Thanks for your help.  Unfortunately, reslicing does not fix the problem.  I am able to get DBM to run though.  It still gives me that strange output of Xs, however, and the jy_image that it outputs is not correct.  The jy_image looks like a plaid pattern with values ranging from .999962.... to 1.0000439... There is no brain shape.  When I run the same images using SPM2, the output seems to look as it should, however the inhomogeneity in the images seems to influence the deformations.  I believe that SPM5 has additional features for DBM including a homogeneity correction, so I would like to be able to use the SPM5 version if possible.  I have run several of my images with both SPM2 and SPM5 and get this same pattern of results.  I have also tried different inhomogeneity parameters in SPM5 and still get the same results.  

Also, regarding inhomogeneity correction, I am wondering as to the validity or advantage of doing iterative inhomogeneity corrections.  I came across a posting on the listserv saying that bias correction would be most accurate if done iteratively during segmentation, but that the current version of SPM does not do this.  I thought to try this:

1) Spitting out a bias corrected (m* image) from the segmentation/normalization procedure. 
2) Rerunning segmentation/normalization with the bias corrected image and spitting out a bias corrected image
3) Rerunning segmentation/normalization with the newest bias corrected image and spitting out a bias corrected image, etc.

I ran this iterative procedure on one of my images pre-treatment and post-treatment and the difference image between the two realigned images was much improved (i.e. the magnitude of the differences were smaller and more consistent spatially) when compared with the realigned images after using just one bias correction.   From this empirical observation, I would recommend performing an iterative bias correction for images with lots of inhomogeneity, however, wanted to make sure this would not introduce other errors or bias into the data.  Any thoughts?


On Jan 14, 2008, at 8:54 AM, John Ashburner wrote:

I'm afraid I can't figure out the cause of this problem.  Did you reslice 
after aligning, or just align?  Maybe do a reslicing as well.  That's all I 
can think of that may help.

Best regards,
-John

I'm beginning to explore the technique of deformation-based morphometry.  I
have longitudinal T1 images from the same subject.  I've performed
preprocessing on the images including resetting the origin, skullstripping,
and registering (aligning) the later scan to the earlier scan. When I try
to run high dimensional warping on the images in SPM5, however, I get the
following output:

Initialising SPM.........done

SPM present working directory:
/Users/neurolabII/Desktop/newly_processed_scans/80
--------------------------
Running "High-Dimensional Warping"
Generating uniform affine transformation field
Warping (iterations=8 regularisation=4)
9.9772625
nan
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

The program keeps printing "Xs" and I have to force quit Matlab.  I am able
to use the SPM2 deformations utility on these images, however, and obtain a
jacobian determinant image (jy_*). Any idea why I am having this trouble
with SPM5, but not SPM2?  Is there any advantage of SPM5 over SPM2 for high
dimensional warping?    Thanks in advance for any insights you may be able
to offer.

-Lynne

Lynne Gauthier
Graduate Research Associate
Neuroimaging Lab
CI Therapy Research Group
University of Alabama - Birmingham
857-998-7785
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