03.mha

PLASTIMATCH AUTOLABEL

       The autolabel command is an experimental program the uses  machine  learning  to  identify  the  thoracic
       vertibrae in a CT scan.

       The command line usage is given as follows:

          Usage: plastimatch autolabel [options]
          Options:
            -h, --help            Display this help message
                --input <arg>     Input image filename (required)
                --network <arg>   Input trained network filename (required)
                --output <arg>    Output csv filename (required)

PLASTIMATCH BOUNDARY

       The boundary command takes a binary label image as input, and generates an image of the image boundary as
       the output.  The boundary is defined as the voxels within the label which have neighboring voxels outside
       the label.

       The command line usage is given as follows:

          Usage: plastimatch boundary [options] input_file
          Required:
            --output <arg>   filename for output image

PLASTIMATCH CROP

       The  crop  command crops out a rectangular portion of the input file, and saves that portion to an output
       file.  The command line usage is given as follows:

          Usage: plastimatch crop [options]
          Required:
              --input=image_in
              --output=image_out
              --voxels="x-min x-max y-min y-max z-min z-max" (integers)

       The voxels are indexed starting at zero.  In other words, if the size of the image is M imes  N  imes  P,
       the x values should range between 0 and M-1.

   Example
       The  following  command selects the region of size 10 imes 10 imes 10, with the first voxel of the output
       image being at location (5,8,12) of the input image:

          plastimatch crop \
            --input in.mha \
            --output out.mha \
            --voxels "5 14 8 17 12 21"

PLASTIMATCH COMPARE

       The compare command compares two files by subtracting one file from the other, and  reporting  statistics
       of  the difference image.  The two input files must have the same geometry (origin, dimensions, and voxel
       spacing).  The command line usage is given as follows:

          Usage: plastimatch compare image_in_1 image_in_2

   Example
       The following command subtracts synth_2 from synth_1, and reports the statistics:

          $ plastimatch compare synth_1.mha synth_2.mha
          MIN -558.201904 AVE 7.769664 MAX 558.680847
          MAE 85.100204 MSE 18945.892578
          DIF 54872 NUM 54872

       The reported statistics are interpreted as follows:

          MIN      Minimum value of difference image
          AVE      Average value of difference image
          MAX      Maximum value of difference image
          MAE      Mean average value of difference image
          MSE      Mean squared difference between images
          DIF      Number of pixels with different intensities
          NUM      Total number of voxels in the difference image

PLASTIMATCH COMPOSE

       The compose command is used to compose two transforms.  The command line usage is given as follows:

          Usage: plastimatch compose file_1 file_2 outfile

          Note:  file_1 is applied first, and then file_2.
                    outfile = file_2 o file_1
                    x -> x + file_2(x + file_1(x))

       The transforms can be of any type, including translation, rigid, affine, itk B-spline,  native  B-spline,
       or vector fields.  The output file is always a vector field.

       There  is  a further restriction that at least one of the input files must be either a native B-spline or
       vector field.  This restriction is required because that is how the resolution and voxel spacing  of  the
       output vector field is chosen.

   Example
       Suppose  we  want  to  compose  a rigid transform (rigid.tfm) with a vector field (vf.mha), such that the
       output transform is equivalent to applying the rigid transform first, and the vector field second.

          plastimatch compose rigid.tfm vf.mha composed_vf.mha

PLASTIMATCH CONVERT

       The convert command is used to convert files  from  one  format  to  another  format.   As  part  of  the
       conversion  process,  it  can also apply (linear or deformable) geometric transforms to the input images.
       In fact, convert is just an alias for the warp command.

       The command line usage is given as follows:

          Usage: plastimatch convert [options]
          Options:
           --algorithm <arg>         algorithm to use for warping, either
                                      "itk" or "native", default is native
           --ctatts <arg>            ct attributes file (used by dij warper)
           --default-value <arg>     value to set for pixels with unknown
                                      value, default is 0
           --dicom-with-uids <arg>   set to false to remove uids from created
                                      dicom filenames, default is true
           --dif <arg>               dif file (used by dij warper)
           --dim <arg>               size of output image in voxels "x [y z]"
           --direction-cosines <arg>
                                     oriention of x, y, and z axes; Specify
                                      either preset value,
                                      {identity,rotated-{1,2,3},sheared}, or 9
                                      digit matrix string "a b c d e f g h i"
           --dose-scale <arg>        scale the dose by this value
           --fixed <arg>             fixed image (match output size to this
                                      image)
           --input <arg>             input directory or filename; can be an
                                      image, structure set file (cxt or
                                      dicom-rt), dose file (dicom-rt,
                                      monte-carlo or xio), dicom directory, or
                                      xio directory
           --input-cxt <arg>         input a cxt file
           --input-dose-ast <arg>    input an astroid dose volume
           --input-dose-img <arg>    input a dose volume
           --input-dose-mc <arg>     input an monte carlo volume
           --input-dose-xio <arg>    input an xio dose volume
           --input-prefix <arg>      input a directory of structure set
                                      images (one image per file)
           --input-ss-img <arg>      input a structure set image file
           --input-ss-list <arg>     input a structure set list file
                                      containing names and colors
           --interpolation <arg>     interpolation to use when resampling,
                                      either "nn" for nearest neighbors or
                                      "linear" for tri-linear, default is
                                      linear
           --metadata <arg>          patient metadata (you may use this
                                      option multiple times), option written
                                      as "XXXX,YYYY=string"
           --modality <arg>          modality metadata: such as {CT, MR, PT},
                                      default is CT
           --origin <arg>            location of first image voxel in mm "x y
                                      z"
           --output-colormap <arg>   create a colormap file that can be used
                                      with 3d slicer
           --output-cxt <arg>        output a cxt-format structure set file
           --output-dicom <arg>      create a directory containing dicom and
                                      dicom-rt files
           --output-dij <arg>        create a dij matrix file
           --output-dose-img <arg>   create a dose image volume
           --output-img <arg>        output image; can be mha, mhd, nii,
                                      nrrd, or other format supported by ITK
           --output-labelmap <arg>   create a structure set image with each
                                      voxel labeled as a single structure
           --output-pointset <arg>   create a pointset file that can be used
                                      with 3d slicer
           --output-prefix <arg>     create a directory with a separate image
                                      for each structure
           --output-prefix-fcsv <arg>
                                     create a directory with a separate fcsv
                                      pointset file for each structure
           --output-ss-img <arg>     create a structure set image which
                                      allows overlapping structures
           --output-ss-list <arg>    create a structure set list file
                                      containing names and colors
           --output-type <arg>       type of output image, one of {uchar,
                                      short, float, ...}
           --output-vf <arg>         create a vector field from the input xf
           --output-xio <arg>        create a directory containing xio-format
                                      files
           --patient-id <arg>        patient id metadata: string
           --patient-name <arg>      patient name metadata: string
           --patient-pos <arg>       patient position metadata: one of
                                      {hfs,hfp,ffs,ffp}
           --prefix-format <arg>     file format of rasterized structures,
                                      either "mha" or "nrrd"
           --prune-empty             delete empty structures from output
           --referenced-ct <arg>     dicom directory used to set UIDs and
                                      metadata
           --series-description <arg>
                                     series description metadata: string
           --simplify-perc <arg>     delete <arg> percent of the vertices
                                      from output polylines
           --spacing <arg>           voxel spacing in mm "x [y z]"
           --version                 display the program version
           --xf <arg>                input transform used to warp image(s)
           --xor-contours            overlapping contours should be xor'd
                                      instead of or'd

   Examples
       The first example demonstrates how to convert a DICOM volume to NRRD.  The DICOM images that comprise the
       volume  must  be  stored in a single directory, which for this example is called "dicom-in-dir".  Because
       the --output-type option was not specified, the output type will be matched to  the  type  of  the  input
       DICOM volume.  The format of the output file (NRRD) is determined from the filename extension.

          plastimatch convert \
            --input dicom-in-dir \
            --output-img outfile.nrrd

       This example further converts the type of the image intensities to float.

          plastimatch convert \
            --input dicom-in-dir \
            --output-img outfile.nrrd \
            --output-type float

       The  next  example  shows  how to resample the output image to a different geometry.  The --origin option
       sets the position of the (center of) the first voxel of the image, the --dim option sets  the  number  of
       voxels,  and the --spacing option sets the distance between voxels.  The units for origin and spacing are
       assumed to be millimeters.

          plastimatch convert \
            --input dicom-in-dir \
            --output-img outfile.nrrd \
            --origin "-200 -200 -165" \
            --dim "250 250 110" \
            --spacing "2 2 2.5"

       Generally speaking, it is tedious to manually specify the geometry of the output file.  If  you  want  to
       match the geometry of the output file with an existing file, you can do this using the --fixed option.

          plastimatch convert \
            --input dicom-in-dir \
            --output-img outfile.nrrd \
            --fixed reference.nrrd

       This  next  example  shows  how  to  convert  a  DICOM  RT  structure  set  file  into an image using the
       --output-ss-img option.  Because structures in DICOM RT are polylines, they are rasterized to create  the
       image.   The voxels of the output image are 32-bit integers, where the i^th bit of each integer has value
       one if the voxel lies with in the corresponding structure, and value zero if the voxel lies  outside  the
       structure.  The structure names are stored in separate file using the --output-ss-list option.

          plastimatch convert \
            --input structures.dcm \
            --output-ss-img outfile.nrrd \
            --output-ss-list outfile.txt

       In  the previous example, the geometry of the output file wasn't specified.  When the geometry of a DICOM
       RT structure set isn't specified, it is assumed to match the geometry of the DICOM (CT,  MR,  etc)  image
       associated  with  the  contours.  If the associated DICOM image is in the same directory as the structure
       set file, it will be found automatically.  Otherwise, we have to tell plastimatch  where  it  is  located
       with the --referenced-ct option.

          plastimatch convert \
            --input structures.dcm \
            --output-ss-img outfile.nrrd \
            --output-ss-list outfile.txt \
            --referenced-ct ../image-directory

PLASTIMATCH DICE

       The  plastimatch dice compares binary label images using Dice coefficient, Hausdorff distance, or contour
       mean distance.  The input images are treated as boolean, where non-zero values mean that voxel is  inside
       of the structure and zero values mean that the voxel is outside of the structure.

       The command line usage is given as follows:

          Usage: plastimatch dice [options] reference-image test-image
          Options:
           --all            Compute Dice, Hausdorff, and contour mean
                             distance (equivalent to --dice --hausdorff
                             --contour-mean)
           --contour-mean   Compute contour mean distance
           --dice           Compute Dice coefficient (default)
           --hausdorff      Compute Hausdorff distance and average Hausdorff
                             distance

   Example
       The following command computes all three statistics for mask1.mha and mask2.mha:

          plastimatch dice --all mask1.mha mask2.mha

PLASTIMATCH DIFF

       The  plastimatch diff command subtracts one image from another, and saves the output as a new image.  The
       two input files must have the same geometry (origin, dimensions, and voxel spacing).

       The command line usage is given as follows:

          Usage: plastimatch diff image_in_1 image_in_2 image_out

   Example
       The following command computes file1.nrrd minus file2.nrrd, and saves the result in outfile.nrrd:

          plastimatch diff file1.nrrd file2.nrrd outfile.nrrd

PLASTIMATCH DMAP

       The plastimatch dmap command takes a binary label image as input, and creates a distance map image as the
       output.   The  output  image has the same image geometry (origin, dimensions, voxel spacing) as the input
       image.

       The command line usage is given as follows:

          Usage: plastimatch dmap [options]
          Required:
           --input <arg>        input directory or filename
           --output <arg>       output image
          Optional:
           --algorithm <arg>    a string that specifies the algorithm used
                                 for distance map calculation, either
                                 "maurer", "danielsson", or "itk-danielsson"
                                 (default is "danielsson")
           --inside-positive    voxels inside the structure should be
                                 positive (by default they are negative)
           --maximum-distance <arg>
                                voxels with distances greater than this
                                 number will have the distance truncated to
                                 this number
           --squared-distance   return the squared distance instead of
                                 distance

   Example
       The following command computes a distance map file dmap.nrrd from a binary labelmap image label.nrrd.:

          plastimatch dmap --input label.nrrd --output dmap.nrrd

PLASTIMATCH DRR

       A digitally reconstructed radiograph (DRR) is a synthetic  radiograph  which  can  be  generated  from  a
       computed  tomography (CT) scan.  It is used as a reference image for verifying the correct setup position
       of a patient prior to radiation treatment.

       The drr program that comes with plastimatch takes a CT image as input, and generates one or  more  output
       images.  The output images can be either pgm, pfm, or raw format.  The command line usage is:

          Usage: plastimatch drr [options] [infile]
          Options:
           -i, --algorithm <arg>         Choose algorithm {exact,uniform}
               --autoscale               Automatically rescale intensity
               --autoscale-range <arg>   Range used for autoscale in form "min
                                          max" (default: "0 255")
           -z, --detector-size <arg>     The physical size of the detector in
                                          format "row col", in mm
           -r, --dim <arg>               The output resolution in format "row
                                          col" (in mm)
           -e, --exponential             Do exponential mapping of output values
           -y, --gantry-angle <arg>      Gantry angle for image source in degrees
           -N, --gantry-angle-spacing <arg>
                                         Difference in gantry angle spacing in
                                          degrees
           -G, --geometry-only           Create geometry files only
           -h, --help                    display this help message
           -P, --hu-conversion <arg>     Choose HU conversion type
                                          {preprocess,inline,none}
           -c, --image-center <arg>      The image center in the format "row
                                          col", in pixels
           -I, --input <arg>             Input file
           -s, --intensity-scale <arg>   Scaling factor for output image
                                          intensity
           -o, --isocenter <arg>         Isocenter position "x y z" in DICOM
                                          coordinates (mm)
           -n, --nrm <arg>               Normal vector of detector in format "x y
                                          z"
           -a, --num-angles <arg>        Generate this many images at equal
                                          gantry spacing
           -O, --output <arg>            Prefix for output file(s)
           -t, --output-format <arg>     Select output format {pgm, pfm, raw}
           -S, --raytrace-details <arg>
                                         Create output file with complete ray
                                          trace details
               --sad <arg>               The SAD (source-axis-distance) in mm
                                          (default: 1000)
               --sid <arg>               The SID (source-image-distance) in mm
                                          (default: 1500)
           -w, --subwindow <arg>         Limit DRR output to a subwindow in
                                          format "r1 r2 c1 c2",in pixels
           -A, --threading <arg>         Threading option {cpu,cuda,opencl}
                                          (default: cpu)
               --version                 display the program version
               --vup <arg>               The vector pointing from the detector
                                          center to the top row of the detector in
                                          format "x y z"

       An  input  file is required.  The drr program can be used in either single image mode or rotational mode.
       In single image mode, you specify the complete geometry of the x-ray  source  and  imaging  panel  for  a
       single  image.   In  rotational  mode,  the  imaging  geometry  is  rotated  in a circular arc around the
       isocenter, with a fixed source to axis distance (SAD), and projection images generated at  fixed  angular
       intervals.

   Examples
       The following example illustrates the use of single image mode:

          drr -nrm "1 0 0" \
              -vup "0 0 1" \
              -g "1000 1500" \
              -r "1024 768" \
              -z "400 300" \
              -c "383.5 511.5" \
              -o "0 -20 -50" \
              input_file.mha

       In  the  above example, the isocenter is chosen to be (0, -20, -50), the location marked on the CT image.
       The orientation of the projection image is controlled by the nrm and  vup  options.   Using  the  default
       values of (1, 0, 0) and (0, 0, 1) yields the DRR shown on the right: [image] [image]

       By  changing  the  normal  direction  (nrm),  we can choose different beam direction within an isocentric
       orbit.  For example, an anterior-posterior (AP) DRR is generated with a normal of (0,  -1,  0)  as  shown
       below: [image]

       The  rotation  of the imaging panel is selected using the vup option.  The default value of vup is (0, 0,
       1), which means that the top of  the  panel  is  oriented  toward  the  positive  z  direction  in  world
       coordinates.   If  we wanted to rotate the panel by 45 degrees counter-clockwise on our AP view, we would
       set vup to the (1, 0, 1) direction, as shown in the image below.   Note  that  vup  doesn't  have  to  be
       normalized.  [image]

       In  rotional  mode, multiple images are created.  The source and imaging panel are assumed to rotate in a
       circular orbit around the isocenter.  The circular orbit is performed around the Z axis, and  the  images
       are generated every -N ang degrees of the orbit.  This is illustrated using the following example:

          drr -N 20 \
              -a 18 \
              -g "1000 1500" \
              -r "1024 768" \
              -z "400 300" \
              -o "0 -20 -50" \
              input_file.mha

       In the above example, 18 images are generated at a 20 degree interval, as follows: [image]

PLASTIMATCH DVH

       The  dvh  command  creates  a dose value histogram (DVH) from a given dose image and structure set image.
       The command line usage is given as follows:

          Usage: plastimatch dvh [options]
          Options:
               --bin-width <arg>       specify bin width in the histogram in
                                        units of Gy (default=0.5)
               --cumulative            create a cumulative DVH (this is the
                                        default)
               --differential          create a differential DVH instead of a
                                        cumulative DVH
               --dose-units <arg>      specify units of dose in input file as
                                        either cGy as "cgy" or Gy as "gy"
                                        (default="gy")
           -h, --help                  display this help message
               --input-dose <arg>      dose image file
               --input-ss-img <arg>    structure set image file
               --input-ss-list <arg>   structure set list file containing names
                                        and colors
               --normalization <arg>   specify histogram values as either voxels
                                        "vox" or percent "pct" (default="pct")
               --num-bins <arg>        specify number of bins in the histogram
                                        (default=256)
               --output-csv <arg>      file to save dose volume histogram data in
                                        csv format
               --version               display the program version

       The required inputs are --input-dose, --input-ss-img, --input-ss-list, and --output-csv.   The  units  of
       the  input  dose  must be either Gy or cGy.  DVH bin values will be generated for all structures found in
       the structure set files.  The output will be generated as an ASCII csv-format spreadsheet file,  readable
       by OpenOffice.org or Microsoft Excel.

       The  default  is a differential (standard) histogram, rather than the cumulative DVH which is most common
       in radiotherapy.  To create a cumulative DVH, use the --cumulative option.

       The default is to create 256 bins, each with a width of 1 Gy.  You can  adjust  these  values  using  the
       --num-bins and --bin-width option.

   Example
       To generate a DVH for a single 2 Gy fraction, we might choose 250 bins each of width 1 cGy.  If the input
       dose is already specified in cGy, you would use the following command:

          plastimatch dvh \
            --input-ss-img structures.mha \
            --input-ss-list structures.txt \
            --input-dose dose.mha \
            --output-csv dvh.csv \
            --input-units cgy \
            --num-bins 250 \
            --bin-width 1

PLASTIMATCH FDK

       The term FDK refers to the authors Feldkamp, Davis, and Kress who  wrote  the  seminal  paper  "Practical
       cone-beam  algorithm" in 1984.  Their paper describes a filtered back-projection reconstruction algorithm
       for cone-beam geometries.  The fdk program in plastimatch is an implmenetation of the FDK algorithm.   It
       takes a directory of 2D projection images as input, and generates a single 3D volume as output.

       The command line usage is:

          Usage: plastimatch fdk [options]
          Options:
           -x, --detector-offset <arg>   The translational offset of the detector
                                          "x0 y0", in pixels
           -r, --dim <arg>               The output image resolution in voxels
                                          "num (num num)" (default: 256 256 100
           -f, --filter <arg>            Choice of filter {none,ramp} (default:
                                          ramp)
           -X, --flavor <arg>            Implementation flavor {0,a,b,c,d}
                                          (default: c)
           -h, --help                    display this help message
           -a, --image-range <arg>       Use a sub-range of available images
                                          "first ((skip) last)"
           -I, --input <arg>             Input file
           -s, --intensity-scale <arg>   Scaling factor for output image
                                          intensity
           -O, --output <arg>            Prefix for output file(s)
           -A, --threading <arg>         Threading option {cpu,cuda,opencl}
                                          (default: cpu)
               --version                 display the program version
           -z, --volume-size <arg>       Physical size of reconstruction volume
                                          "s1 s2 s3", in mm (default: 300 300 150)

       The usage of the fdk program is best understood by following along with the tutorials: fdk_tutorial_i and
       fdk_tutorial_ii.

       Three different formats of input files are supported.  These are:

       • Pfm format image files with geometry txt files

       • Raw format image files with geometry txt files

       • Varian hnd files

       The pfm and raw files are similar, in that they store the image  as  an  array  of  4-byte  little-endian
       floats.   The  only difference is that the pfm file has a header which stores the image size, and the raw
       file does not.

       Each pfm or raw image file must have a geometry file in the same directory with the .txt extension.   For
       example,  if  you  want  to  use  image_0000.pfm  in  a  reconstruction,  you  should supply another file
       image_0000.txt which contains the geometry.  A brief description of the geometry file format is given  in
       proj_mat_file_format.

       The sequence of files should be stored with the pattern:
          XXXXYYYY.ZZZ

       where  XXXX  is a prefix, YYYY is a number, and .ZZZ is the extension of a known type (either .hnd, .pfm,
       or .raw).

       For example the following would be a good directory layout for pfm files:

          Files/image_00.pfm
          Files/image_00.txt
          Files/image_01.pfm
          Files/image_01.txt
          etc...

       The Varian hnd files should be stored in the original layout.  For example:

          Files/ProjectionInfo.xml
          Files/Scan0/Proj_0000.hnd
          Files/Scan0/Proj_0001.hnd
          etc...

       No geometry txt files are needed to reconstruct from Varian hnd format.

       By default, when you generate a DRR, the image is oriented as if the virtual x-ray source were a  camera.
       That  means  that  for a right lateral film, the columns of the image go from inf to sup, and the rows go
       from ant to post.  The Varian OBI system produces HND files, which are oriented differently. For a  right
       lateral  film,  the  columns  of the HND images go from ant to post, and the rows go from sup to inf.  An
       illustration of this idea is shown in the figure below.
         [image]

PLASTIMATCH FILL

       The fill command is used to fill an image region with a constant intensity.  The region filled is defined
       by a mask file, with voxels with non-zero intensity in the mask image being filled.

       The command line usage is given as follows:

          Usage: plastimatch fill [options]
          Options:
            --input <arg>         input directory or filename; can be an image
                                   or dicom directory
            --mask <arg>          input filename for mask image
            --mask-value <arg>    value to set for pixels within mask (for
                                   "fill"), or outside of mask (for "mask"
            --output <arg>        output filename (for image file) or directory
                                   (for dicom)
            --output-format <arg> arg should be "dicom" for dicom output
            --output-type <arg>   type of output image, one of {uchar, short,
                                   float, ...}

   Examples
       Suppose  we  have  a file prostate.nrrd which is zero outside of the prostate, and non-zero inside of the
       prostate.  We can fill the prostate with an intensity of 1000,  while  leaving  non-prostate  areas  with
       their original intensity, using the following command.

          plastimatch fill \
            --input infile.nrrd \
            --output outfile.nrrd \
            --mask-value 1000 \
            --mask prostate.nrrd

PLASTIMATCH FILTER

       The  filter  command applies a filter to an input image, and creates a filtered image as its output.  The
       filter can be either built-in, or custom.

       The command line usage is given as follows:

          Usage: plastimatch filter [options] input_image
          Options:
           --gabor-k-fib <arg>     choose gabor direction at index i within
                                    fibonacci spiral of length n; specified as
                                    "i n" where i and n are integers, and i is
                                    between 0 and n-1
           --gauss-width <arg>     the width (in mm) of a uniform Gaussian
                                    smoothing filter
           --kernel <arg>          kernel image filename
           --output <arg>          output image filename
           --output-kernel <arg>   output kernel filename
           --pattern <arg>         filter type: {gabor, gauss, kernel},
                                    default is gauss

       The built-in filters supported are "gabor" and "gauss".  For a Gaussian, the width of the Gaussian can be
       controlled  using the --gauss-width option.  The Gabor filter is currently limited to automatic selection
       of filter directions, which are spaced quasi-uniformly on the unit sphere.  Custom filters are  specified
       by supplying a kernel file, which is convolved with the image.

   Example
       The  following  command  will  generate  a filtered image from the first gabor filter within a bank of 10
       filters.:

          plastimatch filter --pattern gabor Testing/rect-1.mha \
            --gabor-k-fib "0 5" --output g-05.mha

PLASTIMATCH GAMMA

       The gamma command compares two images using the so-called gamma criterion.  The gamma criterion specifies
       that images are similar at a givel location within a reference image if there exists a voxel with similar
       intensity nearby in the comparison image.  Both local gamma and global gamma can be performed using  this
       command.

       The command line usage is given as follows:

          Usage: plastimatch gamma [options] image_1 image_2
          Options:
           --analysis-threshold <arg>
               Analysis threshold for dose in float (for
                example, input 0.1 to apply 10% of the
                reference dose). The final threshold dose
                (Gy) is calculated by multiplying this
                value and a given reference dose (or
                maximum dose if not given). (default is
                0.1)
           --compute-full-region    With this option, full gamma map will be
                generated over the entire image region
                (even for low-dose region). It is
                recommended not to use this option to
                speed up the computation. It has no
                effect on gamma pass-rate.
           --dose-tolerance <arg>   The scaling coefficient for dose
                difference. (e.g. put 0.02 if you want to
                apply 2% dose difference criterion)
                (default is 0.03)
           --dta-tolerance <arg>    The distance-to-agreement (DTA) scaling
                coefficient in mm (default is 3)
           --gamma-max <arg>        The maximum value of gamma to compute;
                smaller values run faster (default is
                2.0)
           --inherent-resample <arg>
               Spacing value in [mm]. The reference
                image itself will be resampled by this
                value (Note: resampling compare-image to
                ref-image is inherent already). If arg <
                0, this option is disabled. (default is
                -1.0)
           --interp-search          With this option, smart interpolation
                search will be used in points near the
                reference point. This will eliminate the
                needs of fine resampling. However, it
                will take longer time to compute.
           --local-gamma            With this option, dose difference is
                calculated based on local dose
                difference. Otherwise, a given reference
                dose will be used, which is called
                global-gamma.
           --output <arg>           Output image
           --output-failmap <arg>   File path for binary gamma evaluation
                result.
           --output-text <arg>      Text file path for gamma evaluation
                result.
           --reference-dose <arg>   The prescription dose (Gy) used to
                compute dose tolerance; if not specified,
                then maximum dose in reference volume is
                used
           --resample-nn            With this option, Nearest Neighbor will
                be used instead of linear interpolation
                in resampling the compare-image to the
                reference image. Not recommended for
                better results.

   Example
       A  gamma  image  is  produced  from two input images using the default parameters.  This will be a global
       gamma, using maximum intensity of the reference image as the gamma normalization value.:

          plastimatch gamma --output gamma.mha \
            reference-image.mha compare-image.mha

PLASTIMATCH HEADER

       The header command is used to display simple properties about the volume, such as the image data type and
       image geometry.

       The command line usage is given as follows:

          Usage: plastimatch header [options] input_file [input_file ...]
          Options:
           -h, --help      display this help message
               --version   display the program version

   Example
       We  can  display  the  geometry  of any supported file type, such as mha, nrrd, or dicom.  We can run the
       command as follows:

          $ plastimatch header input.mha
          Type = float
          Planes = 1
          Origin = -180 -180 -167.75
          Size = 512 512 120
          Spacing = 0.7031 0.7031 2.5
          Direction = 1 0 0 0 1 0 0 0 1

       From the header information, we see that the image has 120 slices, and each slice is 512  x  512  pixels.
       The slice spacing is 2.5 mm, and the in-plane pixel spacing is 0.7031 mm.

PLASTIMATCH JACOBIAN

       The  jacobian command computes the Jacobian determinant of a vector field.  Either a Jacobian determinant
       image, or its summary statistics, can be computed.

       The command line usage is given as follows:

          Usage: plastimatch jacobian [options]
          Options:
            --input <arg>          input directory or filename of image
            --output-img <arg>     output image; can be mha, mhd, nii, nrrd,
                                    or other format supported by ITK
            --output-stats <arg>   output stats file; .txt format

   Example
       To create a Jacobian determinant image from a vector field file vf.mha, run the following:

          plastimatch jacobian \
            --input vf.mha --output-img vf_jac.mha

PLASTIMATCH LM-WARP

       The landmark_warp executable performs landmark-based deformable registration  by  matching  corresponding
       point landmarks on the fixed and moving images.

       The command line usage is given as follows:

          Usage: plastimatch lm-warp [options]
          Options:
           -a, --algorithm <arg>         RBF warping algorithm
                                          {tps,gauss,wendland}
           -d, --default-value <arg>     Value to set for pixels with unknown
                                          value
               --dim <arg>               Size of output image in voxels "x [y z]"
           -F, --fixed <arg>             Fixed image (match output size to this
                                          image)
           -f, --fixed-landmarks <arg>   Input fixed landmarks
           -h, --help                    display this help message
           -I, --input-image <arg>       Input image to warp
           -v, --input-vf <arg>          Input vector field (applied prior to
                                          landmark warping)
           -m, --moving-landmarks <arg>
                                         Output moving landmarks
           -N, --numclusters <arg>       Number of clusters of landmarks
               --origin <arg>            Location of first image voxel in mm "x y
                                          z"
           -O, --output-image <arg>      Output warped image
           -L, --output-landmarks <arg>
                                         Output warped landmarks
           -V, --output-vf <arg>         Output vector field
           -r, --radius <arg>            Radius of radial basis function (in mm)
               --spacing <arg>           Voxel spacing in mm "x [y z]"
           -Y, --stiffness <arg>         Young modulus (default = 0.0)
               --version                 display the program version

       Options "-a", "-r", "-Y", "-d" are set by default to:

          -a=gauss          Gaussian RBFs with infinite support
          -r=50.0           Gaussian width 50 mm
          -Y=0.0            No regularization of vector field
          -d=-1000          Air

       You may want to choose different algorithm:

          -a=tps            Thin-plate splines (for global registration)
          -a=wendland       Wendland RBFs with compact support (for
                             local registration)

       In the case of Wendland RBFs "-r" option sets the radius of support.

       Regularization  of  vector  field  is  available for "gauss" and "wendland" algorithms. To regularize the
       output vector field increase "-Y" to '0.1' and up with increment '0.1'.

   Example
       To create a vector field from coresponding landmarks in fixed.fcsv and moving.fcs using  Gaussian  radial
       basis functions, do the following:

          plastimatch lm-warp \
              --output-vf vf.nrrd \
              --fixed-landmarks fixed.fcsv --moving-landmarks moving.fcsv

PLASTIMATCH MABS

       The  mabs command performs a multi-atlas based segmentation (MABS) operation.  The command can operate in
       one of several training mode, or in segmentation mode.

       The command line usage is given as follows:

          Usage: plastimatch mabs [options] command_file
          Options:
            --atlas-selection         run just atlas selection
            --convert                 pre-process atlas
            --output <arg>            output (non-dicom) directory when doing
                                       a segmentation
            --output-dicom <arg>      output dicom directory when doing a
                                       segmentation
            --pre-align               pre-process atlas
            --segment <arg>           use mabs to segment the specified image
                                       or directory
            --train                   perform full training to find the best
                                       registration and segmentation parameters
            --train-atlas-selection   run just train atlas selection
            --train-registration      perform limited training to find the
                                       best registration parameters only

       Prior to running the mabs command, you must create a  configuration  file,  and  you  must  arrange  your
       training  data  into  the proper directory format.  For a complete description of the command file syntax
       and usage examples, please refer to the mabs_guidebook and the segmentation_command_file_reference.

PLASTIMATCH MASK

       The mask command is used to fill an image region with a constant intensity.  The region filled is defined
       by  a mask file, with voxels with zero intensity in the mask image being filled.  Thus, it is the inverse
       of the fill command.

       The command line usage is given as follows:

          Usage: plastimatch mask [options]
          Options:
            --input <arg>           input directory or filename; can be an
                                     image or dicom directory
            --mask <arg>            input filename for mask image
            --mask-value <arg>      value to set for pixels within mask (for
                                     "fill"), or outside of mask (for "mask"
            --output <arg>          output filename (for image file) or
                                     directory (for dicom)
            --output-format <arg>   arg should be "dicom" for dicom output
            --output-type <arg>     type of output image, one of {uchar, short,
                                     float, ...}

   Examples
       Suppose we have a file called patient.nrrd, which is zero outside of the patient, and non-zero inside the
       patient.   If  we  want to fill in the area outside of the patient with value -1000, we use the following
       command.

          plastimatch mask \
            --input infile.nrrd \
            --output outfile.nrrd \
            --negate-mask \
            --mask-value -1000 \
            --mask patient.nrrd

PLASTIMATCH ML-CONVERT

       To be written.

PLASTIMATCH PROBE

       The plastimatch probe command is used to examine the image intensity or vector field displacement at  one
       or  more  positions  within a volume.  The probe positions can be specified in world coordinates (in mm),
       using the --location option, or as image indices using the --index option.  The locations or indices  are
       linearly interpolated if they lie between voxels.

       The command line usage is given as follows:

          Usage: plastimatch probe [options] file
          Options:
           -i, --index <arg>      List of voxel indices, such as
                                   "i j k;i j k;..."
           -l, --location <arg>   List of spatial locations, such as
                                   "i j k;i j k;..."

       The  command  will  output  one  line  for each probe requested.  Each output line includes the following
       fields.:

          PROBE#        The probe number, starting with zero
          INDEX         The (fractional) position of the probe as a voxel index
          LOC           The position of the probe in world coordinates
          VALUE         The intensity (for volumes) or displacement
                         (for vector fields)

   Example
       We use the index option to see an image intensity at coordinate (2,3,4), and the location option  to  see
       image intensities at two different locations:

          plastimatch probe \
             --index "2 3 4" \
             --location "0 0 0; 0.5 0.5 0.5" \
             infile.nrrd

       The  output  will  include  three  probe  results.   Each probe shows the probe index, voxel index, voxel
       location, and intensity.

          0:    2.00,    3.00,    4.00;  -22.37,  -21.05,  -19.74; -998.725891
          1:   19.00,   19.00,   19.00;    0.00,    0.00,    0.00; -0.000197
          2:   19.38,   19.38,   19.38;    0.50,    0.50,    0.50; -9.793450

PLASTIMATCH REGISTER

       The plastimatch register command is used to peform linear or deformable registration of two images.   The
       command line usage is given as follows:

          Usage: plastimatch register command_file

       The  command file is an ordinary text file, which contains a single global section and one or more stages
       sections.  The global section begins with a line containing only the string "[GLOBAL]",  and  each  stage
       begins with a line containing the string "[STAGE]".

       The  global section is used to set input files, output files, and global parameters, while the each stage
       section defines a sequential stage of processing.  For a complete description of the command file syntax,
       please refer to the registration_command_file_reference.

   Examples
       If  you  want  to register image_2.mha to match image_1.mha using B-spline registration, create a command
       file like this:

          # command_file.txt
          [GLOBAL]
          fixed=image_1.mha
          moving=image_2.mha
          img_out=warped_2.mha
          xform_out=bspline_coefficients.txt

          [STAGE]
          xform=bspline
          impl=plastimatch
          threading=openmp
          max_its=30
          regularization_lambda=0.005
          grid_spac=100 100 100
          res=4 4 2

       Then, run the registration like this:

          plastimatch register command_file.txt

       The above example only performs a single registration stage.  If you want to do multi-stage registration,
       use multiple [STAGE] sections.  Like this:

          # command_file.txt
          [GLOBAL]
          fixed=image_1.mha
          moving=image_2.mha
          img_out=warped_2.mha
          xform_out=bspline_coefficients.txt

          [STAGE]
          xform=bspline
          impl=plastimatch
          threading=openmp
          max_its=30
          regularization_lambda=0.005
          grid_spac=100 100 100
          res=4 4 2

          [STAGE]
          max_its=30
          grid_spac=80 80 80
          res=2 2 1

          [STAGE]
          max_its=30
          grid_spac=60 60 60
          res=1 1 1

       For more examples, please refer to the image_registration_guidebook.

PLASTIMATCH RESAMPLE

       The resample command can be used to change the geometry of an image.

       The command line usage is given as follows:

          Usage: plastimatch resample [options]
          Options:
              --default-value <arg>   value to set for pixels with unknown value,
                                       default is 0
              --dim <arg>             size of output image in voxels "x [y z]"
              --direction-cosines <arg>
                                      oriention of x, y, and z axes; Specify either
                                       preset value,
                                       {identity,rotated-{1,2,3},sheared}, or 9 digit
                                       matrix string "a b c d e f g h i"
          -F, --fixed <arg>           fixed image (match output size to this image)
          -h, --help                  display this help message
              --input <arg>           input directory or filename; can be an image or
                                       vector field
              --interpolation <arg>   interpolation type, either "nn" or "linear",
                                       default is linear
              --origin <arg>          location of first image voxel in mm "x y z"
              --output <arg>          output image or vector field
              --output-type <arg>     type of output image, one of {uchar, short,
                                       float, ...}
              --spacing <arg>         voxel spacing in mm "x [y z]"
              --subsample <arg>       bin voxels together at integer subsampling rate
                                       "x [y z]"
              --version               display the program version

   Example
       We  can use the --subsample option to bin an integer number of voxels to a single voxel.  So for example,
       if we want to bin a cube of size 3x3x1 voxels to a single voxel, we would do the following.

          plastimatch resample \
            --input infile.nrrd \
            --output outfile.nrrd \
            --subsample "3 3 1"

PLASTIMATCH SCALE

       The scale command scales an image or vector field by multiplying each voxel by a constant value.

       The command line usage is given as follows:

          Usage: plastimatch scale [options] input_file
          Options:
            --output <arg>   filename for output image or vector field
            --weight <arg>   scale the input image or vector field by this
                              value (float)

   Example
       This command creates an output file with image intensity (or voxel length) twice as large  as  the  input
       values:

          plastimatch scale --output output.mha --weight 2.0 input.mha

PLASTIMATCH SEGMENT

       The  segment  command  does  simple  threshold-based  semgentation.   The  command line usage is given as
       follows:

          Usage: plastimatch segment [options]
          Options:
            -h, --help                    Display this help message
                --input <arg>             Input image filename (required)
                --lower-threshold <arg>   Lower threshold (include voxels
                                           above this value)
                --output-dicom <arg>      Output dicom directory (for RTSTRUCT)
                --output-img <arg>        Output image filename
                --upper-threshold <arg>   Upper threshold (include voxels
                                           below this value)

   Example
       Suppose we have a CT image of a water tank, and we wish to create an image which has ones where there  is
       water, and zeros where there is air.  Then we could do this:

          plastimatch segment \
            --input water.mha \
            --output-img water-label.mha \
            --lower-threshold -500

       If  we  wanted  instead to create a DICOM-RT structure set, we should specify a DICOM image as the input.
       This will allow plastimatch to create the DICOM-RT with the correct patient name, patient id,  and  UIDs.
       The output file will be called "ss.dcm".

          plastimatch segment \
            --input water_dicom \
            --output-dicom water_dicom \
            --lower-threshold -500

PLASTIMATCH STATS

       The plastimatch stats command displays a few basic statistics about the image onto the screen.

       The command line usage is given as follows:

          Usage: plastimatch stats file [file ...]

       The input files can be either 2D projection images, 3D volumes, or 3D vector fields.

   Example
       The following command displays statistics for the 3D volume synth_1.mha.

          $ plastimatch stats synth_1.mha
          MIN -999.915161 AVE -878.686035 MAX 0.000000 NUM 54872

       The reported statistics are interpreted as follows:

          MIN      Minimum intensity in image
          AVE      Average intensity in image
          MAX      Maximum intensity in image
          NUM      Number of voxels in image

   Example
       The following command displays statistics for the 3D vector field vf.mha:

          $ plastimatch stats vf.mha
          Min:            0.000     -0.119     -0.119
          Mean:          13.200      0.593      0.593
          Max:           21.250      1.488      1.488
          Mean abs:      13.200      0.594      0.594
          Energy: MINDIL -6.79 MAXDIL 0.166 MAXSTRAIN 41.576 TOTSTRAIN 70849
          Min dilation at: (29 19 19)
          Jacobian: MINJAC -6.32835 MAXJAC 1.15443 MINABSJAC 0.360538
          Min abs jacobian at: (28 36 36)
          Second derivatives: MINSECDER 0 MAXSECDER 388.82 TOTSECDER 669219
            INTSECDER 1.524e+06
          Max second derivative: (29 36 36)

       The rows corresponding to "Min, Mean, Max, and Mean abs" each have three numbers, which correspond to the
       x, y, and z coordinates.  Therefore, they compute these statistics for each vector direction separately.

       The remaining statistics are described as follows:

          MINDIL        Minimum dilation
          MAXDIL        Maximum dilation
          MAXSTRAIN     Maximum strain
          TOTSTRAIN     Total strain
          MINJAC        Minimum Jacobian
          MAXJAC        Maximum Jacobian
          MINABSJAC     Minimum absolute Jacobian
          MINSECDER     Minimum second derivative
          MAXSECDER     Maximum second derivative
          TOTSECDER     Total second derivative
          INTSECDER     Integral second derivative

PLASTIMATCH SYNTH

       The synth command creates a synthetic image.  The following kinds of images can be created, by specifying
       the  appropriate  --pattern  option.   Each  of  these  patterns  come with a synthetic structure set and
       synthetic dose which can be used for testing.

       • donut -- a donut shaped structure

       • gauss -- a Gaussian blur

       • grid -- a 3D grid

       • lung -- a synthetic lung with a tumor

       • rect -- a uniform rectangle within a uniform background

       • sphere -- a uniform sphere within a uniform background

       • xramp -- an image that linearly varies intensities in the x direction

       • yramp -- an image that linearly varies intensities in the y direction

       • zramp -- an image that linearly varies intensities in the z direction

       The command line usage is given as follows:

          Usage: plastimatch synth [options]
          Options:
           --background <arg>        intensity of background region
           --cylinder-center <arg>   location of cylinder center in mm "x [y
                                      z]"
           --cylinder-radius <arg>   size of cylinder in mm "x [y z]"
           --dicom-with-uids <arg>   set to false to remove uids from created
                                      dicom filenames, default is true
           --dim <arg>               size of output image in voxels "x [y z]"
           --direction-cosines <arg>
                                     oriention of x, y, and z axes; Specify
                                      either preset value,
                                      {identity,rotated-{1,2,3},sheared}, or 9
                                      digit matrix string "a b c d e f g h i"
           --donut-center <arg>      location of donut center in mm "x [y z]"
           --donut-radius <arg>      size of donut in mm "x [y z]"
           --donut-rings <arg>       number of donut rings (2 rings for
                                      traditional donut)
           --dose-center <arg>       location of dose center in mm "x y z"
           --dose-size <arg>         dimensions of dose aperture in mm "x [y
                                      z]", or locations of rectangle corners
                                      in mm "x1 x2 y1 y2 z1 z2"
           --fixed <arg>             fixed image (match output size to this
                                      image)
           --foreground <arg>        intensity of foreground region
           --gabor-k-fib <arg>       choose gabor direction at index i within
                                      fibonacci spiral of length n; specified
                                      as "i n" where i and n are integers, and
                                      i is between 0 and n-1
           --gauss-center <arg>      location of Gaussian center in mm "x [y
                                      z]"
           --gauss-std <arg>         width of Gaussian in mm "x [y z]"
           --grid-pattern <arg>      grid pattern spacing in voxels "x [y z]"
           --input <arg>             input image (add synthetic pattern onto
                                      existing image)
           --lung-tumor-pos <arg>    position of tumor in mm "z" or "x y z"
           --metadata <arg>          patient metadata (you may use this
                                      option multiple times)
           --noise-mean <arg>        mean intensity of gaussian noise
           --noise-std <arg>         standard deviation of gaussian noise
           --origin <arg>            location of first image voxel in mm "x y
                                      z"
           --output <arg>            output filename
           --output-dicom <arg>      output dicom directory
           --output-dose-img <arg>   filename for output dose image
           --output-ss-img <arg>     filename for output structure set image
           --output-ss-list <arg>    filename for output file containing
                                      structure names
           --output-type <arg>       data type for output image: {uchar,
                                      short, ushort, ulong, float}, default is
                                      float
           --patient-id <arg>        patient id metadata: string
           --patient-name <arg>      patient name metadata: string
           --patient-pos <arg>       patient position metadata: one of
                                      {hfs,hfp,ffs,ffp}
           --pattern <arg>           synthetic pattern to create: {cylinder,
                                      donut, dose, gabor, gauss, grid, lung,
                                      noise, rect, sphere, xramp, yramp,
                                      zramp}, default is gauss
           --penumbra <arg>          width of dose penumbra in mm
           --rect-size <arg>         width of rectangle in mm "x [y z]", or
                                      locations of rectangle corners in mm "x1
                                      x2 y1 y2 z1 z2"
           --spacing <arg>           voxel spacing in mm "x [y z]"
           --sphere-center <arg>     location of sphere center in mm "x y z"
           --sphere-radius <arg>     radius of sphere in mm "x [y z]"
           --volume-size <arg>       size of output image in mm "x [y z]"

   Examples
       Create a cubic water phantom 30 x 30 x 40 cm with zero position at the center of the water surface:

          plastimatch synth \
            --pattern rect \
            --output water_tank.mha \
            --rect-size "-150 150 0 400 -150 150" \
            --origin "-245.5 245.5 -49.5 449.5 -149.5 149.5" \
            --spacing "1 1 1" \
            --dim "500 500 300"

       Create lung phantoms with two different tumor positions, and output to dicom:

          plastimatch synth \
            --pattern lung \
            --output-dicom lung_inhale \
            --lung-tumor-pos "0 0 10"
          plastimatch synth \
            --pattern lung \
            --output-dicom lung_exhale \
            --lung-tumor-pos "0 0 -10"

PLASTIMATCH SYNTH-VF

       The synth-vf command creates a synthetic vector field.  The following  kinds  of  vector  fields  can  be
       created, by specifying the appropriate option.

       • gauss -- a gaussian warp

       • radial -- a radial expansion or contraction

       • translation -- a uniform translation

       • zero -- a vector field that is zero everywhere

       The command line usage is given as follows:

          Usage: plastimatch synth-vf [options]
          Options:
           --dim <arg>             size of output image in voxels "x [y z]"
           --direction-cosines <arg>
                                   oriention of x, y, and z axes; Specify
                                    either preset value, {identity,
                                    rotated-{1,2,3}, sheared}, or 9 digit
                                    matrix string "a b c d e f g h i"
           --fixed <arg>           An input image used to set the size of the
                                    output
           --gauss-center <arg>    location of center of gaussian warp "x [y
                                    z]"
           --gauss-mag <arg>       displacment magnitude for gaussian warp in
                                    mm "x [y z]"
           --gauss-std <arg>       width of gaussian std in mm "x [y z]"
           --origin <arg>          location of first image voxel in mm "x y
                                    z"
           --output <arg>          output filename
           --radial-center <arg>   location of center of radial warp "x [y
                                    z]"
           --radial-mag <arg>      displacement magnitude for radial warp in
                                    mm "x [y z]"
           --spacing <arg>         voxel spacing in mm "x [y z]"
           --volume-size <arg>     size of output image in mm "x [y z]"
           --xf-gauss              gaussian warp
           --xf-radial             radial expansion (or contraction)
           --xf-trans <arg>        uniform translation in mm "x y z"
           --xf-zero               Null transform

PLASTIMATCH THRESHOLD

       The threshold command creates a binary labelmap image from an input intensity image.

       The command line usage is given as follows:

          Usage: plastimatch threshold [options]
          Options:
              --above <arg>    value above which output has value high
              --below <arg>    value below which output has value high
          -h, --help           display this help message
              --input <arg>    input directory or filename
              --output <arg>   output image
              --range <arg>    a string that forms a list of threshold ranges of the
                                form "r1-lo,r1-hi,r2-lo,r2-hi,...", such that voxels
                                with intensities within any of the ranges
                                ([r1-lo,r1-hi], [r2-lo,r2-hi], ...) have output value
                                high
              --version        display the program version

   Example
       The  following  command  creates a binary label image with value 1 when input intensities are between 100
       and 200, and value 0 otherwise.:

          plastimatch threshold \
            --input input_image.nrrd \
            --output output_labe.nrrd \
            --range "100,200"

PLASTIMATCH THUMBNAIL

       The thumbnail command generates a two-dimensional thumbnail image of an axial slice of the input  volume.
       The  output  image is not required to correspond exactly to an integer slice number.  The location of the
       output image within the slice is always centered.

       The command line usage is given as follows:

          Usage: plastimatch thumbnail [options] input-file
          Options:
            --input file
            --output file
            --thumbnail-dim size
            --thumbnail-spacing size
            --slice-loc location

   Example
       We create a two-dimensional image with resolution 10 x 10 pixels, at axial location 0, and of size  20  x
       20 mm:

          plastimatch thumbnail \
            --input in.mha --output out.mha \
            --thumbnail-dim 10 \
            --thumbnail-spacing 2 \
            --slice-loc 0

PLASTIMATCH UNION

       The  union command creates a binary volume which is the logical union of two input images.  Voxels in the
       output image have value one if the voxel is non-zero in either input image, or value zero if the voxel is
       zero in both input images.

       The command line usage is given as follows:

          Usage: plastimatch union [options] input_1 input_2
          Options:
           -h, --help           display this help message
               --output <arg>   filename for output image
               --version        display the program version

   Example
       The following command creates a volume that is the union of two input images:

          plastimatch union \
            --output itv.mha \
            phase_1.mha phase_2.mha

PLASTIMATCH WARP

       The  warp  command  is an alias for convert.  Please refer to plastimatch convert for the list of command
       line parameters.

   Examples
       To warp an image using the B-spline coefficients generated by the plastimatch register command (saved  in
       the file bspline.txt), do the following:

          plastimatch warp \
            --input infile.nrrd \
            --output-img outfile.nrrd \
            --xf bspline.txt

       In  the  previous  example,  the  output  file geometry was determined by the geometry information in the
       bspline coefficient file.  You can resample to a different geometry using --fixed,  or  --origin,  --dim,
       and --spacing.

          plastimatch warp \
            --input infile.nrrd \
            --output-img outfile.nrrd \
            --xf bspline.txt \
            --fixed reference.nrrd

       When  warping  a structure set image, where the integer bits correspond to structure membership, you need
       to use nearest neighbor interpolation rather than linear interpolation.

          plastimatch warp \
            --input structures-in.nrrd \
            --output-img structures-out.nrrd \
            --xf bspline.txt \
            --interpolation nn

       Sometimes, voxels located outside of the geometry of the input image will be warped into the geometry  of
       the  output  image.  By default, these areas are "filled in" with an intensity of zero.  You can choose a
       different value for these areas using the --default-value option.

          plastimatch warp \
            --input infile.nrrd \
            --output-img outfile.nrrd \
            --xf bspline.txt \
            --default-value -1000

       In addition to images and structures, landmarks exported from 3D Slicer can also be warped.

          plastimatch warp \
            --input fixed_landmarks.fcsv \
            --output-pointset warped_landmarks.fcsv \
            --xf bspline.txt

       Sometimes, it may be desirable to apply a transform explicitly defined by a vector field instead of using
       B-spline  coefficients.   To allow this, the --xf option also accepts vector field volumes.  For example,
       the previous example would become.

          plastimatch warp \
            --input fixed_landmarks.fcsv \
            --output-pointset warped_landmarks.fcsv \
            --xf vf.mha

PLASTIMATCH XF-CONVERT

       The xf-convert command converts between transform types.  A transform can be either a B-spline transform,
       or  a  vector field.  There are two different kinds of B-spline transform formats: the plastimatch native
       format, and the ITK format.  In addition to converting the transform type,  the  xf-convert  command  can
       also change the grid-spacing of B-spline transforms.

       The command line usage is given as follows:

          Usage: plastimatch xf-convert [options]
          Options:
            --dim <arg>            Size of output image in voxels "x [y z]"
            --grid-spacing <arg>   B-spline grid spacing in mm "x [y z]"
            --input <arg>          Input xform filename (required)
            --nobulk               Omit bulk transform for itk_bspline
            --origin <arg>         Location of first image voxel in mm "x y z"
            --output <arg>         Output xform filename (required)
            --output-type <arg>    Type of xform to create (required), choose
                                    from {bspline, itk_bspline, vf}
            --spacing <arg>        Voxel spacing in mm "x [y z]"

   Example
       We  want  to  convert  a  B-spline  transform  into  a  vector  field.   If  the B-spline transform is in
       native-format, the vector field geometry is defined by the values found in the transform header.:

          plastimatch xf-convert \
            --input bspline.txt \
            --output vf.mha \
            --output-type vf

       Likewise, if we want to convert a vector field into a set of B-spline coefficients with  a  control-point
       spacing of 30 mm in each direction.

          plastimatch xf-convert \
            --input vf.mha \
            --output bspline.txt \
            --output-type bspline \
            --grid-spacing 30

AUTHOR

       Plastimatch    is    a    collaborative    project.    For   additional   documentation,   please   visit
       http://plastimatch.org.     For    questions,    comments,    and    bug    reports,     please     visit
       http://groups.google.com/group/plastimatch.

COPYRIGHT

       Plastimatch  development  team  (C)  2010-2019.   You are free to use, modify, and distribute plastimatch
       according to a BSD-style license.  Please see LICENSE.TXT for details.