Thanks Doug! Will try the --init-fsl or --init-spm for bbregister. -Liang On Wed, Dec 10, 2014 at 10:50 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote:
> > 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 >
_______________________________________________ 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.
