Re: [Freesurfer] Project functional region into white matter

External Email - Use Caution

Would it be best to do option 1 in the CVS space or in subject space?

On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

Yes. The 2nd would dilate in all dimensions, but you would only keep those voxels that were in WM. but the 1st is definitely cleaner

On 12/18/19 2:52 PM, Corinna Bauer wrote:

...

    External Email - Use Caution

Ok thanks! The first option sounds like it might provide a cleaner result, since the second would dilate in all dimensions. I'll let you know if I run into any trouble with it.

Thanks again,

Corinna

On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

off the top of my head I can think of a couple of ways
1. replicate the wmparc.mgz stream. For this you will need to
create an
annotation from your GM ROIs by combining them into a
ssegmenation, then
using mri_vol2surf to create a surface-based segmentation, then using
mris_seg2annot, then use mri_aparc2aseg to create an
aparc+aseg.mgz type
file, then mri_aparc2aseg again to create the wmparc.mgz type
file. This
will take some trial an error as the command lines are a bit picky
(esp
mris_seg2annot)
2. simple dilation of the GM ROIs followed by taking an intersection
with the WM mask. You can use mri_binarize to create the WM mask,
then,
for each GM ROI, use mri_binarize with the --dilate option to
dilate a
few voxels, then something like fscalc wmmask.mgz and
roidilated.mgz -o
roidilated-in-wm.mgz


On 12/18/19 2:33 PM, Corinna Bauer wrote:
>
>         External Email - Use Caution
>
> Hi Doug,
> Yes, I have GM ROIs in CVS space and I'd like to create a
> corresponding WM ROI for each of them that extends 2-3 voxels
into the WM.
> Would it be possible to create something akin to wmparc.mgz with
these
> ROIs?
>
> Corinna
>
> On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
wrote:
>
>     Hi Corinna, if I understand correctly, you basically have
cortical GM
>     ROIs in CVS space and you want to create an ROI of the adjacent
>     WM. Is
>     that right? How far do you want to extend the ROI into WM?
Do you
>     want
>     to do something like a wmparc.mgz?
>     doug
>
>     On 12/18/19 9:55 AM, Corinna Bauer wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Hello all,
>     >
>     > I have a series of functionally-defined ROI volumes (.nii
>     format) that
>     > I'd like to project into the white matter to then be used for
>     > tractography.
>     >
>     > So far the vols have been brought from cvs_avg35 space
into subject
>     > space from using mri_vol2vol and the corresponding m3z file.
>     This was
>     > followed by mri_vol2vol using the registration from

bbregister

...

>     to get
>     > the functional regions into diffusion space.
>     >
>     > I have done this for the ROIs in their original GM volume,

but

...

>     would
>     > now like to also have corresponding WM volumes for
tractography.
>     >
>     > What is the best way to go about doing this?
>     >
>     > Thanks,
>     >
>     > Corinna
>     >
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto: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>
<mailto: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 <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