As mentioned in the first email somehow tkmedit seems to skip some slices if one tries to edit them manually and the resolution of the volume is not 1mm^3. Attached is a screenshot of the filled.mgz which I tried to edit on the left from the coronal view and on the right from the sagittal view.
The resolution of the volume used in this case is 0.6mm. If I use the "Slice" thing to browse through the slices nearly every second slice is skipped. Increasing or decreasing the volume index by 1 in the direction I would like to move on doesn't work either. For example if I change the volume index from 162 338 124 to 163 338 124 the same slice is being shown. 161 338 124 and 164 338 124 are different as it should be, but it is not possible to view 163 and so it is impossible to edit this slice. Are there any other tools available to edit volumes like tkmedit does? It doesn't need to be included within FreeSurfer but it would be better if it could handle the .mgz format. Regards, Falk -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Falk Lüsebrink Sent: Monday, May 18, 2009 2:36 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_fill Hi Bruce, Actually I need to skip the whole aseg process as this is incompatible to the high resolution volumes I'm using. I read that prior to the aseg files the talairach transform was used to delete the cerebellum and that the cutting planes correctly. Is it possible to use this again? I also tried using seed points, though the cerebellum was never erased. Regards, Falk -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 18, 2009 2:07 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_fill p.s. you can pick seed points in the callosum and pons in tkmedit and see if that fixes your problem, but if there is something else going on then it may not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink wrote: > Hi FreeSurfers, > > > > At the end of mri_fill Im told to check the filled volume as the > cerebellum may be included. It is and also the brainstem. But > actually I dont know how to fix this. Do I need to include the seed > points for cc and pons for better cutting planes? Do I need to manually edit the volume? > > > > If the latter is better are there any other tools available besides tkmedit? > If I try to add or delete voxels of a high resolution volume tkmedit > seems to skin every second slice. > > > > Regards, > > Falk > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<<attachment: filled.JPG>>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
