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 > ma...@nmr.mgh.harvard.edu <mailto:ma...@nmr.mgh.harvard.edu> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
