This is a script that displays brain scan volumes as slices in three different views at the same time. It can show up to two different brain volumes at once for comparison. It can also overlay binary images to visualize segmentations.

This script uses scans in a .nii.gz format, so the nibabel package is required. You also need opencv and numpy.

To install them, simply type the following, and press enter:

pip install -r requirements.txt

To run the script, type the following and press enter:

python neurodisplay.py -i <volume_name.nii.gz> [-j <volume_name2.nii.gz> ...]

Replace the string <volume_name.nii.gz> from above with the path to your volume and add the following optional parameters as desired:

• -j: path to a secondary brain volume for comparison which will be displayed below de first one.
• -x: path to a binary segmentation volume which will be overlaid on the first volume.
• -y: path to a secondary binary segmentation volume which will be overlaid on the second volume.

It is possible to provide only one brain volume and two segmentations. In that case, the same volume will be displayed on both rows.

Single brain volume:

python neurodisplay.py -i images/t1.nii.gz

Single brain volume with overlaid segmentation:

python neurodisplay.py -i images/t1.nii.gz -x pred/t1.nii.gz

Two brain volumes with overlaid segmentation:

python neurodisplay.py -i images/t1.nii.gz -j images_t1ce/t1ce.nii.gz -x pred/t1.nii.gz -y labels/lab.nii.gz

usage: neurodisplay.py [-h] -i I [-j J] [-x X] [-y Y]

Display neuroimages with binary labels. At least one brain image (-i) is required

optional arguments:
  -h, --help  show this help message and exit
  -i I        path to the top brain image (required)
  -j J        path to the bottom brain image
  -x X        path to the top label image
  -y Y        path to the bottom label image