External Email - Use Caution Thanks again Doug, that makes sense. I was aware that the matrix could be inverted but I thought we would need --inv for that. Does mri_label2vol also convert label-to-temp when --label is used, or is this specific to seg-to-temp conversion? I'm asking because I also created labels with mri_annotation2label and tried to convert them to functional space with this command: mri_label2vol --label labels/lh.precuneus.label --reg reg.dat --subject s01 --o label-in-func.nii --temp example_func.nii --fill-ribbon --hemi lh # reg.dat comes from bbregister -mov example_func.nii but this did not work. The label-in-func.nii kept the voxel size and orientation of the orig.mgz. Do you have any idea what I'm doing wrong? Best regards, Sam
On Thu, Apr 18, 2019 at 6:13 PM Greve, Douglas N.,Ph.D. < [email protected]> wrote: > 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. > > <[email protected] <mailto:[email protected]>> 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 > > > [email protected] > > <mailto:[email protected]> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] <mailto: > [email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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