I don't think slicer has the capability to display the diffusion vectors as
RGB.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of David B. FitzGerald, MD
Sent: Wednesday, November 11, 2009 3:34 PM
To: [log in to unmask]
Subject: [FSL] using slicer to generate RGB jpgs of DTI images with RGB
corresponding to V1
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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