Hello, 

I have written my first script for MRIcroGL! I have added two overlays and specified their colours, now I would like to add a legend that shows the colours and a corresponding label that I would like to specify. 

Also, I have used mosaic to show S, C and A slices but they are poorly aligned. How can I move the S slice up a bit?

Is that possible?

Cheers!

You can use the colorbarposition function to adjust whether the colorer is visible or hidden
 gl.colorbarposition(2)
You can export your image as a bitmap with this function:
 gl.savebmp('mybitmap.png')
which will allow you to decorate your image with your favorite bitmap editor. My own suggestion would be to create your mosaics without text labels ("-L") and then use a vector-art tool like illustrator to add text. The vector text will appear sharper in high resolution layouts than bitmaps.

The Scripting/Templates/help provides an exhaustive list of the in-built Python functions. The Scripting/Templates/mosaic scripts also illustrate showing high quality images.

Okay, then I'll create my legend outside of MRIcroGL. 

However, my sagittal slice is still cut off at the bottom, is there a way to properly align this?

The sagittal slice is not cut off at the bottom. The brain field of view only shows a limited amount of the neck. You can see that the sagittal slice is perfectly aligned with the coronal images and the sagitall rendering by including a coronal slice that includes more of the spinal column, for example y = -50mm in MNI space:

import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.mosaic("C 20 -50 S 0 20 S X R 0");

It is true that your image is longer in the A-P direction (Y) than the I-S (Z) direction, so the axial slice will appear taller than the coronal and sagittal slices. This reflects the field of view of your image. You may want to use the semicolon  ";" to place your axial slices on a separate row from the coronal and sagittal slices. The screen height for axial slices is the Y-dimension, while it is the Z-dimension for the coronal and sagittal slices. In contrast, the screen width is the X-dimension for the axial and coronal slices, but the Y dimension for sagittal slices. You can always create your own template images with any field of view you wish.

import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.mosaic("A 10 20 30 40 ; C 20 -50 S 0 20 ");