I've figured out how to use slicer to generate axial, coronal and sagittal
jpgs of my FA images. I would like to generate jpgs of using the principal
eigenvector (V1) colorcoded with the RGB convention to indicate direction as
well as FA values. So far, the LUT option seems to only get me so far, as it
appears to only do a one:one translation of a color with an FA value, not
the principal direction.
here is the code
foreach slicenumber (-0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10 \
-11 -12 -13 -14 -15 -16 -17 -18 -19 -20 \
-21 -22 -23 -24 -25 -26 -27 -28 -29 -30 \
-31 -32 -33 -34 -35 -36 -37 -38 -39 -40 \
-41 -42 -43 -44 -45 -46 -47 -48 -49 -50 \
-51 -52 -53 -54 -55 -56 -57 -58 -59)
slicer dti_FA.nii.gz dti_L1.nii.gz -l $FSLDIR/etc/luts/render1.lut \
-z $slicenumber'.' dti_FA_slices-axial$slicenumber.jpg
end
Any suggestions would be appreciated!
Thanks
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