Making a glass brain

This example shows how to create a glass brain image using a brain mask to visualize and contextualize fiber bundles. Best viewed in mrview but can work in MI-Brain.

The series of commands is inspired from this but adapted to use scilpy instead. Adjust the variable RES to change the voxel size of the output image. A lower value will give a smoother result but will take longer to compute and be heavier on memory.

IN=brainmask.nii.gz
OUT=glass_brain.nii.gz
RES=0.2

scil_volume_resample.py ${IN} resampled.nii.gz --voxel_size ${RES} --interp cubic -f
scil_volume_math.py blur resampled.nii.gz 2 smooth.nii.gz -f --data_type float32
scil_volume_math.py lower_threshold smooth.nii.gz 0.3 threshold.nii.gz -f --data_type uint8
scil_volume_math.py dilation threshold.nii.gz 2 dilated.nii.gz -f
scil_volume_math.py subtraction dilated.nii.gz threshold.nii.gz ${OUT} -f

To view the output in mrview, first open a subject’s image you want to visualize other than the glass brain. Then, add the glass brain as an overlay. Go to “View” and select “Volume render” (or press F3). At the bottom of the overlay window: deactivate interpolation, change the color scheme to “Gray” and reduce opacity.

To view the output in MI-Brain, load the output. Right-click the image and select “Create a polygon model”. Reduce the opacity of the polygon model to something low and change the color to something gray-ish.

Here are some examples of the output images: