Preprocessing script: from dicom to aligned nifty for SynthRAD2023 Grand Challenge
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Table of Contents

• Goal
• Getting Started
  • Prerequisites
  • Installation
• Usage
  • Function Descriptions
• Roadmap
• Contributing
• License
• Contact

Goal

To pre-process CBCT, MRI and CT images for the synthRAD2023 deep learning challenge. This includes file format conversions from .dcm to .nii.gz, resampling, allignment, masking, defacing and cropping.

Getting Started

To get a local copy up and running follow these simple steps.

Prerequisites

• numpy

pip install numpy

• SimpleITK/SimpleElastix

pip install SimpleITK-SimpleElastix

• PyDicom

pip install pydicom

• openpyxl

pip install openpyxl

Installation

1. Clone the repo

git clone https://github.com/SynthRAD2023/preprocessing.git

or

git clone git@github.com:SynthRAD2023/preprocessing.git

Usage

The main file pre_process_tools.py contains tools for:

• Converting from .dcm to .nii.gz (MRI,CBCT and CT);
• Resampling CTs to 1x1x1 mm³ for brain and to 1x1x2.5 mm³ for pelvis;
• Registering MRI/CBCT to CT (as a result MRI/CBCT will also have 1x1x1 or 1x1x2.5 spacing) using Elastix;
• Segmenting patient outline on MRI/CBCT an dilate the resulting mask;
• Crop MRI, CBCT, CT and the mask with a small extra margin to the dilated mask;

The Elastix parameter files adopted can be found in param_files.

If desired, there is also functions to:

• Apply the mask to MRI and CT;

Each task can be run as a subfunction of the main file, as described in the next section.

Examples of how to run pre-processing for a batch of patients can be found in the directory examples:

• pre_process_batch_MR.py for python-based pre-processing;
• pre_process_batch_MR.sh for bash-based (terminal) pre-processing in Unix. This file reads the list of patients provided in pat_list_brain_mri2ct.txt.

The file extract_tags_tools.py provides functions to:

• Read a list of tags from a text file;
• Extract tags from dicom files and returns a dictionary containing the key: value pairs
• Get dimensions and spacing of pre-processed images
• Write the tags to a CSV/excel file

An example of a tag extraction is provided in the directory examples:

• extract_tags_UMCG.py shows an example of how to use the above functions for a dataset containing multiple patients and images directly in python;
• pre_process_batch_MR.sh contains instructions on how to call the above functions from the terminal.

Futher example of the code from two insititutions has been provided. N.B. this is intended as example of script, it should be adapted for your own use.

Function Description

Pre-processing:

convert_dicom_nifti(input, output)

description:
convert a dicom image to compressed nifti using SimpleITK

arguments:
input: folder containing dicom series (example 'C:\path\containing\Dicom_series')
output: output file path for compressed nifti (example: 'C:\path\to\folder\image.nii.gz')

command line usage:
python pre_process_tools.py convert_dicom_to_nifti --i 'C:\path\containing\Dicom_series' --o 'C:\path\to\folder\image.nii.gz'

resample(input, output, spacing)

description:
resample nii.gz image using custom spacing (in mm)

arguments:
input: file path input image (example: 'C:\path\to\folder\image.nii.gz')
output: file path resampled image (example: 'C:\path\to\folder\image_resampled.nii.gz')
spacing: new spacing in mm (example: (1,1,1))

command line usage:
python pre_process_tools.py resample --i 'C:\path\to\folder\image.nii.gz' --o 'C:\path\to\folder\image_resampled.nii.gz' --s 1 1 1

read_parameter_map(parameter_fn)

description:
read an elastix parameter map from a .txt file and return the parameter map object

arguments:
parameter_fn: file path parameter file

register(fixed, moving, parameter, output)

description:
register two images using elasix parameter map

arguments:
fixed: file path to fixed image for registration (example: 'C:\path\to\folder\fixed.nii.gz')
moving: file path to moving image for registration (example: 'C:\path\to\folder\moving.nii.gz')
parameter: file path to parameter map .txt file (example: 'C:\path\to\folder\parameters.txt')
output: file path to registered image (example: 'C:\path\to\folder\moving_registered.nii.gz')

command line usage:
python pre_process_tools.py register --f C:\path\to\folder\fixed.nii.gz' --m 'C:\path\to\folder\moving.nii.gz' --p 'C:\path\to\folder\parameters.txt'--o 'C:\path\to\folder\moving_registered.nii.gz'

segment(input, output, radius)

description:
create a rough body mask for MR/CBCT/CT image

arguments:
input: file path input image (example: 'C:\path\to\folder\image.nii.gz')
output: file path mask (example: 'C:\path\to\folder\mask.nii.gz')
radius: currently not used (radius to fill holes in mask), default value =  (12,12,12)

command line usage:
python pre_process_tools.py segment --i 'C:\path\to\folder\moving_registered.nii.gz' --o 'C:\path\to\folder\moving_mask.nii.gz' 

correct_mask_mr(mr,ct,transform,mask,mask_corrected)

description:
limit the mask, generated with above segment function, to the MR FOV

argumnents:
mr: file path to mr (original unaltered mr image)
ct: file path to resampled ct
transform: path to registration paramters which the register function saves in a file (*_parameters.txt)
mask: file path to mask generated by segment function
mask_corrected: file path for corrected mask output

command line usage:
not yet implemented

mask_mr or mask_ct(input, mask_in, output)

description:
mask an image with provided mask (e.g. created by segment above). The background value is -1000 for CT, and 0 for MRI.

arguments:
input: file path input image (example: 'C:\path\to\folder\image.nii.gz')
mask_in: file path to mask (example: 'C:\path\to\folder\mask.nii.gz')
output: file path to masked image (example: 'C:\path\to\folder\image_masked.nii.gz')

crop(input, mask_crop, output)

description:
crop an image with bounding box of mask image

arguments:
input: file path input image (example: 'C:\path\to\folder\image.nii.gz')
mask_crop: file path to mask, used to calculate bounding box (example: 'C:\path\to\folder\mask.nii.gz')
output: file path to cropped image (example: 'C:\path\to\folder\image_cropped.nii.gz')

generate_overview(input_path,ref_path,mask_path,output_path,title)

description:
generate a figure with CBCT/MR, CT and MASK to check pre-processing

arguments:
input_path: path to pre-processed CBCT/MR
ref_path: path to pre-processed reference CT
mask_path: path to pre-processed mask
output_path: output path of figure file
title: Title used in figure

Other utilities

In addition to the main functions above, following functions were used for specific datasets and specifc anatomies:

• limit_pixel_values: sets a fixed minimum value for all voxels
• clean_border: removes artifacts from the patient border
• create_FOV_cbct: creates a FOV ROI for cbcts
• fix_fov_cbct_umcg: fixes the mask so the mask does not contain voxels outside the FOV
• transform_mask: Warps a mask from CBCT coordinatesto CT coordinate system
• generate_mask_cbct: combines many functions (including some of the above) to generate a final mask for cbcts

Dicom tag extraction:

read_tags(input_txt)

description:
read dicom tag strings from a txt file

arguments:
input_txt: file path to text file containg dicom tags (see example in param_files)

returns: 
python list containing dicom tags

extract_tags(dcm_folder_path,tag_list,pre_processed=None)

description:
extracts tags from a folder containg dicom files (only from the first element) and from pre-processed nifti images

arguments:
dcm_folder_path: path to folder containing dicom image slices
tag_list: list defining which tags to extract
pre_processed: path to pre-processed nifti file (can be left out if tags should be only extracted from dicom files)

returns:
python dict with dicom tags as key:value pairs

write_dict_to_csv(input_dict,output_csv,tag_list)

description:
takes a dict containing dicom tags and writes it to a csv file

arguments:
input_dict: dict containing extracted tags
output_csv: filename of output csv file
tag_list: list of dicom tags, necessary to create header in csv file

write_csv_to_xlsx(input_csv,output_xlsx)

description:
takes a csv and creates an xlsx file

arguments:
input_csv: path to csv file
output_xlsx: filepath of output xlsx file

Roadmap

See the open issues for a list of proposed features (and known issues).

Contributing

Contributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are greatly appreciated.

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request
   
   

License

Distributed under the GNU General Public License v3.0. See LICENSE for more information.

Contact

Adrian Thummerer - a[dot]thummerer[at]umcg[dot]nl
Matteo Maspero - @matteomasperonl - m.maspero@umcutrecht.nl

Project Link: https://github.com/SynthRAD2023/preprocessing