minor changes

applications/fsleyes/fsleyes_render.md

@@ -34,7 +34,8 @@ Let's make this brain look funkier. Start by toggling off the sagittal and coron
 
 Next, toggle off the location cursor. You should now see this:
 
-![snapshot1](data/snapshot1.png "snapshot1")
+<img src="data/snapshot1.png" alt="snapshot1" style="width:400px;"/>
+
 
 Now change the colormap to "Cool" (of course), and open the Overlay display panel (cogwheel at the top left). Then follow these steps (or do your own prittification):
 
@@ -46,18 +47,20 @@ Close the display panel and open the View settings (spanner below cogwheel), the
 
 If you did the above you should now see:
 
-![snapshot2](data/snapshot2.png "snapshot2")
+<img src="data/snapshot2.png" alt="snapshot2" style="width:400px;"/>
 
 
 Now wouldn't it be nice if one could generate the same thing from scratch without going through the above steps by hand? Here is how you do it:  
 
-<code>Settings -> Ortho View 1 -> Show command line for scene</code>
+**Settings -> Ortho View 1 -> Show command line for scene**
 
 You can even click on copy to clipboard. Do that, then open a new text file (e.g. with emacs) and paste the result into the text file. The command you get looks very long so I am highlighting in <span style="color:blue">blue</span> the bit about the scene and in <span style="color:red">red</span> the bit about the overlay. 
 
+----
 
-<code>fsleyes <span style="color:blue">--scene ortho --worldLoc -0.49994659423828125 -17.50005340576172 18.49994659423828 --displaySpace /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --xcentre  0.00000  0.00000 --ycentre  0.00000  0.00000 --zcentre  0.00000  0.00000 --xzoom 100.0 --yzoom 100.0 --zzoom 100.0 --hideLabels --layout horizontal --hidex --hidey --hideCursor --bgColour 1.0 1.0 1.0 --fgColour 0.0 0.0 0.0 --cursorColour 0.0 1.0 0.0 --colourBarLocation top --colourBarLabelSide top-left --colourBarSize 100.0 --labelSize 12 --performance 3 --movieSync </span>/usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz <span style="color:red">--name "MNI152_T1_1mm" --overlayType volume --alpha 100.0 --brightness 52.4977497749775 --contrast 64.99649964996499 --cmap cool --negativeCmap greyscale --displayRange 1000.0 8000.0 --clippingRange 1000.0 10098.99 --modulateRange 0.0 9999.0 --gamma 0.0 --cmapResolution 7 --interpolation spline --numSteps 100 --blendFactor 0.1 --smoothing 0 --resolution 100 --numInnerSteps 10 --clipMode intersection --volume 0</span></code>
+<code>fsleyes <span style="color:blue">--scene ortho --worldLoc -0.49994659423828125 -17.50005340576172 18.49994659423828 --displaySpace /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --xcentre  0.00000  0.00000 --ycentre  0.00000  0.00000 --zcentre  0.00000  0.00000 --xzoom 100.0 --yzoom 100.0 --zzoom 100.0 --hideLabels --layout horizontal --hidex --hidey --hideCursor --bgColour 1.0 1.0 1.0 --fgColour 0.0 0.0 0.0 --cursorColour 0.0 1.0 0.0 --colourBarLocation top --colourBarLabelSide top-left --colourBarSize 100.0 --labelSize 12 --performance 3 --movieSync </span> /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz <span style="color:red">--name "MNI152_T1_1mm" --overlayType volume --alpha 100.0 --brightness 52.4977497749775 --contrast 64.99649964996499 --cmap cool --negativeCmap greyscale --displayRange 1000.0 8000.0 --clippingRange 1000.0 10098.99 --modulateRange 0.0 9999.0 --gamma 0.0 --cmapResolution 7 --interpolation spline --numSteps 100 --blendFactor 0.1 --smoothing 0 --resolution 100 --numInnerSteps 10 --clipMode intersection --volume 0</code>
 
+----
 
 If you run it all in a Terminal it will open FSLeyes and set it up to look like the above screenshot. Try that!