Hi Marco, I think it might be that your PET volume is left-right reversed. I reran bbregister after left-right reversing the pet data and it looks much better.

mri_convert PBR_CLBP001_average8-28_BET_hdrOK.nii --left-right-reverse-pix lrrev.nii

There's always the chance that the T1 was reversed, but I suspect the PET :).

doug

On 08/20/2012 11:36 PM, Marco Loggia, PhD wrote:

Hi Doug and Freesurfer team,

I am trying to coregister some PET maps with their relative high resolution MEMPRAGE files. I was thinking that bbregister might be my best option but the results are still not satisfactory, likely due to the intrinsic features of my radioligand (the resulting maps are quite 'noisy' in terms of anatomical details). Do you have any suggestions on how to improve the results of bbregister (e.g., flags to use, or preprocessing steps prior to running bbregister)?

-the PET map for one subject is here: /autofs/space/katahdin_005/users/marco/PBR28/data/PBR_CLBP001/PET/PBR_CLBP001_average8-28_BET_hdrOK.nii -my SUBJECTS_DIR is here /autofs/space/katahdin_005/users/marco/PBR28/data/

• The command I ran is: bbregister --init-fsl --mov

PBR_CLBP001_average8-28_BET_hdrOK.nii --t2 --s PBR_CLBP001 --reg PET2brain.BB.reg --o PET2brain.BB.nii

Thanks!

Marco

---

Marco L. Loggia, PhD Postdoctoral Fellow Massachusetts General Hospital Brigham and Women's Hospital Harvard Medical School

149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer