Hi Helen, it is not aligned. You will need to apply the registration with mri_vol2vol or use the --o option to output a volume. I did not follow how you are trying to incorporate this into the SPM pipeline. Also note that if you are using SPM8, make sure to added --spm-nii or else you will get LR reversals. doug
On 02/28/2013 04:24 PM, Chen, Xiaoyan wrote: > Dear freesurfer experts, > I have a question regarding how to > incorporating bbregister coregistered mean image into the SPM batch. > > After realignment step, I convert the mean functional image from the analyze > format to nii format (to avoid flipping brain using bbregister) > > Then, I use bbregister to co-register the mean functional image to subjects' > surfaces using following command > > > bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold > --reg register.dat -- spm-nii > > > After this step, is the mean.nii the coregistered image already? If it is, in > SPM, shall I skip the coregistration and segmentation step? If I do skip > them, in the Normalization step, is the following correct? > > source image: mean.nii that has been coregistered in bbregister > > image to write: (Dependency) realigned session1 and realigned session2 > > template image: EPI > > > Thank you very much for your help. > > > > Helen > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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.
