Dear Michael,
Try specifying your lut file with its full pathname. I'm not sure if
'-l ./custom1.lut' works but '-l /home/ba/dev/blue.lut' works for me.
Best,
- BettyAnn
> Hello FSL experts,
>
> I am trying to produce images of a seed region overlaid on the
> MNI standard using slicer. The quick version of my question is:
> how do I change the color of the overlaid mask? The long version
> follows. Note: In all of the below, the links lead to an image
> hoster so as to not send multiple images in the email.
>
> I have tried the following:
>
> overlay 1 0
> /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -a
> FOC84.nii.gz 1 100 foc_overlay_out
>
> This creates an overlaid mask the way I would expect. And is
> viewed properly in fslview . When I run the following, I get an
> acceptable slicer version of the image:
>
> slicer foc_overlay_out.nii.gz -S 2 750 foc_out.png
>
> However, and this is where my question lies, I cannot seem to
> change the color and get a problem with custom look up tables
> (luts). I created custom lut files with the command:
>
> create_lut custom
>
> But when I try any varation of the following commands, I get the
> same incorrect black and white image.
>
> slicer foc_overlay_out.nii.gz -l custom1.lut -S 2 750 foc_out.png
>
> slicer foc_overlay_out.nii.gz -l render3.lut -S 2 750
> foc_out_3.png
>
> slicer foc_overlay_out.nii.gz -l garbage -S 2 750
> foc_out_garbage.png
>
> Where custom1= a custom file I modified that should run
> green-lightgreen, render3.lut= the render 3 lut I copied out of
> the fsl directory, and garbage=a bad file name
>
> The fact that the garbage name produced the same result makes me
> think that none of the luts are being loaded correctly. Can some
> one pelase tell me where I am going wrong?
>
> Thank you,
>
> Michael
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