Good point, I will do that! But so far when I looked, the L-R flip did not happen.
Thank you!
Aga
Aga Burzynska
Max Planck Institute for Human Development
Neurocognition of Decision Making
Lentzeallee 94
14195 Berlin
Ph: + 49 30 82406 335
-----Ursprüngliche Nachricht-----
Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
Gesendet: Mi 2011-02-09 17:11
An: Burzynska, Aga
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: AW: [Freesurfer] reg-feat2anat: a problem!
Yea, though I might just go to 179 to make sure there's not a flip.
doug
Burzynska, Aga wrote:
>
> 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:greve@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" <greve@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
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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