The registration actually goes from anat to func. mri_label2vol knows this. In any case, it is just a matrix that can easily be inverted.
On 4/18/19 11:58 AM, Sam W. wrote: > > External Email - Use Caution > > Hi Doug, > Thanks! After registering with bbregister -mov example_func.nii (to > get reg.dat), I tried > mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o > aseg-in-func.nii --temp example_func.nii > the result looks good, but I'm wondering why it worked. The reg.dat > specifies the conversion from func to orig doesn't it? And the > mri_label2vol command above does the registration from seg to > example_func, which is the opposite direction to what reg.dat encodes. > Could you clarify that to me please? > Best regards, > Sam > > > On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > If you want to transfer a segmentation, then it is better to use > mri_label2vol with the --seg option. Run it with --help to get > examples. > Probably even better is to transfer your functional to anatomical > space > (mri_vol2vol) so that it is in registration with the anatomical; > transferring it to anat space handles partial voluming better. > > On 4/16/19 8:21 PM, Sam W. wrote: > > > > External Email - Use Caution > > > > Hi, > > > > I just finished reconall and now I'd like to convert the > aseg.mgz to > > native functional space. > > My first thought was to simply convert the aseg.mgz to native > > functional space with mri_vol2vol: > > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz > --o > > aseg-in-rawavg.nii --regheader > > Is this a valid procedure to convert the aseg to functional space? > > I think the recommended way is to register the example_func to > > anatomical first: > > bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat > > and then use mri_vol2vol with the --inv flag > > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz > --o > > aseg-in-rawavg.nii --regheader --inv > > But I'm not sure... Could someone confirm which of the above (or > > maybe none of them) is correct? > > > > Best regards, > > Sam > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
