Skip to content

Latest commit

 

History

History
68 lines (45 loc) · 2.68 KB

README.MD

File metadata and controls

68 lines (45 loc) · 2.68 KB

MIA (Medical Image Anonymizer)

MIA is a software that allows to anonymize medical images in DICOM format (.dcm) and convert them to NIFTI format (.nii).

Requirements

The listed requirements can be installed with the command "pip install [package name]", make sure you have the latest version of pip installed.

You can upgrade pip using:

python -m pip install --upgrade pip

Software Instalation Command
dicognito pip install dicognito
nibabel pip install nibabel
itk pip install itk
numpy pip install numpy
dicom-numpy pip install dicom-numpy
medio pip install medio

How to run

  • Clone or download the repo.
  • Enter to the folder
  • Run the main.py file with the command:
    • python main.py [args]

Arguments

Argument Function
-h, --help show a help message and exit
-dir, --directory Path to the folder where the images are located, by default is ./
-out, --output Path to the folder where the images are located, by default is ./output/
-ext --extension The extension of medical images you are looking to anonimize, by default is .dcm
-C, --convert Boolean value which defines if converts the images to nifti by default is False
-A, --anonymize Boolean value which defines if anonymize the images or not by default is False

Examples

Anonymize

Supose there is a folder aside the main.py file called "images" to anonymize these image you should run either:

  • python main.py -A
  • python main.py --anonymize

Custon dir anonymize

Supose there is a folder in your desktop (~/usr/desktop/) called "images", which contains the images to anonymize, you should then run either:

  • python main.py -dir "~/usr/desktop/images" -A
  • python main.py -dir "~/usr/desktop/images" --anonymize

Custom output dir anonymize

Supose there is a folder in your desktop (~/usr/desktop/) called "images", which contains the images to anonymize, and you want then to output in your documents (~/usr/documents/), you should then run either:

  • python main.py -dir "~/usr/desktop/images" -out "~/usr/documents/" -A
  • python main.py -dir "~/usr/desktop/images" -out "~/usr/documents/" --anonymize

Convert

Supose there is a folder aside the main.py file called "images" to anonymize and convert these image you should run either:

  • python main.py -A -C
  • python main.py --anonymize --convert