Preprocess Volumes for Deep Learning

Read Volumetric Data

Supported file formats for volumetric image data include MAT-files, Digital Imaging and Communications in Medicine (DICOM) files, and Neuroimaging Informatics Technology Initiative (NIfTI) files.

Read volumetric image data into an ImageDatastore. Read volumetric pixel label data into a PixelLabelDatastore (Computer Vision Toolbox). For more information, see Datastores for Deep Learning.

The table shows typical usages of imageDatastore and pixelLabelDatastore for each of the supported file formats. When you create the datastore, specify the FileExtensions name-value argument as the file extensions of your data. Specify the ReadFcn property as a function handle that reads data of the file format. The filepath argument specifies the path to the files or folder containing image data. For pixel label images, the additional classNames and pixelLabelID arguments specify the mapping of voxel label values to class names.

Image File Format	Create Image Datastore or Pixel Label Datastore
MAT	volds = imageDatastore(filepath, ... "FileExtensions",".mat","ReadFcn",@(x) fcn(x)); pxds = pixelLabelDatastore(filepath,classNames,pixelLabelID, ... "FileExtensions",".mat","ReadFcn",@(x) fcn(x)); fcn is a custom function that reads data from a MAT file. For example, this code defines a function called matRead that loads volume data from the first variable of a MAT file. Save the function in a file called matRead.m. function data = matRead(filename) inp = load(filename); f = fields(inp); data = inp.(f{1}); end
DICOM volume in single file	volds = imageDatastore(filepath, ... "FileExtensions",".dcm","ReadFcn",@(x) dicomread(x)); pxds = pixelLabelDatastore(filepath,classNames,pixelLabelID, ... "FileExtensions",".dcm","ReadFcn",@(x) dicomread(x)); For more information about reading DICOM files, see dicomread (Image Processing Toolbox).
DICOM volume in multiple files	Follow these steps. For an example, see Create Image Datastore Containing Single and Multi-File DICOM Series (Image Processing Toolbox). Aggregate the files into a single study by using the dicomCollection (Image Processing Toolbox) function. Read the DICOM data in the study by using the dicomreadVolume (Image Processing Toolbox) function. Write each volume as a MAT file. Create the ImageDatastore or PixelLabelDatastore from the collection of MAT files by following the procedure for MAT files.
NIfTI	volds = imageDatastore(filepath, ... "FileExtensions",".nii","ReadFcn",@(x) niftiread(x)); pxds = pixelLabelDatastore(filepath,classNames,pixelLabelID, ... "FileExtensions",".nii","ReadFcn",@(x) niftiread(x)); For more information about reading NIfTI files, see niftiread (Image Processing Toolbox).

Pair Image and Label Data

To associate volumetric image and label data for semantic segmentation, or two volumetric image datastores for regression, use a randomPatchExtractionDatastore (Image Processing Toolbox). A random patch extraction datastore extracts corresponding randomly-positioned patches from two datastores. Patching is a common technique to prevent running out of memory when training with arbitrarily large volumes. Specify a patch size that matches the input size of the network and, for memory efficiency, is smaller than the full size of the volume, such as 64-by-64-by-64 voxels.

You can also use the combine function to associate two datastores. However, associating two datastores using a randomPatchExtractionDatastore has some benefits over combine.

• randomPatchExtractionDatastore supports parallel training, multi-GPU training, and prefetch reading. Specify parallel or multi-GPU training using the ExecutionEnvironment name-value argument of trainingOptions. Specify prefetch reading using the DispatchInBackground name-value argument of trainingOptions. Prefetch reading requires Parallel Computing Toolbox™.

• randomPatchExtractionDatastore inherently supports patch extraction. In contrast, to extract patches from a CombinedDatastore, you must define your own function that crops images into patches, and then use the transform function to apply the cropping operations.

• randomPatchExtractionDatastore can generate several image patches from one test image. One-to-many patch extraction effectively increases the amount of available training data.

Preprocess Volumetric Data

Deep learning frequently requires the data to be preprocessed and augmented. For example, you may want to normalize image intensities, enhance image contrast, or add randomized affine transformations to prevent overfitting.

To preprocess volumetric data, use the transform function. transform creates an altered form of a datastore, called an underlying datastore, by transforming the data read by the underlying datastore according to the set of operations you define in a custom function. Image Processing Toolbox™ provides several functions that accept volumetric input. For a full list of functions, see 3-D Volumetric Image Processing (Image Processing Toolbox). You can also preprocess volumetric images using functions in MATLAB^® that work on multidimensional arrays.

The custom transformation function must accept data in the format returned by the read function of the underlying datastore.

Underlying Datastore	Format of Input to Custom Transformation Function
ImageDatastore	The input to the custom transformation function depends on the ReadSize property. When ReadSize is 1, the transformation function must accept an integer array. The size of the array is consistent with the type of images in the ImageDatastore. For example, a grayscale image has size m-by-n, a truecolor image has size m-by-n-by-3, and a multispectral image with c channels has size m-by-n-by-c. When ReadSize is greater than 1, the transformation function must accept a cell array of image data corresponding to each image in the batch. For more information, see the read function of ImageDatastore.
PixelLabelDatastore	The input to the custom transformation function depends on the ReadSize property. When ReadSize is 1, the transformation function must accept a categorical matrix. When ReadSize is greater than 1, the transformation function must accept a cell array of categorical matrices. For more information, see the read (Computer Vision Toolbox) function of PixelLabelDatastore.
RandomPatchExtractionDatastore	The input to the custom transformation function must be a table with two columns. For more information, see the read (Image Processing Toolbox) function of RandomPatchExtractionDatastore.

The transform function must return data that matches the input size of the network. The transform function does not support one-to-many observation mappings.

To apply random affine transformations to volumetric data in RandomPatchExtractionDatastore, you must use the transform function. The DataAugmentation property of this datastore does not support volumetric data.

Examples

Transform Batch of Volumetric Data in Image Datastore

This example shows how to transform volumetric data in an image datastore using a sample image preprocessing pipeline.

Specify a set of volumetric images saved at MAT files.

filepath = fullfile(matlabroot,"toolbox","images","imdata","mristack.mat");
files = [filepath; filepath; filepath];

Create an image datastore that stores multiple volumetric images. Specify that the ReadSize of the datastore is greater than 1. Specify a custom read function, matRead. This function is defined in the Supporting Functions section of this example.

volDS = imageDatastore(files,FileExtensions=".mat", ...
    ReadSize=3,ReadFcn=@(x) matRead(x));

Specify the input size of the network.

inputSize = [128 128];

Preprocess the volumetric images in volDS using the custom preprocessing pipeline defined in the preprocessVolumetricIMDS supporting function.

dsTrain = transform(volDS,@(x) preprocessVolumetricIMDS(x,inputSize));

Read a batch of data.

minibatch = read(dsTrain)

minibatch=3×1 cell array
    {128x128x21 uint8}
    {128x128x21 uint8}
    {128x128x21 uint8}

Supporting Functions

The matRead function loads volume data from the first variable of a MAT file.

function data = matRead(filename)
    inp = load(filename);
    f = fields(inp);
    data = inp.(f{1});
end

The preprocessVolumetricIMDS function performs the desired transformations of data read from an underlying image datastore. Because the read size of the image datastore is greater than 1, the function must accept a cell array of image data. The function loops through each read image and transforms the data according to this preprocessing pipeline:

• Randomly rotate the image about the z-axis.

• Resize the volume to the size expected by the network.

• Create a noisy version of the image with Gaussian noise.

• Return the image in a cell array.

function batchOut = preprocessVolumetricIMDS(batchIn,inputSize)
 
numRows = size(batchIn,1);
batchOut = cell(numRows,1);
 
for idx = 1:numRows
    
    % Perform randomized 90 degree rotation about the z-axis
    imRotated = imrotate3(batchIn{idx,1},90*(randi(4)-1),[0 0 1]);

    % Resize the volume to the size expected by the network
    imResized = imresize(imRotated,inputSize);
    
    % Add zero-mean Gaussian noise with a normalized variance of 0.01
    imNoisy = imnoise(imResized,"gaussian",0.01);

    % Return the preprocessed data
    batchOut(idx) = {imNoisy};
    
end
end

Transform Volumetric Data in Random Patch Extraction Datastore

This example shows how to transform pairs of volumetric data in a random patch extraction datastore using a sample image preprocessing pipeline.

Specify two sets of volumetric images saved at MAT files. Each set contains five volumetric images.

dir = fullfile(matlabroot,"toolbox","images","imdata","BrainMRILabeled");
filesVol1 = fullfile(dir,"images");
filesVol2 = fullfile(dir,"labels");

Store each set of volumetric images in an image datastore. Specify a custom read function, matRead. This function is defined in the Supporting Functions section of this example. Use the default ReadSize of 1.

vol1DS = imageDatastore(filesVol1,FileExtensions=".mat",ReadFcn=@(x) matRead(x));
vol2DS = imageDatastore(filesVol2,FileExtensions=".mat",ReadFcn=@(x) matRead(x));

Specify the input size of the network.

inputSize = [128 128];

Create a random patch extraction datastore that extracts corresponding patches from the two datastores. Select three patches per image.

patchVolDS = randomPatchExtractionDatastore(vol1DS,vol2DS,inputSize,PatchesPerImage=3);

Preprocess the volumetric images in patchVolDS using the custom preprocessing pipeline defined in the preprocessVolumetricPatchDS supporting function.

dsTrain = transform(patchVolDS,@(x) preprocessVolumetricPatchDS(x));

Read a batch of data.

minibatch = read(dsTrain)

minibatch=15×2 table
         InputImage            ResponseImage   
    ____________________    ___________________

    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}
    {128x128x155 uint16}    {128x128x155 uint8}

Supporting Functions

The matRead function loads volume data from the first variable of a MAT file.

function data = matRead(filename)
    inp = load(filename);
    f = fields(inp);
    data = inp.(f{1});
end

The preprocessVolumetricPatchDS function performs the desired transformations of data read from the underlying random patch extraction datastore. The function must accept a table. The function transforms the data according to this preprocessing pipeline:

• Randomly select one of five augmentations.

• Apply the same augmentation to the data in both columns of the table.

• Return the augmented image pair in a table.

function batchOut = preprocessVolumetricPatchDS(batchIn)

numRows = size(batchIn,1); 
batchOut = batchIn;

% 5 augmentations: nil,rot90,fliplr,flipud,rot90(fliplr)
augType = {@(x) x,@rot90,@fliplr,@flipud,@(x) rot90(fliplr(x))};

for idx = 1:numRows

    img = batchIn{idx,1}{1};
    resp = batchIn{idx,2}{1};
    
    rndIdx = randi(5,1);
    imgAug = augType{rndIdx}(img);
    respAug = augType{rndIdx}(resp);
    
    batchOut(idx,:) = {imgAug,respAug};

end
end