Provided by: plastimatch_1.7.4+dfsg.1-2_amd64 bug

NAME

       plastimatch - register, convert, warp, or manipulate 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 1.7.4
          Usage: plastimatch command [options]
          Commands:
           add           adjust        average       bbox          boundary
           crop          compare       compose       convert       dice
           diff          dmap          dose          drr           dvh
           fill          filter        gamma         header        jacobian
           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 and linear scaling.

       The command line usage is given as follows:

          Usage: plastimatch adjust [options]
          Required:
            --input <arg>       input directory or filename
            --output <arg>      output image
          Optional:
            --pw-linear <arg>   a string that forms a piecewise linear
                                 map from input values to output values,
                                 of the form "in1,out1,in2,out2,..."

       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.

   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"

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 0.3.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

       This command is under construction.

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]
             --input-ss-img file
             --input-ss-list file
             --input-dose file
             --output-csv file
             --input-units {gy,cgy}
             --cumulative
             --num-bins
             --bin-width

       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 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 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 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 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 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 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) 2010-2015.  You are free to use, modify,  and  distribute
       plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.