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. < dgr...@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. > > <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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
