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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 [log in to unmask]