Converting that matrix will not be easy. If you want to try, look at our wiki page on coordinate systems and see how your coordinate systems match up. It won't be easy. Your bbregister command is not going to work for sure, you cannot use --init-header (which should only be used for two MRIs acquired in the same session). Try --init-fsl or --init-spm. Most PET tracers have an effective T2 weighting
On 12/08/2014 04:52 PM, Liang Wang wrote: > Hi Bruce, > Thanks a lot for the suggestions! Here are some followup questions. > 1) The functional volume was PET data and anatomical data have been > processed with Freesurfer. I run the bbregister as: > bbregister --mov PET.nii --s subject_name --reg register.dat --t1 > --init-header > It does not register the PET to anatomical images well. Since PET > contrast does not like the typical t1/t2, I am not sure how to set the > "--contrast" argument (already tried to both t1 and t2). Also, as PET > and anatomical are both in native space, not sure how to set the "--init-" > 2) Actually, the PET image has been aligned with orig.mgz well (in the > native space) using a in-house method. The registration matrix likes > below: > 0.992629 0.109294 0.052358 10.4812 > -0.102034 0.986829 -0.125525 16.5118 > -0.065387 0.119257 0.990708 -23.4735 > 0.000000 0.000000 0.000000 1.0000 > I wonder if there is a way that can convert this matrix to a readable > format for "mri_vol2surf". > 3) I tried to run mri_vol2surf (using a --regheader option as pet.nii > and orig.mgz already aligning well) as: > mri_vol2surf --mov PET.nii --hemi lh --regheader subject_name --o > lh.pet.mgh. But the results does not look right. > Any suggestions for these questions would be very appreciated! > > -Liang > > On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > Hi Liang > > try bbregister. > > cheers > Bruce > > On Fri, 5 Dec 2014, Liang Wang wrote: > > Hi Experts, > > At subject level, I want to convert a functional volume (in a > subject's > native space) to this subject's native surface. The functional > volume has > been registered to this subject T1 images in native space. I know > "mri_vol2surf' would do the job but unsure how to generate > the registration > matrix for --reg option. I appreciate any suggestions. > > Thanks > -Liang > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
