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fsleyes_brain_gif.sh
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fsleyes_brain_gif.sh
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#!/bin/env bash
# inputs
image=/Users/fmorfini/Downloads/sub-NEUpilotFM_ses-localizer_desc-preproc_T1w.nii.gz
lastslice=96
firstslice=-50
# call fsleyes
echo "generating images from fsleyes. this takes a while"
for ((firstslice<$lastslice; firstslice++)); do
output=$(printf "%03u" $z).png
# the first time to get this comand: open fsleyes, set up the views as you like manually, then [setting] [ortho view 1] [show command line for scene] copy and paste
fsleyes render -of $output --scene ortho --worldLoc 3.2318436975690474 -9.78085491242608 $z --displaySpace $image --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 0.0 0.0 0.0 --fgColour 1.0 1.0 1.0 --cursorColour 0.0 1.0 0.0 --colourBarLocation top --colourBarLabelSide top-left --colourBarSize 100.0 --labelSize 12 --performance 3 --movieSync $image --name "mybrain_desc-preproc_T1w" --overlayType volume --alpha 100.0 --brightness 50.0 --contrast 52.0 --cmap random --negativeCmap greyscale --displayRange 278.3576562500002 13639.52515625 --clippingRange 278.3576562500002 14057.061640625 --modulateRange 0.0 13917.8828125 --gamma -0.972916573745412 --cmapResolution 14 --interpolation spline --numSteps 100 --blendFactor 0.1 --smoothing 0 --resolution 100 --numInnerSteps 10 --clipMode intersection --volume 0
done
#combine png into a gif
convert -delay 10 -loop 0 *.png tmp_movie.gif
#make background (black) transparent and trim border
convert tmp_movie.gif -transparent black -trim tmp_transp.gif
echo "generating gif"
#combine png into a gif, make background (black) transparent and trim border
convert -delay 10 -loop 0 -transparent black -trim -dispose previous *.png tmp_movie.gif
#make cycle patrol (goes back and forth)
magick tmp_movie.gif -coalesce -duplicate 1,-2-1 -quiet -layers OptimizePlus -loop 0 Francesca_Morfini_my_brain_gif.gif
mkdir allframes
mv *png tmp* allframes
echo "all done"