Commit ee9270ac authored by Saad Jbabdi's avatar Saad Jbabdi
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parent 98c1b94a
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
......@@ -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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