more edits

applications/fsleyes/data/tracts.txt

+fsleyes --scene ortho --worldLoc 23.747230186891017 -17.50005340576172 5.207819563619225 --displaySpace /usr/local/fsl/data/atlases/XTRACT/xtract-tract-atlases-prob-1mm.nii.gz --xcentre  0.00229  0.00274 --ycentre  0.00274  0.00274 --zcentre  0.00274  0.00229 --xzoom 276.59102519755277 --yzoom 287.54133813086855 --zzoom 287.54133813086855 --layout horizontal --hidez --bgColour 0.0 0.0 0.0 --fgColour 1.0 1.0 1.0 --cursorColour 0.0 1.0 0.0 --showColourBar --colourBarLocation left --colourBarLabelSide top-left --colourBarSize 30.0 --labelSize 12 --performance 3 --movieSync /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --name "MNI152_T1_2mm" --overlayType mip --alpha 100.0 --brightness 37.37961476725522 --contrast 74.91974317817014 --cmap brain_colours_bone --linkHighRanges --displayRange 5000.0 10000.0 --clippingRange 5000.0 10000.0 --gamma 0.0 --cmapResolution 256 --interpolation spline --window 50.0 --volume 0 /usr/local/fsl/data/atlases/XTRACT/xtract-tract-atlases-prob-1mm.nii.gz --name "xtract-tract-atlases-prob-1mm" --overlayType mip --alpha 100.0 --brightness 49.79941272735595 --contrast 49.91995750020426 --cmap red-yellow --displayRange 0.0 100.80234909057617 --clippingRange 0.0 101.0 --gamma 0.0 --cmapResolution 256 --interpolation none --window 50.0 --volume 14

applications/fsleyes/fsleyes_render.md

@@ -229,6 +229,7 @@ Do the following:
 - Change the display type of both from "3d/4D volume" to "Maximum intensity projection"
 - Change the MNI brain to have "Spline interpolation"
 - Select volume number 14 for the tracts
+- Use the spanner to add a colourbar on the left with size 30
 - Untoggle the axial view
 - Copy the command line onto the clipboard as before
 
@@ -240,7 +241,32 @@ Now use FSleyes render to create a nice looking figure. We will also control the
 fsleyes render --outfile my_tract.png --size 800 600 <COPY REST OF THE COMMAND HERE>
 ```
 
+If you want to compare what you produced to what I made, have a look at [this](data/snapshot5.png)
+
 > Exercise : create a FOR loop that produces a snapshot like the one above for all the XTRACT tracts.
 
 
+----
+
+Ok one last thing. Let's imagine that you want to check that your registration has worked properly and also wanted to make a PNG to show others that it does. 
+
+For this, we will need two images that have been aligned with each other. These two arree included with the practical material:
+
+```
+fsleyes data/example_func2highres.nii.gz data/highres.nii.gz & 
+```
+
+Then follow this recipe:
+
+- Change the display mode of the highres to "3d/4D mask image"
+- Change the color to Red
+- Click on the cogwheel
+- Change the threshold to 600-1400
+- Click on "Show outline only"
+- Change outline width to 3
+
+Copy the command line to the clipboard and use the command line to render an image. The result should look like this:
+
+
+
 The End.
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