Hi all
I ran the following code (part of UK Biobank pipeline) to reduce the FOV on a T1 image, but it gave a strange result, namely an output image (T1_tmp) that had the top half of the brain missing:
head_top=`${FSLDIR}/bin/robustfov -i T1_orig_ud | grep -v Final | head -n 1 | awk '{print $5}'`
${FSLDIR}/bin/fslmaths T1_orig_ud -roi 0 -1 0 -1 $head_top 170 0 1 T1_tmp
The head_top value was 66.000+e01. When this was input to the second line (fslmaths), the ROI extracted started at the wrong z value (closer to 30, not 66). But if I entered the value 66 into that line (instead of "$head_top") it worked correctly. It looks like fslmaths can't deal with exponential format numbers - is this correct?
I corrected the problem by adding in an intermediate line:
printf -v head_top "%.f" "$head_top"
But as this has obviously worked before as part of the Biobank pipeline, is this to do with my setup or is it something to do with using different FSL versions? (I'm using 6 but Biobank pipeline is normally run on 5)?
Many thanks
Chris
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