Not well tested, but should work in most cases. Test of the CLI were only performed on WIN10, so there might be some issues popping up.

Please post an issue, if there is something not working as expected.

Install

As always I would recommend, creating a new python environment for this tool!

You can then install the package via pip from Github.

pip install git+https://github.com/SRSteinkamp/simons_mask_binarizer.git

The installation should install all the necessary packages namely (nilearn and nibabel) and expose the command line tool below.

How to use

Currently exposes a CLI directly, to transform single files. In your terminal run:

nifti_binarizer INPUTPATH -o OUTPUTPATH -p PREFIX

Where the INPUTPATH (path of the image to be converted) has to be provided.

• -o or --outputpath argument is optional to provide the destination of the converted image. Defualt image is converted inside INPUTPATH folder.

• -p or --prefix argument is optional, prefix defaults to bin_.

Examples:

nifti_binarizer C:\some_folder\my_mask.nii.gz`

Creates a new file named as C:\some_folder\bin_my_mask.nii.gz.

nifti_binarizer C:\some_folder\my_mask.nii.gz -o C:\other_folder\`

Creates a new file in C:\other_folder\bin_my_mask.nii.gz.

nifti_binarizer C:\some_folder\my_mask.nii.gz -o C:\other_folder\ -p 'p'`

Creates a new file in C:\other_folder\pmy_mask.nii.gz.