Hi Allison and Nick, Thanks for the info. The wiki didn't mention that either freeview or scuba (dev only) would be available in the current release.
I tried both scuba and freeview and I'm wondering if there is some easy way to browse through the slices from either the sagital, coronal or axial view. Using scuba I could enter the RAS or index coords or is there something else I'm missing? In freeview I think I have to switch between the navigation tool and voxel edit tool or is there another way? At first glance freeview does appeal more to me in terms of simply erasing some voxels, so I think I will stick with it. Thanks in advance, Regards, Falk -----Original Message----- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Tuesday, May 19, 2009 5:38 PM To: Nick Schmansky Cc: Falk Lüsebrink Subject: RE: [Freesurfer] mri_fill Falk, I can help you get started with scuba or freeview. For freeview, you type: freeview -v volume.mgz and it will load your volume. There is a help guide in there to take you through all the tools. Let me know if you need any help. Allison -- On Tue, 19 May 2009, Nick Schmansky wrote: > Falk, > > There are two tools included with freesurfer that can be used to perform > edits on hi-res data: scuba, and freeview. I do not have experience > with either. tkmedit is not setup to edit hi-res data, as it resamples > to 1mm^3. > > Nick > > On Tue, 2009-05-19 at 11:46 +0200, Falk Lüsebrink wrote: >> 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 Iÿÿm told to check the filled volume as the >>> cerebellum may be included. It is and also the brainstem. But >>> actually I donÿÿt 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 >> _______________________________________________ >> 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
