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>> 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
>     >
>     >
>     >
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