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> 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 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

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 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
>
>
> _______________________________________________
> 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