Thanks. It didn't quite work as I'm guessing the step sizes in original.mnc are negative, but I am able to reshape the minc file afterwards to get it exactly the same.
>From my (limited) understanding of mri_vol2vol, when you invoke it with the --regheader is it taking the ras to voxel transform as listed from mri_info aseg.mgz and then applying that to the image to get into the original.mnc space? thanks, mishkin On Dec 13, 2007 11:47 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: > Mishkin, > > try this: > > mri_vol2vol --mov aseg.mgz \ > --targ original.mnc \ > --o aseg-in-native.mnc \ > --regheader \ > --interp nearest > > Nick > > > On Thu, 2007-12-13 at 22:05 -0500, Mishkin Derakhshan wrote: > > Hi, > > I am having troubles getting the right options with mri_convert. > > > > I ran: > > recon-all -autorecon1 -i original.mnc -s subj1 > > recon-all -subcortseg -s subj1 > > > > I now want to convert aseg.mgz into aseg.mnc but in the same space and > > with the same orientation as my original.mnc file. > > > > My original.mnc file has the following attributes: > > double zspace ; > > zspace:comments = "Z increases from patient inferior to superior" ; > > zspace:step = -0.9765625 ; > > zspace:start = 127.418768256005 ; > > zspace:direction_cosines = -0.0275245718714001, > > -0.000514697647100001, 0.999620994692302 ; > > double yspace ; > > yspace:comments = "Y increases from patient posterior to anterior" ; > > yspace:step = -0.9765625 ; > > yspace:start = 146.850463958339 ; > > yspace:direction_cosines = -0.0186971433325, 0.999825193136882, > > -2.319984599e-08 ; > > double xspace ; > > xspace:comments = "X increases from patient left to right" ; > > xspace:step = 1.49999999999996 ; > > xspace:start = -95.4780255890689 ; > > xspace:direction_cosines = 0.999446254069973, 0.0186900576545041, > > 0.0275293837630133 ; > > short image(zspace, yspace, xspace) ; > > > > Any help would be much appreciated. > > thanks, > > mishkin > > _______________________________________________ > > 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
