whippersnappy 1.1.0

A package to plot and capture FastSurfer and FreeSurfer-style surface overlays.

WhipperSnapPy

WhipperSnapPY is a small Python OpenGL program to render FreeSurfer and FastSurfer surface models and color overlays and generate screen shots.

Contents:

• Capture 4x4 surface plots (front & back, left and right)
• OpenGL window for interactive visualization

Note, that currently no off-screen rendering is supported. Even in snap mode an invisible window will be created to render the openGL output and capture the contents to an image. In order to run this on a headless server, inside Docker, or via ssh we recommend to install xvfb and run

apt update && apt install -y python3 python3-pip xvfb
pip3 install pyopengl glfw pillow numpy pyrr PyQt5==5.15.6
pip3 install .
xvfb-run whippersnap ...

Installation:

The WhipperSnapPy package can be installed from this repository using:

python3 -m pip install .

Usage:

Local:

After installing the Python package, the whippersnap program can be run using the installed command line tool such as in the following example:

whippersnap -lh $OVERLAY_DIR/$LH_OVERLAY_FILE \
            -rh $OVERLAY_DIR/$RH_OVERLAY_FILE \
            -sd $SURF_SUBJECT_DIR \
            -o $OUTPUT_DIR/whippersnappy_image.png \

Note that adding the --interactive flag will start an interactive GUI that includes a visualization of one hemisphere side and a simple application through which color threshold values can be configured.

Docker:

the whippersnap program can be run within a docker container to capture a snapshot by building the provided Docker image and running a container as follows:

docker build --rm=true -t whippersnappy -f ./Dockerfile .

docker run --rm --init --name my_whippersnappy -v $SURF_SUBJECT_DIR:/surf_subject_dir \
                                               -v $OVERLAY_DIR:/overlay_dir \
                                               -v $OUTPUT_DIR:/output_dir \
                                               --user $(id -u):$(id -g) whippersnappy:latest \
                                               --lh_overlay /overlay_dir/$LH_OVERLAY_FILE \
                                               --rh_overlay /overlay_dir/$RH_OVERLAY_FILE \
                                               --sdir /surf_subject_dir \
                                               --output_path /output_dir/whippersnappy_image.png

In this example: $SURF_SUBJECT_DIR contains the surface files, $OVERLAY_DIR contains the overlays to be loaded on to the surfaces, $OUTPUT_DIR is the local output directory in which the snapshot will be saved, and ${LH/RH}_OVERLAY_FILE point to the specific overlay files to load.

Note: The --init flag is needed for the xvfb-run tool to be used correctly.

Links:

We also invite you to check out our lab webpage at https://deep-mi.org