[VoxBo] realignment issue

[Daniel Kimberg]

Hi all.  In tracking down the cause of the problem that Ranjani posted to the list recently, I discovered what may (or may not) be a long-standing bug in the SPM2 realign jobtype.  This jobtype is used by the bigprep script that I believe has been used as a starting point for various folks writing VoxBo prep scripts.

I'm still looking at various things, but it's possible that script lines beginning with "spm2_realign" don't currently realign anything, they just calculate the transformation but don't apply it.  It's also possible the problem was introduced at some indeterminate time over the last few years.

It would be a great help if anyone who's used a script using spm2_realign could take a quick visual look at a few data files to see if there are obvious alignment problems.  The easiest way to check quickly is to load up 4D files from separate runs side-by-side in vbview, and flip back and forth between them to see if there's notable mis-alignment.  Probably it would be easiest to spot on a coronal or sagittal view, using a subject with appreciable head movement.

Please email me what you find (kimberg at mail.med.upenn.edu) or post here if you have other comments/questions.  I'll post a summary as soon as I have a better idea of the scope of the problem.  In the meantime, I'll try to produce some better working jobtypes for future use.

dan