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, Thanks for the update

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

2012-08-22 Thread Douglas Greve
? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [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

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

2012-08-21 Thread Douglas N Greve
, 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 it, you would edit the dura from

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

2012-08-20 Thread Sarosh, Cyrus
] 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. 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

2012-08-20 Thread Douglas N Greve
, 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 it, you would edit the dura from

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

2012-08-14 Thread Sarosh, Cyrus
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

2012-08-14 Thread Douglas N Greve
-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, this may or may not be a problem. The cortical label

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: Doug

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

2012-08-14 Thread Douglas N Greve
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 a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all

[Freesurfer] Edits to aparc+aseg.mgz

2012-08-13 Thread Sarosh, Cyrus
Hello FreeSurfer Users, I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.html. Basically, pieces of the subarachnoid space/pia

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.