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. < DGREVE@mgh.harvard.edu> 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 CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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