DICOM (.dcm, .dic)

Import and Export fully support DICOM files conforming to Section PS 3.10 of the DICOM standard.
Import can also read ACR/NEMA Version 2.0 files.

Background & Context

- MIME type: application/dicom
- DICOM medical imaging format.
- Commonly used in medical imaging equipment and picture archiving and communication systems.
- DICOM is an acronym for Digital Imaging and Communications in Medicine.
- Stores multiple raster images together with patient and device information.
- Binary format.
- Supports a variety of image encoding and data compression methods.
- DICOM Version 3.0 was introduced in 1993.

Import & Export

Import["file.dcm"] imports a DICOM file, returning an Image object.
Import["file.dcm",elem] imports the specified element from a DICOM file.
The import format can be specified with Import["file","DICOM"] or Import["file",{"DICOM",elem,…}].
Export["file.dcm",expr] exports graphics or any other expression as an image to a DICOM file.
When exporting Wolfram Language graphics or arbitrary expressions to DICOM, the resulting image has the same raster size as its displayed form.
Image objects are by default exported at their raster size.
Because DICOM is a raster image format, all fonts are rasterized on export.
See the following reference pages for full general information:

	Import, Export	import from or export to a file
	CloudImport, CloudExport	import from or export to a cloud object
	ImportString, ExportString	import from or export to a string
	ImportByteArray, ExportByteArray	import from or export to a byte array

Import Elements

General Import elements:
"Elements" list of elements and options available in this file

"Summary" summary of the file

"Rules" list of rules for all available elements
Data representation elements:

	"Data"	array of values
	"Graphics"	Graphics object representing an image
	"Image"	raster graphics given as an Image object
	"ImageList"	a list of images

"RawData" array of color map indices

"RawPixelData" DICOM pixel data without scaling
Overlay elements:
"Overlays" an overlay image or a list of overlays
Import by default uses "Image" for single-frame DICOM files and "ImageList" for multi-frame DICOM files.
Advanced Import elements:

	"BitDepth"	bits used to represent each color channel in the file
	"Channels"	the number of color channels used in the file
	"ColorMap"	color reduction palette, given as a list of color values
	"ColorSpace"	color encoding used in the file
	"ImageSize"	raster dimensions
	"MetaInformation"	metainformation stored in the file
	"RawMetaInformation"	raw metainformation stored in the file
	"Summary"	summary of the file

Export Elements

General Export element:
"Rules" a list of imported elements in the form of elemexpr
Export["file.dcm",{elem₁->expr₁,…},"Rules"] uses rules to specify the elements to be exported.
Available Export elements:

	"Data"	numeric data
	"Image"	an Image object
	"Image3D"	an Image3D object
	"ImageList"	a list of image frames
	"MetaInformation"	an association of metadata tags and values
	"Overlays"	a list of association

The "Overlays" associations can have the following keys:

	"Description"	the overlay description
	"Image"	one or a list of overlay images
	"Label"	the overlay label
	"Type"	the type of the overlay
	"Subtype"	the subtype of the overlay

Values for "Type" can be either "Graphics" or "RegionOfInterest". "Subtype" can be either "User" or "Automated".

Options

Import and Export options:

"ImageTopOrientation"	Top	orientation of the image as stored in the file
ImageSize	Automatic	overall image size
IncludeMetaInformation	All	amount of metadata to import and export

Possible settings for IncludeMetaInformation include:

	All	include all available metadata
	None	include no metadata
	"Anonymized"	include anonymized metadata
	"FullyAnonymized"	include fully anonymized metadata

Import option:
"DataTransformation" Automatic set of transformations applied to the data stored in the file
"DataTransformation" can be an association with the following keys:

"Modality"	Automatic	modality transform to make data manufacturer independent
"Polarity"	Automatic	whether to assume minimum value as black or white
"Presentation"	Automatic	whether to transform to human perceptual response
"ScalingWindow"	Automatic	scaling method to use for importing data, also known as values of interest (VOI)

By default, the modality transformation specified in the file is used. Use "Modality"None to disable this transform.
By default, the polarity transformation specified in the file is used. Possible settings are:
"Normal" assume minimum value to be black

"Reverse" assume minimum value to be white
By default, the presentation transformation specified in the file is used. Use "Presentation"None to disable this transform.
"ScalingWindow" can take the following settings:

	Automatic	automatic scaling
	None	no scaling
	"MinMax"	scale to min and max of data in all frames
	"MinMaxPerFrame"	scale to min and max of each frame
	{center,w}	scale to the range {center-w,center+w}
	<\|"Center"center,"Width"w\|>	scale to the range {center-w,center+w}
	<\|"Min"min,"Max"max\|>	scale to the range {min,max}

With "ScalingWindow"->Automatic, values are scaled using scaling values stored in the file. If no scaling specification is stored, values are scaled using the "MinMax" method.
Export options:

ColorSpace	Automatic	color space to be used in the file
CompressionLevel	Automatic	compression level to use
ImageSize	Automatic	overall image size
"BitDepth"	Automatic	bit depth per channel used to store image data
"ImageEncoding"	None	the image encoding to use
"ImageTopOrientation"	Automatic	orientation of the image as stored in the file

Supported ColorSpace settings are "Grayscale" and "RGB".
Possible values for "ImageEncoding" are "JPEGLossless", "JPEGLosslessNonhierarchical", "JPEGLSLossless", "JPEGLSLossy", "JPEGLossy8Bit", "JPEGLossy12Bit" and "RLE".

Examples

open allclose all

Basic Examples (3)Summary of the most common use cases

Import a DICOM file containing a gray-level image:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-qvth9o

Out[1]=1

Summary of an image:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-edvlsz

Out[1]=1

Export an image to DICOM:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-0dzamt

Out[1]=1

Scope (2)Survey of the scope of standard use cases

Show all Import elements available in the file:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-g7tsey

Out[1]=1

Import the metadata from a DICOM file:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-1i8t43

Import Elements (15)

Available Elements (3)

List of available elements:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-1g2ndh

Out[1]=1

Import all elements as a list of rules:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-myzd73

Import some image options:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-bvl5fv

Out[1]=1

The "Options" element does not return all options that are present in the imported image:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-kx49o5

Data Representation (4)

"Data" (1)

Import the image data:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-o8nr5i

Out[1]=1

Create an image from imported data:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-n493vs

Out[2]=2

"Graphics" (1)

Import as a Graphics object:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-oxk5kn

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-oxk2tw

Out[2]=2

"Image" (1)

Import as an Image object:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-vtuh6c

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-1f07e2

Out[2]=2

This is the default import element for DICOM:

In[3]:=3

✖

https://wolfram.com/xid/0hkhc4k5q8-s0naad

Out[3]=3

"RawPixelData" (1)

Import DICOM pixel data as stored in the file:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-gzb4jz

Out[1]=1

The values are returned without any scaling and may not be visible when displayed in an image:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-qsfjwi

Out[2]=2

Adjust the values to see more of the data:

In[3]:=3

✖

https://wolfram.com/xid/0hkhc4k5q8-kcwg4r

Out[3]=3

Metadata (8)

"BitDepth" (1)

Get the number of bits used for representing each color channel:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-v4dei0

Out[1]=1

"Channels" (1)

Get the number of image channels:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-oedubm

Out[1]=1

"ColorSpace" (1)

Get the color encoding used on export:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-wb968h

Out[1]=1

Use ImageColorSpace to get the color space of an imported image:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-ca8qqr

Out[2]=2

"ImageSize" (1)

Get the dimensions of the image stored in the file:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-ma62cc

Out[1]=1

Using ImageDimensions on an imported image gives the same result:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-hjusgl

Out[2]=2

"MetaInformation" (1)

Read the metainformation from a DICOM file:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-kvi5nk

A dataset of metainformation:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-rzhrs6

Out[2]=2

"RawMetaInformation" (2)

Unlike "MetaInformation", "RawMetaInformation" does not validate imported values against the DICOM Standard and does not perform any conversions to Wolfram Language expressions. Read the raw metainformation from a DICOM file:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-48sw08

A dataset of raw metainformation:

In[2]:=2

✖

https://wolfram.com/xid/0hkhc4k5q8-yxtpw1

Out[2]=2

The "RawMetaInformation" element may return more tags than "MetaInformation":

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-9bwuh5

Out[1]=1

"Summary" (1)

Get the image summary:

In[1]:=1

✖

https://wolfram.com/xid/0hkhc4k5q8-4is8p9

Out[1]=1