I have no idea. An RA wrote the guts of spmregister about 10 years ago. You might try using mri_coreg in the dev environemnt. Don't know how to convert an spm mat into FSL.

On 09/08/2016 04:02 PM, Albrecht, Daniel S. wrote:

Hello,

I've been using spmregister in order to coregister a static PET image to an MPRAGE, typically with good results. A representative run is as follows:

spmregister --mov $file.nii --s $subj --reg SUV_lin_T1.dat --fsvol orig

We then convert *.dat to *.mat with tkregister2, and apply the *.mat to the PET with FLIRT.

However, the registration was unsatisfactory for a recent subject. While working through a couple different coregistration options, I tried running coregister (estimate and reslice) in SPM. The result from this was quite good. I was confused why this would give a different result from spmregister when I'm not changing any of the default parameters in SPM. Any ideas on why running a coregistration directly through SPM would give a different result?

And as a secondary follow-up, are there any tools available to convert an SPM transformation matrix (e.g. x from x=spm_coreg) to a *.mat that can be used in FSL FLIRT?

Thanks,

Daniel S. Albrecht, PhD Research Fellow in Radiology Martinos Center for Biomedical Imaging

Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-6748 Fax: (617) 726-7422 dsalbrecht@mgh.harvard.edu https://owa.partners.org/cvpn/aHR0cHM6Ly9wcm94eS1vd2EucGFydG5lcnMub3Jn/owa/redir.aspx?C=8A9OJCUaPkOLxUmmjc0_cF-xdjAP2NEI4aEbq2JpVjitXhs_QYjcIRXVbcEtTXWjym0XzqsaDNI.&URL=mailto%3amarco%40nmr.mgh.harvard.edu

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