Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-22 Thread Douglas Greve
...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: Monday, August 20, 2012 2:18 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz >> >> Hi Cyrus, my apolo

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-22 Thread Sarosh, Cyrus
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 21, 2012 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Run it with -autorecon3 doug On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote: > Doug, > > Thank

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-21 Thread Douglas N Greve
I need to edit a different file or was my >> command line incorrect? >> >> Thanks, >> >> Cyrus >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >>

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-21 Thread Sarosh, Cyrus
...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-20 Thread Douglas N Greve
mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, August 14, 2012 1:43 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz > > > For GM volume and thickness, you will certainly want to fix it.

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-20 Thread Sarosh, Cyrus
Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 1:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-14 Thread Douglas N Greve
surfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, August 14, 2012 11:28 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz > > > Depending upon how bad it is and what you are going to do with it, it may be &g

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-14 Thread Sarosh, Cyrus
@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: > D

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-14 Thread Douglas N Greve
; -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, August 13, 2012 4:13 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz &

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-14 Thread Sarosh, Cyrus
de it appear. Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 13, 2012 4:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus,

Re: [Freesurfer] Edits to aparc+aseg.mgz

2012-08-13 Thread Douglas N Greve
Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the surface-based method will exclude the dura in these situations. Are the surfaces accurate or are they including dura as well? BTW, you should not be editing the aparc+aseg.mgz. d