Hello SPMers,

I am using SPM 8 since some time to register and then warp brain images 
to MNI templates. More exactly, I use
1. estimate & write to register & warp the anatomical MRI and then
2. estimate with the resulting transformation matrix to warp a (binary) 
segmentation mask

This procedure always worked, but now our institute updated to MATLAB 
R2014a and the second transformation of the binary segmentation does not 
produce the expected results: Instead of a transformed segmentation, I 
am presented with an empty image. No error or remark by SPM.

I've tried to combine the two steps into a single when, adding the 
segmentation as a second image to write to the Data->Subject(1) beside 
the anatomical MRI. Now, curiously, both of the warping fail: The 
anatomical MRI is heavily distorted, while the binary segmentation is 
still black. Again, no error or remark from SPM.

Applying the such resulting transformation matrix to the anatomical MRI 
alone yields the expected results. I therefore assume the problem lies 
with the warping, not with the registration/estimation.

In my despair, I've switched to SPM12 and (after some time getting used 
to the new interface and wondering about the impossibility to define a 
weight image), I had to observe exactly the same strange behaviour: 
anatomical MRI alone works, adding the binary segmentation caused both 
warping to fail.

I can only assume that SPM somehow warps both image at the same time. 
Otherwise I couldn't explain to myself how the binary segmentation image 
can influence the warping of the anatomical MRI.

Furthermore, I suspect the problem lies with the new MATLAB version. 
Sadly, I can't switch back, as our license for the old version expired.

Did anyone observe a similar behaviour? Does anyone now what might cause 
it? And, most importantly, does anyone know a workaround or a fix? Maybe 
another program that can read and apply SPM transformation matrices?

Best and thanks already,
Oskar

-- 
Oskar Maier, M.Sc.
     Wissenschaftlicher Mitarbeiter

UNIVERSITÄT ZU LÜBECK
     INSTITUT FÜR MEDIZINISCHE INFORMATIK

     building 64, 2 floor, room 3
     Ratzeburger Allee 160
     23538 Lübeck
     Germany

     Tel +49 451 500 5645
     Fax +49 451 500 5610
     [log in to unmask]

     www.imi.uni-luebeck.de