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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