write

Write affine medical volume data to NIfTI file

Since R2022b

Syntax

write(medVol,filename)

write(medVol,filename,info)

Description

write(medVol,filename) writes the voxel data and spatial information of the affine medicalVolume object medVol to the file filename in the Neuroimaging Informatics Technology Initiative (NIfTI) file format. The write function creates a combined NIfTI file that contains both metadata and volumetric data. The object function populates the metadata using appropriate default values and volume properties, such as size and data type.

write(medVol,filename,info) sets metadata attributes by using the metadata structure info. If the specified metadata structure does not match the image contents and size, then write returns an error.

Examples

Write Medical Volume Object Data to NIfTI File

Write data from a medical volume object, created using a chest CT volume saved as a directory of DICOM files. The CT volume is part of a data set containing three CT volumes. The size of the entire data set is approximately 81 MB. Download the data set from the MathWorks® website, then unzip the folder.

zipFile = matlab.internal.examples.downloadSupportFile("medical","MedicalVolumeDICOMData.zip");
filepath = fileparts(zipFile);
unzip(zipFile,filepath)

Specify the directory of DICOM files for the first CT volume in the data set.

dataFolder = fullfile(filepath,"MedicalVolumeDICOMData","LungCT01"); 

Create a medical volume object for the CT volume.

medVol = medicalVolume(dataFolder);

The Voxels property contains the intensity values of each voxel. The VolumeGeometry property contains a medicalref3d object defining the spatial referencing for the image volume.

V = medVol.Voxels;
R = medVol.VolumeGeometry;

Modify the voxel data by applying a 3-D Gaussian filter.

sigma = 2;
filterV = imgaussfilt3(V,sigma);

Create a new medicalVolume object that contains the smoothed voxel values. To maintain the same spatial referencing as the original volume, specify the original medicalref3d object R.

medVolSmooth = medicalVolume(filterV,R);

Write the smoothed image data to a new NIfTI file.

niftiFilename = "LungCT01_smoothed.nii";
write(medVolSmooth,niftiFilename)

Write Medical Volume Object Data to Compressed NIfTI File

Write data from a medical volume object, created using a chest CT volume saved as a directory of DICOM files. The CT volume is part of a data set containing three CT volumes. The size of the entire data set is approximately 81 MB. Download the data set from the MathWorks® website, then unzip the folder.

zipFile = matlab.internal.examples.downloadSupportFile("medical","MedicalVolumeDICOMData.zip");
filepath = fileparts(zipFile);
unzip(zipFile,filepath)

Specify the directory of DICOM files for the first CT volume in the data set.

dataFolder = fullfile(filepath,"MedicalVolumeDICOMData","LungCT01"); 

Create a medical volume object for the CT volume.

medVol = medicalVolume(dataFolder);

Write the CT data to a compressed NIfTI file by including the extension .nii.gz in the filename.

niftiFilename = "LungCT01.nii.gz";
write(medVol,niftiFilename)

Input Arguments

medVol — Medical volume

medicalVolume object

Medical volume, specified as a medicalVolume object. medVol must be an affine image volume.

An image volume is affine if these conditions are met:

• All slices are parallel to each other.

• The spacing between slices in each dimension is uniform.

• The upper-left voxels of all slices are collinear.

• No two slices are coincident, meaning no two slices are located at the same position in space.

filename — Name of NIfTI file

string scalar | character vector

Name of the NIfTI file, specified as a string scalar or a character vector. The write function creates a combined NIfTI file that contains both metadata and volumetric data. If you omit an extension from filename or include the extension .nii, then the function writes an uncompressed NIfTI file with extension .nii. If you include the extension .nii.gz, then the function writes a compressed file with extension .nii.gz using gzip.

info — NIfTI file metadata

structure

NIfTI file metadata, specified as a structure in the format returned by the niftiinfo function.

Version History

Introduced in R2022b

R2024a: Write volume data to compressed NIfTI file

Write a compressed NIfTI file by specifying a filename with the extension .nii.gz. Files compressed using gzip are smaller and require less disk space than uncompressed files. For example, this code writes the image data in medVol to the compressed file brain.nii.gz:

write(medVol,"brain.nii.gz")