Hello,
I have seen many posts with the same problem but I did not quite understand what is the solution.
My aim is to present my TBSS analysis showing the reference brain, the skeleton in green and the stats in red-yellow. To build that I would like to use the command 'slicer'
When I use the command "fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green -b 0.2,0.7 myfile_tfce_corrp_fstat1 -l Red-Yellow -b 0.95,1" I get my skeleton in green and stats in red-yellow as I want, however, snapshot will not be a good option for me as I will need to put many slices in a picture in different orientations.
When I use the command "overlay 0 0 $FSLDIR/data/standard/MNI152_T1_1mm -a mean_FA_skeleton 0.2 0.7 myfile_tfce_corrp_fstat1 0.95 1 output.nii.gz" I get the skeleton in red-yellow and the stats in green, which I would like to invert. I do understand that I cannot choose colours in the 'overlay' command but only in the 'slicer'. However, I have not managed to use 'slicer' to stack 3 images together. It only deals with two.
I tied overlaying brain + skeleton without the stats a first step to then add the stats in slicer, but yet the skeleton comes in red.
What is the way around it?
Regards,
Thais Minett
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