Merge branch 'fsleyes_branch' into 'master'

Mo fixed a few typos in commands.

See merge request !14

applications/fsleyes/data/.ipynb_checkpoints/cmd-checkpoint.txt

+--scene 3d --worldLoc 9.918212890625e-05 -18.000099182128906 17.999900817871094 --displaySpace world --cameraRotation -60.10  177.44 -1.96 --zoom 75.0 --hideLegend --lightPos 181.9999008178711 199.99970245361328 17.999900817871094 --offset 0.0 0.0 --hideCursor --bgColour 0.6 0.6 0.753 --fgColour 0.0 1.0 0.0 --cursorColour 0.0 1.0 0.0 --colourBarLocation top --colourBarLabelSide top-left --colourBarSize 100.0 --labelSize 12 --performance 3 --movieSync /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --name "MNI152_T1_2mm" --overlayType volume --alpha 100.0 --brightness 59.98929424740918 --contrast 80.01069122355028 --cmap yellow --negativeCmap greyscale --clipPlane 50.000 5.883 $angle1 --clipPlane 50.000 -2.917 $angle2 --displayRange 1000.0 4985.0685976730165 --clippingRange 1000.0 10067.68 --modulateRange 0.0 9968.0 --gamma 0.0 --cmapResolution 256 --interpolation none --numSteps 100 --blendFactor 0.1 --smoothing 0 --resolution 100 --numInnerSteps 10 --clipMode intersection --volume 0

applications/fsleyes/data/cmd.txt

+--scene 3d --worldLoc 9.918212890625e-05 -18.000099182128906 17.999900817871094 --displaySpace world --cameraRotation -60.10  177.44 -1.96 --zoom 75.0 --hideLegend --lightPos 181.9999008178711 199.99970245361328 17.999900817871094 --offset 0.0 0.0 --hideCursor --bgColour 0.6 0.6 0.753 --fgColour 0.0 1.0 0.0 --cursorColour 0.0 1.0 0.0 --colourBarLocation top --colourBarLabelSide top-left --colourBarSize 100.0 --labelSize 12 --performance 3 --movieSync /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --name "MNI152_T1_2mm" --overlayType volume --alpha 100.0 --brightness 59.98929424740918 --contrast 80.01069122355028 --cmap yellow --negativeCmap greyscale --clipPlane 50.000 5.883 $angle1 --clipPlane 50.000 -2.917 $angle2 --displayRange 1000.0 4985.0685976730165 --clippingRange 1000.0 10067.68 --modulateRange 0.0 9968.0 --gamma 0.0 --cmapResolution 256 --interpolation none --numSteps 100 --blendFactor 0.1 --smoothing 0 --resolution 100 --numInnerSteps 10 --clipMode intersection --volume 0

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

+# Creating figures and movies with FSLeyes
+
+You may be familiar with using FSLeyes for looking at your data. Perhaps you have taken screenshots and pasted those into a talk or a paper. Here we will learn how to script such things and ask FSLeyes to create complex figures directly from the command line. 
+
+This has several advantages. For example, you can re-create the same or similar figures simply by editing the script, instead of re-doing all the FSLeyes tinkering. It is also useful if you need to create complex figures for many datasets/subjects.
+
+
+## Content
+
+* [Using FSLeyes render to create a PNG](#create-png)
+* [Creating a movie for a talk with FSLeyes and ImageMagick](#create-movie)
+* [Creating a figure for a paper](#create-for-paper)
+
+
+<a class="anchor" id="create-png"></a>
+## Using fsleyes render
+
+The first thing we will learn is how to generate a complex command line for FSLeyes. 
+
+Everything you can set manually by clicking on the FSLeyes graphical interface can be reproduced through the command line. You can learn all about the command line arguments by reading the [documentation](https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/command_line.html) or looking at the FSLeyes full help (`fsleyes -fh`). 
+
+Here we will instead cheat and use the lazy approach. We will first use the graphical interface to produce a nice looking image. Then we will generate a full command line in FSLeyes and use that as the basis for creating more similar figures.
+
+### Creating an examplar
+Start by opening FSLeyes. The command below also loads a MNI brain (copy this onto a Terminal shell):
+
+```bash
+fsleyes -std1mm &
+```
+
+
+Let's make this brain look funkier. Start by toggling off the sagittal and coronal views. We only want to see the axial view. 
+
+Next, toggle off the location cursor. You should now see this:
+
+<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):
+
+- Change interpolation to "Spline interpolation"
+- Change the colourmap resolution from 256 to 7
+- Change the Display range to min=1000 and max=8000
+
+Close the display panel and open the View settings (spanner below cogwheel), then change the background color to be white. 
+
+If you did the above you should now see:
+
+<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:  
+
+**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. 
+
+
+----
+<img src="data/snapshot7.png" alt="snapshot7" style="width:800px;"/>
+
+<!--- <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!
+
+Now as I said the command line is long and contains many things that are default behaviour anyway. So let's strip it down a little bit as it will make this document shorter. In the below, I am only keeping a subset of the options, but I did not add new ones:
+
+```bash
+fsleyes --scene ortho --hideLabels --layout horizontal --hidex --hidey --hideCursor --bgColour 1.0 1.0 1.0 --fgColour 0.0 0.0 0.0 /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --overlayType volume --cmap cool --displayRange 1000.0 8000.0 --cmapResolution 7 --interpolation spline 
+
+```
+
+> Check that the above command generates the same view by running it in a terminal!
+
+### Rendering
+
+Instead of opening FSLeyes, wee want to create an image (a PNG for example) to use in a presentation. This can be done very simply by using the above command and adding a render flag to fsleyes:
+
+```
+fsleyes render -outputfile my_image.png <rest of the command>
+```
+
+Run the above code (make sure you replace `<rest of the command>` with the rest of the FSLeyes command we created earlier). This should now output a PNG file. Have a look at it!
+
+> Exercise: Do the same as above but instead of rendering an axial view of the MNI brain, try to render a 3D view. Make it look nice before you render.
+
+<a class="anchor" id="create-movie"></a>
+## Creating a movie
+
+Here we will create a movie of the MNI brain scrolling through z-slices. We'll also add a bit of text showing the slice number for good measure. The result will look like this:
+
+<img src="data/snapshot3.gif" alt="snapshot3" style="width:400px;"/>
+
+First, make sure that you have ImageMagick installed. To do that, go to your terminal and run thee command `convert`. If you get a long help for the convert command you are good to go. Otherwise install ImageMagick from [here](https://imagemagick.org/script/download.php).
+
+We will re-use the previous render command. Start by copying that into a text editor. You can use the code below:
+
+```bash
+fsleyes render --outfile my_image.png --scene ortho --hideLabels --layout horizontal --hidex --hidey --hideCursor --bgColour 1.0 1.0 1.0 --fgColour 0.0 0.0 0.0 /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --overlayType volume --cmap cool --displayRange 1000.0 8000.0 --cmapResolution 7 --interpolation spline 
+```
+
+Now to change the z-location, we will use the `-voxelLoc` flag. We will also use a FOR loop to change the location, and store a different PNG at each step. Here is what the code will look like (copy it onto your text editor):
+
+```bash
+rest_of_command="--scene ortho --hideLabels --layout horizontal --hidex --hidey --hideCursor --bgColour 1.0 1.0 1.0 --fgColour 0.0 0.0 0.0 /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --overlayType volume --cmap cool --displayRange 1000.0 8000.0 --cmapResolution 7 --interpolation spline"
+
+
+mkdir -p my_folder
+for ((z=0;z<=181;z+=4));do
+    zzz=`$FSLDIR/bin/zeropad $z 3`
+    echo "Slice $zzz"
+    
+    out=my_folder/image_${zzz}.png
+    fsleyes render --outfile $out  --voxelLoc 91 109 $z $rest_of_command
+done
+```
+
+Examine the above script line by line. We first create a variable called `rest_of_command` containing all the extra stuff for display that does not change in the FOR loop.
+
+We then use a FOR loop, where we go through every fourth z-slice (can you see that?). We create a variable called `zzz` inside the loop. This is to use for naming the output PNG files so that they are listed in the same order as the z-slices (e.g. instead of image_1.png we have image_001.png). 
+
+Run this script and you should see that many PNGs will get created, one per slice.
+
+Now to combine all these PNGs into a single GIF, run the below ImageMagick command:
+
+```bash
+convert -delay 5 my_folder/image_???.png -loop 0 my_movie.gif
+```
+
+Have a look at the GIF. On a mac you can simply use the space bar on your keyboard to preview the GIF. 
+
+It is still missing the changing text. We will also use ImageMagick for this. Below is the same script as before but with the addition of a call to `convert` that adds the text:
+
+```bash
+rest_of_command="--scene ortho --hideLabels --layout horizontal --hidex --hidey --hideCursor --bgColour 1.0 1.0 1.0 --fgColour 0.0 0.0 0.0 /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz --overlayType volume --cmap cool --displayRange 1000.0 8000.0 --cmapResolution 7 --interpolation spline"
+
+
+mkdir -p my_folder
+for ((z=0;z<=181;z+=4));do
+    zzz=`$FSLDIR/bin/zeropad $z 3`
+    echo "Slice $zzz"
+    
+    out=my_folder/image_${zzz}.png
+    fsleyes render --outfile $out  --voxelLoc 91 109 $z $rest_of_command
+    
+    # Bit that adds annotation to the image
+    out_annot=my_folder/image_annot_${zzz}.png
+    convert $out \
+            -gravity NorthWest  -pointsize 50 \
+            -fill black -annotate 1 "`echo Z = $z`" $out_annot
+
+done
+```
+
+Now run the above, then run the below to make the final GIF:
+
+```bash
+convert -delay 5 my_folder/image_annot_???.png -loop 0 my_annotated_movie.gif
+```
+
+> Note: FSLeyes has/will soon have the option of adding annotations (text, arrows, boxes, etc.), so you don't need to use ImageMagick to add them
+
+> Exercise: Create a similar movie which scrolls through every 6th Sagittal slice
+
+### Rotating head through the GUI
+
+You can of course also create an animateed GIF directly through the GUI without the FOR look in bash and ImageMagick. Here is an example of how to create a rotating head:
+
+Open FSLeyes with a standard brain in 3D mode:
+
+```
+fsleyes --scene 3d -std1mm &
+```
+
+Then follow the below steps:
+
+- Change the colourmap to "Cool"
+- In the display settings (cogwheel) increase Blending to 0.5 and number of samples to 260
+- Change minimum display range to 5000
+- In the view settings (spanner) toggle "Movie mode"
+- Change movie axis to Z
+- Decrease Movie update rate to the minimum
+- Then save the GIF through Settings->3D view->Save animated GIF
+
+Et voilà! You should be able to see something like [this](data/rotating_head.gif)
+
+### Scalped pacman
+
+The video that we have just created is nice. But wouldn't it be even better if we could create a scalped pacman?
+
+Open a new session of FSLeyes with a 2mm standard brain, this time directly in 3D mode:
+
+```bash
+fsleyes -std --scene 3d &
+```
+
+Ok I now that looks a little scary. Let's make the following changes. Open the overlay display panel (Settings->3D View 1->Overlay display panel) and:
+
+- Change the colourmap to Yellow
+- Change the display range to min=1000, max=5000
+- Turn the brain upside down 
+- Add two clipping planes
+
+Copy the command line that creates this scene as we have done before (Settings->3D View 1->Show command line for scence).
+
+Now we are going to create a FOR loop where we will change the angles of the clipping planes and save each angle in a separate PNG files. We will then combine them into a single GIF. In the code below, you can find the FOR loop, all that is missing is the command line fsleyes that you have copied to the clipboard:
+
+```bash
+outputfolder=my_pacman
+mkdir -p $outputfolder
+
+for ((angle1=0,angle2=180;angle1<=16;angle1++,angle2--));do
+    echo $angle1 $angle2
+
+    fsleyes render --outfile $outputfolder/grot_`zeropad $angle1 3`.png [INSERT THE COMMAND HERE AND PUT IN $angle1 AND $angle2 WHERE YOU THINK THEY SHOULD GO ]
+    
+done
+```
+
+Run the command above (after suitable changes - or you can copy my [version](data/cmd.txt)) and then run the below to produce the GIF:
+
+```bash
+convert -delay 1x30 `ls $outputfolder/grot_???.png` `ls -r $outputfolder/grot_???.png` -loop 0 $outputfolder/pacman.gif
+```
+
+Notice we are using the PNGs twice, once for opening the mouth, and once for closing it, where the files are read in reverse order (`ls -r`).
+
+You should be able to see this GIF:
+
+<img src="data/snapshot4.gif" alt="snapshot4" style="width:400px;"/>
+
+<a class="anchor" id="create-for-paper"></a>
+## Figure for a paper
+
+By now hopefully you have seen how you can combine the power of intuitively interacting with the FSLeyes graphical interface and the power of bash scripting. We'll do one more example of creating a nice graphic and then rendering it in a bash script. This one will look very nice.
+
+Run the code below. It will open FSLeyes, with a 2mm MNI brain, and will also load the XTRACT tracts atlas. 
+
+```bash
+    fsleyes -std $FSLDIR/data/atlases/XTRACT/xtract-tract-atlases-prob-1mm &
+```
+
+We will try to make this nice by displaying the two images using maximum intensity projections.
+
+Do the following:
+
+- Change the colourmap of the MNI brain to "Bone"
+- Change its min/max display range to 5000-10000
+- Change the colourmap of the tracts to "Red-Yellow"
+- 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
+
+[This](data/tracts.txt) is what I got after doing the above (feel free to use that).
+
+Now use FSleyes render to create a nice looking figure. We will also control the DPI (digits per inch) of this figure, as some journal publishers insist that you have good quality images. 
+
+```
+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 are 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:
+
+<img src="data/snapshot6.png" alt="snapshot5" style="width:400px;"/>
+
+Now you should be able to use FSLeyes for this kind of thing and hopefully you will never ever need to use `slicesdir` ever again.
+
+----
+
+The End.