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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 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.
> <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
>     >
>     >
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