Hi David,
I've written a little helper utility which converts dti_V1 + dti_FA to a
series of PPMs (a quick hack - not much error checking). Maybe this is
what you are looking for? "PPM to anything else (JPG)" can be achieved
e.g. with convert from ImageMagick.
It is compiled with
gcc -o fsl2ppm -I/usr/include/nifti fsl2ppm.c -lniftiio
Maybe the "-I" option has to be adjusted to your installation. Search
for nifti1_io.h on your system and set the include path to the directory
where nifti1_io.h lives. If libniftiio.so is installed in a non standard
directory add -L to the gcc call.
Christina
David B. FitzGerald, MD schrieb:
> 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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