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

You can install the requirements with:

pip install -r requirements.txt

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'))

Versions 🚀

🆕 NEW

Full course about medical imaging segmentation is coming soon, join the waitlist here:

https://pycad.co/monai-and-pytoch-for-medical-imaging/