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
>     >     >
>     >     >
>     >     >
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