Alignment difficulty introducing errors in ROI

[Ken Sze]

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

[Greg Brown-6]

Hi Kenny
You can manually alter the roi between each slice with the arrow
keys without altering the ROI shape or dimensions.
alternately look in the ImageJ plugin pages for registration tools to
realign the images in a stack to remove relative motion for you.
I use the tools of the BIJ tooolkit
http://bij.isi.uu.nl/
written by Michael Abramoff

If you find a manual registration tool please let me know.
Cheers
Greg


Date sent:       Mon, 30 Jan 2006 04:37:25 -0500
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Ken Sze <[hidden email]>
Subject:         Alignment difficulty introducing errors in ROI
To:             [hidden email]

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
Greg Brown  SMRT
Senior Radiographer - MRI Research and Development
Radiology, Royal Adelaide Hospital
North Terrace Adelaide, South Australia 5000  AUSTRALIA
[hidden email]   Adelaide MRI Website www.users.on.net/vision  
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Greg