Hi,

You can replace the last two lines with:

slicer img.nii -l $FSLDIR/etc/luts/renderhot.lut -z -${L3} test.png

Note that there isn't a lut (lookup table) that is exactly the same as the Red in FSLView, but you can quite easily make one from $FSLDIR/etc/luts/renderhot.lut yourself (it is just a simple text file defining RGB colours) if you want to.

All the best,

Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Moran Artzi <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Saturday, 30 January 2016 07:04
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Auto save .png image

Dear all,

I want to save image of the middle slice (on z axis) of binary image

This slice can be detect using

L1=`fslstats img.nii-w | cut -d' ' -f5`

L2=`fslstats img.nii -w | cut -d' ' -f6`

L3=`echo "$L1 +($L2 / 2)" | bc -l`

fslmaths img.nii -roi 0 600 0 600 $L3 1 0 1 test

fslview img.nii test -l Red

Is it possible to automatically save from the from the command line image in .png format of the axial orientation of this image (as appears in the viewer)

Many thanks

Moran