For the Experts only. Here we're going to make a spinning "Maximum Intensity Projection" rendered on a spinning background slice of the brain!

There are two example input pairs of functional/background images provided, a low resolution pair (zstat2 / example_func), which is useful for testing the script on, and a high resolution pair (hr_zstat1 / highres), for the final rendering.

The output will be an animated GIF, which you can view with your web browser.

1. Inputs
   The inputs are going to be.
   • A zstat image
   • A Background image
   • The incremental rotation (How much the picture should rotate between successive frames)
   • The required z-threshold
   • The output filename
2. Check inputs
   
   • Include a usage clause which will run if the script is run with the wrong number of inputs.
   • Check whether the input files exist.
   • Check that the background image and the zstat image have the same dimensions
3. Making the rotation matrix
   We are going to need a matrix which performs an incremental rotation about a vertical line through centre of the x-y plane. Remember that (0,0,0) isn't at the centre of a volume so we have to be a little clever...
   • Make a matrix which translates the centre of the image to the origin.
   • Make a matrix which rotates by the correct increment about the z-axis
     • Hint 1: You will need to convert the incremental angle to radians using bc: inc_rad=`echo "scale=10; $inc_deg * 3.1417 /180"|bc` ;
     • Hint2: You can calculate sin and cos using bc -l: cosinc=`echo "c($inc_rad)" | bc -l`; and sininc=`echo "s($inc_rad)"|bc -l`;
   • Invert the first matrix to get a matrix which translates the origin to the image centre.
   • Concatenate these three matrices to generate a matrix which rotates around a vertical line through the centre of the x-y plane.
4. Generating the Background Image.
   We want a "background" slice to rotate with our MIP. A good choice for this is the mid-sagittal plane. Use fslmaths with the -roi option to generate an image of the same size as your background but with zeros everywhere apart from the mid-sagittal plane - we're going to rotate this image underneath the MIP.
5. Making the movie
   Make a while loop which will carry on repeating until the total rotation has reached 360 degrees. Inside this loop you will need to:
   • Using fslmaths and the -Xmax option, make mips of the current rotated zstat and mid-sagittal plane images (outputs will be 2D)
   • Using overlay, render the zstat mip on the mid-sag mip with the required threshold
   • Using slicer, create a ppm of the resulting 2D image.
   • Using convert, convert the ppm to a gif - store this gif to a sensible name.
   • Using convert_xfm, create the rotation matrix for the next rotation
   • Using flirt rotate the zstat and mid-sag images to their next position.
6. use whirlgif to merge all the gifs into a single animated gif.
   Get rid of all unneccessary files you've created.
7. Look here for the cheat.