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. > <dgr...@mgh.harvard.edu <mailto:dgr...@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> > > 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
