Dear Doug, The determinant sign is negative for both example_func and orig.mgz (-73.6 and -1, respecitively).
The files differed also in their format, type, vox2ras-fsl and orientation, but I guess it is ok. My feeling was that flirt is unable to fit the brain given the maximum angle of rotation 90, so I doubled this using: re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx I tried this on several subjects and the registration looks very good: I would not make it better manually. Can I assume it works now? Cheers, Aga -----Ursprüngliche Nachricht----- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Mo 2011-02-07 19:36 An: Burzynska, Aga Cc: 'freesurfer@nmr.mgh.harvard.edu' Betreff: Re: [Freesurfer] reg-feat2anat: a problem! That is not a problem. By "anatomical" I meant the FreeSurfer anatomical (eg, orig.mgz) doug Agnieszka Burzynska wrote: > Dear Doug, > Thank you a lot! > Our feat data is always nifti, but anatomical FSL data is sometimes in the > analyze format. Is this already a problem? > > I will now check the rest. > > Thank you, cheers, > Aga > > > On 2/7/11 4:35 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > > >> 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 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.
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