Hi Aga, are you using nifti? If analyze, that could be the problem. Do your functionals and anatomicals have a different sign to their determinants (you can check with mri_info). In principle, reg-feat2anat should handle this but in some cases it does not. The 5.1 version will handle it properly. If they do have the same sign, then look through the log file and find the flirt command. Run that command by itself (you may need to run reg-feat2anat with --nocleanup to keep it from deleting the files). If that fails, then contact the FSL people
doug Agnieszka Burzynska wrote: > Dear all, > I am using the command reg-feat2anat to transform functional data > pre-processed in FSL to the anatomical image in Freesurfer. > > As suggested, I check the registration with reg-feat2anat --feat > run2.feat —manual. > > I have 3 runs of functional data for each subject. Surprisingly, some > runs are registered well but others not (even of the same subject, so > using the same reference anatomical images: see the attached image. > Upper row: bad registration of one run and lower row: good > registration of another run). > > I have no problem to manually correct the registrations, it works > well, but as I have many subjects, I wonder if there may be a way to > change some options of reg-feat2anat to make it work better? Can you > see from the attached image what is the problem with my images? (I > viewed the functional and anatomical data of a few subjects, some woth > good and some with bad registration and see no difference or flip) > > Thanks a lot for your help! > Aga > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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.
