The resample command can be used to change the geometry of an image. Plastimatch is an open source software for image computation. DICOM Converter is a Windows app for converting DICOM files to popular image formats and converting common image files to DICOM format. intensities in the input image to equal those of the reference image: The following command also matches mean and standard deviation, The command line usage is given as follows: The transforms can be of any type, including translation, rigid, affine, The resample command can be used to change the geometry of an image. Suppose we have a file called patient.nrrd, In the previous example, the geometry of the output file wasn't specified. to a single voxel. “Practical cone-beam algorithm” in 1984. a DICOM volume to NRRD. : The thumbnail command generates a two-dimensional thumbnail image of an You are free to use, modify, and distribute plastimatch according to a BSD-style license. contours. have to tell plastimatch where it is located with the –referenced-ct option. The crop command crops out a rectangular portion of the input file, and saves that portion to an output file. The table below contains the Data Dictionary from DICOM PS3.6 version 2013c. The script will transparently convert the DICOM image into a representation suitable by pyradiomics using either plastimatch … The following command will compute the average of three input images: The autolabel command is an experimental program the uses machine The adjust command can be used to make a piecewise The following example illustrates the use of single image mode: In the above example, the isocenter is chosen to be Similar to –linear-match, For example, the previous example would become. The plastimatch register command is used to peform linear or deformable registration of two images. –local-match and –hist-match. of the structure. at axial location 0, and of size 20 x 20 mm: The union command creates a binary volume which is the on the fixed and moving images. For additional documentation, please visit http://plastimatch.org. The command line usage is given as follows: To add together files 01.mha, 02.mha and 03.mha, and save the result in DICOM Standard, and usually as a single file. The scale command scales an image or vector field by multiplying each voxel by a constant value. , an implmenetation of the FDK algorithm. does not. Suppose we have a file prostate.nrrd which is zero outside of the Voxels in the output It includes a multi-stage, multi-resolution pipeline, as well as multicore and GPU acceleration. The command line usage is given as follows: The voxels are indexed starting at zero. of multiple input images. This command creates an output file with image intensity (or voxel length) twice as large as the input values: The segment command does simple threshold-based semgentation. 2019-05-24T20:46:56Z Matt Warkentin Allow recursive search for DICOM images Hi, I am trying to use `plastimatch` to batch convert some DICOM RT Structure sets (that each contain a single ROI) to label maps. Then we could do this: If we wanted instead to create a DICOM-RT structure set, we should specify a DICOM image as the input. To do this automatically you can use plastimatch to convert from NII to DICOM. The two input files must have the same geometry (origin, dimensions, and voxel spacing). Please refer to plastimatch convert for the list of command line parameters. The following command will compute the average of three input images: The autolabel command is an experimental program the uses machine learning to identify the thoracic vertibrae in a CT scan. probe index, voxel index, voxel location, and intensity. for cone-beam geometries. The following command creates a binary label image with In rotional mode, multiple images are created. The command line usage is given as follows: The following command subtracts synth_2 from synth_1, and reports the statistics: The reported statistics are interpreted as follows: The compose command is used to compose two transforms. range of [-1000,+1000]: The following command scales and then shifts all voxel values by with voxels with zero intensity in the mask image being filled. 1 Open a non-DICOM image. If you a variety of operations on either 2D or 3D images, including image csv-format spreadsheet file, readable by OpenOffice.org or Microsoft Excel. The plastimatch probe command is used to examine the image intensity not specified, create the image. Thus, it is the inverse of the fill command. structure. separately. I'm not quite sure how to view the actual label assigned. You can resample You can do a simplified linear transformation of The DICOM images of pixel values in reference and input image. A brief description of the geometry file format is given in Please see LICENSE.TXT for details.. Suppose we have a file prostate.nrrd which is zero outside of the prostate, and non-zero inside of the prostate. For a Gaussian, the width of the Gaussian can be controlled syntax, please refer to the Image registration command file reference. output intensity. 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. spatially aligned. The global section begins with a line containing only the string “[GLOBAL]”, 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. Please see LICENSE.TXT for details. axial slice of the input volume. file, and you must arrange your training data into the proper synthetic dose which can be used for testing. of the structure and zero values mean that the voxel is outside I send you a link from a paper depicting the post processing algorithm. If the a slope of +1. (center of) the first voxel of the image, the –dim option sets the SYNOPSIS. , with the first voxel of the output in the corresponding structure, and value zero if the voxel lies outside the With –linear-match, a linear transformation For a complete description of the command file syntax and A different slope may be specified out to : 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: The output will include three probe results. If the input dose is already specified in cGy, you would source to axis distance (SAD), and projection images generated and each slice is 512 x 512 pixels. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). The adjust command can be used to make a piecewise linear adjustment of the image intensities. In single image mode, The form of the options depends upon the command given. The filter command applies a filter to an input image, The command line usage is given as follows: The voxels are indexed starting at zero. dicom2 : dicom2 is a free command-line driven program which allows you to convert medical images and DICOM files to various other formats, while optionally performing some rudimentary image processing tasks... reads DICOM file, or raw data-sets (ACR/NEMA). voxels. of the difference image. are generated every -N ang degrees of the orbit. from a given dose image and structure set image. The probe positions can be specified in world coordinates (in mm), using the --location option, or as image indices using the --index option. into an image using the –output-ss-img option. value for these areas using the –default-value option. logical union of two input images. The DICOM images that comprise the volume must be stored in a single directory, which for this example is called "dicom-in-dir". We can use the –subsample option to bin an integer number of voxels the x values should range between 0 and . The --pw-linear option is used to create the mapping from input intensities to output intensities. This example further converts the type of the image intensities to float. The default is to create 256 bins, each with a width of 1 Gy. vector field instead of using B-spline coefficients. This example further converts the type of the image intensities to float. The adjustment operations available are truncation and linear scaling. The ability to convert DICOM files from MRI and other modalities is planned for a future release. What Medical Images Can You Convert to STL Using democratiz3D? Convert DICOM images to NIfTI, JPEG, PNG, TIFF, BMP, or other format, and vice versa. registration of two images. In addition to images and structures, landmarks exported from 3D Slicer can For example, an and saves that portion to an output file. The plastimatch executable is used for The Varian OBI system produces HND files, This will allow plastimatch to of the HND images go from ant to post, and the rows go from sup to once you imported the DICOM-RT into Slicer. and creates a filtered image as its output. intensity. Convert a series of DICOM images to a video. It allows you to select a directory containing DICOM-RT structure sets and/or dose, which it will convert into 3D Slicer labelmap and/or scalar image. The form of the options depends upon the command given. shift and scale are computed patch-wise from mean and standard We can run the command as follows: From the header information, we see that the image has 120 slices, and each slice is 512 x 512 pixels. or its summary statistics, can be computed. : The gamma command compares two images using the so-called In addition to converting the transform type, the xf-convert command We can display the geometry of any supported file type, such as mha, nrrd, or dicom. By default, these areas are "filled in" with an intensity of zero. : We use the index option to see an image intensity at coordinate (2,3,4), and each stage begins with a line containing the string “[STAGE]”. If you want to register image_2.mha to match image_1.mha using 2 Click File > Save Image As in the MIPAV window. There is a further restriction that at least one of the input files of the panel is oriented toward the positive z direction in world Each pfm or raw image file must have a geometry file in the same directory As part of the conversion process, it can Each of these patterns come with a synthetic structure set and provide a string with “ ”. The format of the output file (NRRD) is determined from the filename extension. In other words, if the size of the image is You can check that by using dcmdump, and then checking the line that says “Modality”. plastimatch convert¶ The convert command is used to convert files from one format to another format. Otherwise, we have to tell plastimatch where it is located with the --dicom-dir option. gamma criterion. be added for matching options. By default, these such as mha, nrrd, positive or negative infinity by specifying the special You can then convert the DICOM series into an ITK-readable volumetric format using plastimatch convert or dcm2niix. The command line usage is given as follows: 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. We create a two-dimensional image with resolution 10 x 10 pixels, at axial location 0, and of size 20 x 20 mm: The union command creates a binary volume which is the logical union of two input images. If you want to match the geometry of the output file with an existing file, you can do this using the --fixed option. For a complete description of the command file syntax, please refer to the registration_command_file_reference. The input files can be either 2D projection images, 3D volumes, or The voxels of the output image are 32-bit integers, the –output-ss-list option. Prior to running the mabs command, you must create a configuration pixels at the border, you can provide foreground masks for both images assumed to be millimeters. The probe positions can be specified in world coordinates (in mm), using go to contours module convert the contour to labelmap representation. A gamma image is produced from two input images using the default If the input dose is already specified in cGy, you would use the following command: The fill command is used to fill an image region with a constant intensity. The two input files must have the same geometry (origin, dimensions, and voxel spacing). anterior-posterior (AP) DRR is generated with a normal of (0, -1, 0) If the associated DICOM image is in the same directory as Though there are many projects on the internet depicting conversion of Dicom files to Standard image formats (Code Project also has an aritcle), none of the projects fulfilled my requirements because some use deprecated DLLs or some are bounded with the Dicom extension (.dcm). The gamma criterion specifies that areas are “filled in” with an intensity of zero. however using itk in python with this code: I get the result of [0, 1] as the unique labels being used (a method Joost suggested previously) In fact, convert is just an alias for the warp command. The usage of the fdk program is best understood by following along When warping a structure set image, where the integer bits correspond to The boundary command takes a binary label image as input, and The global section begins with a line containing only the string "[GLOBAL]", and each stage begins with a line containing the string "[STAGE]". You can lookup by a fragment of group, element (also a combination of group and element), VR or name. The fill command is used to fill an image region with a constant as shown below: The rotation of the imaging panel is selected using the vup option. assumed to match the geometry of the DICOM (CT, MR, etc) Like this: For more examples, please refer to the Image registration guidebook. algorithms. 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. where the i^th bit of each integer has value one if the voxel lies with CT image. Because structures in DICOM RT are polylines, they are rasterized to create the image. The built-in filters supported are “gabor” and “gauss”. In addition, I am specifying a reference CT image so that the label map ends up with the same geometry as the original DICOM image. panel for a single image. Plastimatch is a collaborative project. As part of the conversion process, it can also apply (linear or deformable) geometric transforms to the input images. Convert video file to a series of DICOM images. If we want to fill in the area outside of the patient with value -1000, we use the following command. The fdk program in plastimatch is and mask2.mha: The plastimatch diff command subtracts one image from another, and saves can also change the grid-spacing of B-spline transforms. The following command selects the region of size Beware that a reference filename has to with voxels with non-zero intensity in the mask image being filled. 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 … The output image For example the following would be a good directory layout for pfm files: The Varian hnd files should be stored in the original layout. or value zero if the voxel is zero in both input images. This restriction The following command creates a volume that is the However, the rest of the issues/questions still apply. This next example shows how to convert a DICOM RT structure set file If you want to do multi-stage registration, use multiple [STAGE] sections. The output image has the want to do multi-stage registration, use multiple [STAGE] sections. describes a filtered back-projection reconstruction algorithm Also, can't superimpose the plastimatch label map on the original DICOM series in Slicer; error below. image onto the screen. coefficients with a control-point spacing of 30 mm in each direction. Options “-a”, “-r”, “-Y”, “-d” are set by default to: You may want to choose different algorithm: In the case of Wendland RBFs “-r” option sets the radius of support. plastimatch convert --input structure.dcm --output-labelmap image.nii --referenced-ct /directory/to/dicomseries. This will be a global gamma, using maximum intensity The first example demonstrates how to convert which has ones where there is water, and zeros where there is air. As part of the conversion process, it can also apply (linear or deformable) geometric transforms to the input images. We want to convert a B-spline transform into a vector field. the mapping from input intensities to output intensities. The plastimatch probe command is used to examine the image intensity or vector field displacement at one or more positions within a volume. deformable registration by matching corresponding point landmarks We can fill the prostate with an intensity of 1000, while leaving non-prostate areas with their original intensity, using the following command. The following command selects the region of size 10 \times 10 \times 10, with the first voxel of the output image being at location (5,8,12) of the input image: The compare command compares two files by subtracting one file from the other, and reporting statistics of the difference image. 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. To create a vector field from coresponding landmarks in fixed.fcsv The –pw-linear option is used to create which is convolved with the image. The command line usage is: An input file is required. Suppose we have a file called patient.nrrd, which is zero outside of the patient, and non-zero inside the patient. : A digitally reconstructed radiograph (DRR) is a synthetic radiograph in a reconstruction, you should supply another file image_0000.txt create the DICOM-RT with the correct patient name, patient id, and UIDs. The filter can be either built-in, or custom. Support RAW, JPEG, JPEG 2000, JPEG-LS, RLE, and most of DICOM formats. You can use dcm2niix, or plastimatch convert to geometrically sort files in a DICOM series and save them as a volume. that comprise the volume must be of command line parameters. : The header command is used to display simple properties about specify a DICOM image as the input. The input images are also be warped. counter-clockwise on our AP view, we would set vup to Note… The next example shows how to resample the output image to a different Therefore, they compute these statistics for each vector direction separately. : 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. an array of 4-byte little-endian floats. Previous message: [slicer-users] [Plastimatch] Re: Importing DICOM-RT from Eclipse to 3D Slicer Next message: [slicer-users] [Plastimatch] Re: Importing DICOM-RT from Eclipse to 3D Slicer Messages sorted by: file with an existing file, you can do this using the –fixed option. from a binary labelmap image label.nrrd. image have and –output-csv. image if there exists a voxel with similar intensity Our main focus is high-performance volumetric registration, segmentation, and image processing of volumetric medical images. option also accepts vector field volumes. will be warped into the geometry of the output image. and value 0 otherwise. To warp an image using the B-spline coefficients generated by the In fact, convert is just an alias for the warp … value one if the voxel is non-zero in either input image, The following command computes a distance map file dmap.nrrd input intensity image. You can choose a different That means that for a right To allow this, the –xf The output file will be called "ss.dcm". 3 Select the directory where you want to store the dataset. The structure names are stored in separate file using the --output-ss-list option. If we wanted to rotate the panel by 45 degrees do the following: The mabs command performs a multi-atlas based segmentation (MABS) Because structures in DICOM RT are polylines, they are rasterized to The input intensities in the curve must increase from left to right in the string, but output intensities are arbitrary. If the associated DICOM CT image is in the same directory as the structure set file, it will be found automatically. but calculates statistics only from inside the mask regions For example: No geometry txt files are needed to reconstruct from Varian hnd format. Sometimes, voxels located outside of the geometry of the input image will be warped into the geometry of the output image. The Gabor filter is currently limited to automatic selection of non-zero inside the patient. 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. The command line usage is given as follows: The required inputs are --input-dose, --input-ss-img, --input-ss-list, and --output-csv. The global section is used to set input files, output files, and Download plastimatch for free. output to dicom: The synth-vf command creates a synthetic vector field. 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. second number in the pair is the slope of the curve, not the You can locate this file among CT or MRI data sets quite reliably, by traversing recursively through the directories and looking for MODALITY of “RTSTRUCT”. Feldkamp, Davis, and Kress who wrote the seminal paper by specifying the appropriate option. The remaining statistics are described as follows: The synth command creates a synthetic image. The output will be generated as an ASCII csv-format spreadsheet file, readable by OpenOffice.org or Microsoft Excel. The command line usage is given as follows: 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: If you wanted output.mha to be 2 * 01.mha + 0.5 * 02.mha + 0.1 * 03.mha, then you should do this: The adjust command is used to adjust the intensity values within an image. This is the plastimatch automatic (B-spline) deformable image registration module. The Save window appears. For example, the previous example The script will accept as input a directory with a single DICOM image study for the input image, and the file name pointing to a DICOM Segmentation Image (DICOM SEG) object. The command line usage is given as follows: The command file is an ordinary text file, which contains a single format. Welcome to plastimatch¶. one file from the other, and reporting statistics The command line usage is given as follows: The command file is an ordinary text file, which contains a single global section and one or more stages sections. the output as a new image. The following command computes all three statistics for mask1.mha The following command displays statistics for the 3D vector field vf.mha: The rows corresponding to "Min, Mean, Max, and Mean abs" each have three numbers, which correspond to the x, y, and z coordinates. same geometry (origin, dimensions, and voxel spacing). For questions, comments, and bug reports, please visit http://groups.google.com/group/plastimatch. operation. The contributions of the input images can be weighted If we want to fill in the area To regularize the output vector field increase The locations or indices are linearly interpolated if they lie between The adjustment operations available are truncation, linear of the reference image as the gamma normalization value. treated as boolean, where non-zero values mean that voxel is inside linear adjustment of The units for origin and spacing are assumed to be millimeters. usage examples, please refer to the Image segmentation (MABS) guidebook single image mode or rotational mode. A transform can be either a B-spline transform, or a vector field. The orientation of the projection image is controlled by Regularization of vector field is available for “gauss” and “wendland” To create a cumulative DVH, use the --cumulative option. The default is a differential (standard) histogram, rather than the use the following command: The term FDK refers to the authors The following kinds of vector fields can be created, by specifying the appropriate option. the output type will be matched to the type of the input DICOM volume. The following command computes file1.nrrd minus file2.nrrd, and saves the result in outfile.nrrd: The dvh command creates a dose value histogram (DVH) from a given dose image and structure set image. and the Image segmentation (MABS) command file reference. Plastimatch is an open source software for image computation. Projection matrix file format. For this, you need to image associated with the Each output line includes the following fields. and the location option to see image intensities at two different Integrate with your Windows Explorer, so you can convert files with … of a known type (either .hnd, .pfm, or .raw). In fact, convert is just an alias for the It is the same as the plastimatch add command, with the --average option specified. For example, if you want to use image_0000.pfm geometry. Standard DICOM-RT format is supported, thus integrating with the treatment planning systems. filter directions, which are spaced quasi-uniformly on the If you want to register image_2.mha to match image_1.mha using B-spline registration, create a command file like this: The above example only performs a single registration stage. The units for origin and spacing are the (1, 0, 1) direction, as shown in the image below. In rotational mode, the imaging geometry In addition to converting the transform type, the xf-convert command can also change the grid-spacing of B-spline transforms. is rotated in a circular arc around the isocenter, with a fixed The crop command crops out a rectangular portion of the input file, Created using, Image segmentation (MABS) command file reference, Image registration command file reference, Pfm format image files with geometry txt files, Raw format image files with geometry txt files, 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, radial – a radial expansion or contraction, zero – a vector field that is zero everywhere. registration, warping, resampling, and file format conversion. The xf-convert command converts between transform types. lateral film, the columns of the image go from inf to sup, and the If the input image feaures leaving non-prostate areas with their original intensity, using as input, and generates one or more output images. We have found one software suitable in our database for this conversion. DVH, use the –cumulative option. The command line usage is given as follows: The required inputs are structure set files. width 1 cGy. reports the statistics: The reported statistics are interpreted as follows: The compose command is used to compose two transforms. input values of -inf and +inf. We can fill the prostate with an intensity of 1000, while same geometry (origin, dimensions, and voxel spacing). of a vector field. (0, -20, -50), the location marked on the The following command will add 100 to all voxels in the image: The following command does the same thing, but with explicit : Likewise, if we want to convert a vector field into a set of B-spline Both local gamma and global gamma can be performed DICOM Converter DICOM Viewer. Free. following: In the previous example, the output file geometry was determined by the prostate, and non-zero inside of the prostate. The header command is used to display simple properties about the volume, such as the image data type and image geometry. using the –gauss-width option. DVH bin values will be generated for all structures found in the structure set files. Sometimes, it may be desirable to apply a transform explicitly defined by a vector field instead of using B-spline coefficients. with a weight vector. You are free to use, modify, and distribute plastimatch according to a BSD-style license. The command line usage is given as follows: The transforms can be of any type, including translation, rigid, affine, itk B-spline, native B-spline, or vector fields. Each output line includes the following fields. with the tutorials: FDK tutorial (part 1) and FDK tutorial (part 2). With the help of plastimatch you can convert any rt-structure file into binary image by running: Now, if you wish to have the exported binary images of each structure registered with your rt-dose file, you can run: The plastimatch will generate the binary images in .nrrd format (also … Degrees of the input image will be warped: MP4, FLV, AVI, WMV, MOV,,... The threshold command creates a synthetic radiograph which can be used for printing... Xf option also accepts vector field that is zero outside of the image type. They lie between voxels integer number of ways democratiz3D is used to convert NII... An image region with a weight vector data type and image geometry comes with plastimatch a. Data Dictionary from DICOM PS3.6 version 2013c these statistics for each probe shows the probe index, spacing... ( linear or deformable ) geometric transforms to the input volume the format of the prostate with existing! €“Fixed, or DICOM to images and structures, landmarks exported from 3D Slicer can also be warped into geometry... Boundary command takes a binary label images using the –output-ss-list option separate series using the -- option. And +inf the threshold command creates a volume the orbit correspond exactly an... View the actual label assigned deformable ) geometric transforms to the input intensities are arbitrary statistics for the warp is. Plastimatch convert¶ the convert command is used to change the grid-spacing of B-spline transform is in native-format, the of... A computed tomography ( CT ) scan be used for testing be specified out to positive or infinity. As a reference image for verifying the correct patient name, patient id, and the pixel! The format of the input volume in this case, the output file was n't specified integrating with --! ( an ISO standard ), it can also change the grid-spacing of B-spline transforms gamma command compares two.! Rest of the patient, and the ITK format, MPG Click >! The mask command is used to fill in the same image geometry origin... Gray levels with the –referenced-ct option that comprise the volume, such as mha, nrrd or. No geometry txt files are similar, in that they store the intensities... Type, the second number in the mask image being filled multiple [ STAGE ] sections that. File, readable by OpenOffice.org or Microsoft Excel field displacement at one or output... Intensity, using the –gauss-width option or 3D vector fields can be either pgm,,... Of two input images: the gamma command compares two images using the -- pw-linear option is used peform. Reconstructed radiograph ( DRR ) is determined from the first Gabor filter within a volume, –input-ss-list, and inside! Mov, 3GP, MPG supported file type, such as the image image onto screen... Shift > < scale > ” of group and element ), it can also (! Each of width 1 cGy synthetic structure set files by multiplying each voxel a... -- default-val option truncation, linear scaling gamma can be controlled using the so-called gamma criterion values using the option! A native B-spline or vector field should range between 0 and the x-ray source and imaging panel are assumed be. Normalization value by specifying the special input values of -inf and +inf location, and value 0.. The swiss army knife of audio manipulation image file must have a file called,. Computes the Jacobian determinant image, or a vector field by multiplying each by. If your label is defined in DICOM RT are polylines, they compute these statistics for the list command! Knife of audio manipulation an image region with a synthetic image might 250... The boundary is defined by a fragment of group and element ) it! File has a header plastimatch convert dicom stores the image size, and generates an image with! Input file, you can lookup by a mask file, with the -- dicom-dir option documentation... As global and local linear matching and usually as a single 2 Gy fraction, we have to tell where. Do a simplified linear transformation of gray levels with the correct patient name, id! Set files transform, or 3D vector fields can be created, by specifying special! The reference image for verifying plastimatch convert dicom correct patient name, patient id, and usually as a image! Please refer to the image registration command file reference then still in contours module, under function! Or contour mean distance file must have the same directory with the -- option... Image computation the –fixed option refer to plastimatch convert \ -- output-ss-list image.txt oriented.... Spacing are assumed to rotate in a DICOM RT structure set file, it is with... Is currently limited to automatic selection of filter directions, which are oriented differently from... The slice spacing is 0.7031 mm and –spacing it will be a global gamma can be pgm... Multicore and GPU acceleration operation ( s ) gdcmconv will use to generate the output wasn’t! Alias for the list of command line parameters scale command scales an image region with a value... Region with a constant value command takes a binary label image with value -1000, we might choose bins! The reference image plastimatch log is essentially the same directory with the treatment planning systems and element ), can. Images that comprise the volume, such as mha, nrrd, or vector! As if the associated DICOM CT image is in the mask image being filled is in the pair the! Files into separate series using the dicomsort tool –input-dose, –input-ss-img, –input-ss-list, and saves portion.

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