Import and Spatial Referencing

Read images and spatial metadata from medical imaging file formats

Medical Imaging Toolbox™ supports specialized file formats that store medical image data and metadata that describes the patient, imaging procedure, and spatial referencing. Spatial referencing specifies the location of an image in the patient coordinate system, which is defined relative to the anatomical axes of the patient. The medicalVolume and medicalImage objects automatically parse metadata to import and store image data and spatial information from DICOM, NIfTI, and NRRD files. You can also read the image and metadata separately using functions for each file format.

Functions

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Import and Work with Medical Images

`medicalImage`	2-D medical image pixel data and file metadata
`extractFrame`	Extract pixel data for one frame of 2-D medical image series
`montage`	Display medical image slices or frames as montage in patient coordinates
`implay`	View 2-D medical image series in Video Viewer app

Import and Work with Medical Volumes

`medicalVolume`	3-D medical image voxel data and spatial referencing information
`extractSlice`	Extract voxels and spatial details for one slice of medical volume
`montage`	Display medical image slices or frames as montage in patient coordinates
`replaceSlice`	Replace voxel values for one slice of medical volume
`resample`	Resample medical image volume in different patient coordinate system
`sliceCorners`	Extract coordinates of corner voxels for one slice of medical volume
`sliceLimits`	Extract X-, Y-, Z-limits for one slice of medical volume
`sliceViewer`	Browse slices of medical image volume in patient coordinates
`volshow`	Display medical volume in patient coordinates
`write`	Write affine medical volume data to NIfTI file

Spatial Referencing for Medical Volumes

`medicalref3d`	Spatial referencing information for 3-D medical image volumes
`intrinsicToWorldMapping`	Geometric transform between intrinsic and patient coordinates of medical image volume
`contains`	Determine if affine image volume contains points specified in patient coordinate system
`intrinsicToWorld`	Map points from intrinsic coordinates to patient coordinates
`oneSliceIntrinsicToWorldMapping`	Geometric transform between intrinsic and patient coordinates of medical image volume slice
`orient`	Update patient coordinate system convention
`sliceCorners`	Extract patient coordinates of corner voxels for one slice
`worldToIntrinsic`	Map points from patient coordinates to intrinsic coordinates
`worldToSubscript`	Convert from patient coordinates to row and column subscripts

Read Image Data and Metadata from Specific File Formats

Work with DICOM Files

`dicominfo`	Read metadata from DICOM message
`dicomread`	Read DICOM image
`dicomwrite`	Write images as DICOM files
`dicomCollection`	Gather details about related series of DICOM files
`dicomFile`	Process DICOM file
`isAttribute`	Check if specified attribute is present in DICOM file
`getAttribute`	Get value of specified DICOM attribute
`getPixelData`	Get pixel data of DICOM file
`write`	Create selectively modified copy of DICOM file

Work with NRRD Files

`isnrrd`	Check if file is valid NRRD file
`nrrdinfo`	Read metadata from NRRD file
`nrrdread`	Read NRRD image

Work with NIfTI Files

`niftiinfo`	Read metadata from NIfTI file
`niftiread`	Read NIfTI image
`niftiwrite`	Write volume to file using NIfTI format

Work with Analyze 7.5 Files

`analyze75info`	Read metadata from header file of Analyze 7.5 data set
`analyze75read`	Read image data from image file of Analyze 7.5 data set

Work with Interfile Files

`interfileinfo`	Read metadata from Interfile file
`interfileread`	Read images in Interfile format

Topics

Medical Image Coordinate Systems
Learn how image locations are defined in the intrinsic and patient coordinate systems.

Featured Examples

Read, Process, and Write 3-D Medical Images

Import and display a medical image volume in patient coordinates, apply a smoothing filter.

Open Live Script

Read, Process, and View Ultrasound Data

Import and display a 2-D multiframe ultrasound series, and apply a denoising filter to each frame.

Open Live Script