Further to my message, I've used this macro:
count = roiManager("count");
if (count==0)
exit("ROI Manager line selection required");
roiManager("select", count-1);
if (selectionType!=5)
exit("Straight line selection required");
run("Rotate...", "angle=90");
roiManager("Add");
roiManager("Show All without labels");
And I can then adjust it to 1px in width.
So, the only question now, is how to get the perpendicular profiles at 15%,45%,65% and 85% of the ROI length.