Convert nifti files into dicoms

This repository contains the complete code for converting nifti files to dicom series. I needed this conversion during my internship while working on tumor segmentation, so I wanted to share the method I discovered with you.

You can simply clone this repository and begin using it. All of the details can be found on my blog, which I dedicated to this function.

Here is the article

The steps

• Using pre-existing dicom file.
• The packages that we need.
• Extract the frame data from the nifti file.
• Prepare the array to be converted.
• Convert one nifti file into dicom series.
• Convert multiple nifti files into multiple dicom series.

The Packages that We Need

As with any other program, we need some packages to complete this conversion, so in this project, you will need to install the following packages individually.

• nibabel: pip install nibabel

• pydicom: pip install pydicom

• numpy: pip install numpy

• tqdm: pip install tqdm (this one is just to print the progress of the conversion)

The main function

This is the main function that does all the work:

def convertNsave(arr,file_dir, index=0):
    """
    `arr`: parameter will take a numpy array that represents only one slice.
    `file_dir`: parameter will take the path to save the slices
    `index`: parameter will represent the index of the slice, so this parameter will be used to put 
    the name of each slice while using a for loop to convert all the slices
    """
    
    dicom_file = pydicom.dcmread('images/dcmimage.dcm')
    arr = arr.astype('uint16')
    dicom_file.Rows = arr.shape[0]
    dicom_file.Columns = arr.shape[1]
    dicom_file.PhotometricInterpretation = "MONOCHROME2"
    dicom_file.SamplesPerPixel = 1
    dicom_file.BitsStored = 16
    dicom_file.BitsAllocated = 16
    dicom_file.HighBit = 15
    dicom_file.PixelRepresentation = 1
    dicom_file.PixelData = arr.tobytes()
    dicom_file.save_as(os.path.join(file_dir, f'slice{index}.dcm'))

Conversion tools

You may face problems with the method provided above, for this reason I found anouther way to do the conversion correctly using SimpleITK example that conversion an array into dicom series.

I tried to put everything together in one GUI to facilitate the work for you and you can do the conversion for one single file or a directory with a single click. It will look like this:

Please see this link for more information about the GUI.

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