Alignment difficulty introducing errors in ROI

Posted by Ken Sze on Jan 30, 2006; 9:37am
URL: http://imagej.273.s1.nabble.com/Alignment-difficulty-introducing-errors-in-ROI-tp3703900.html

Dear all

I am trying to plot a z-axis profile for 2 ROIs for a number of large
stacks of Magnetic Resonance(MR) images of the human kidneys. Because there
are 2 regions of interest- one in the outer part and the second in the
inner part of the kidney (2 very different functional regions of the
organ), it will be interesting to see the different values.

The difficulty i have currently is that due to breathing movements of the
subject, the kidneys in my stacks of MR images vary up and down between
slices. I am hoping to align the kidneys (at least vertically, as there is
greatest variation in this orientation) so that the ROI's I establish will
not measure different compartments of the kidney between slices as a result
of non-alignment.

Does anyone have any pointers?  Advice on this or use of ImageJ, or other
software will be much much appreciated

Regards
Kenny Sze
Medical student, Sydney Australia
Currently in Singapore doing elective term