Hi Ammar,

if you adjust control points you should be running autorecon2-cp not -wm.

cheers Bruce On Fri, 13 May 2011, Moiyadi, Ammar wrote:

Hi I attached the log file for this subject. I tried adjusting control points and performing autorecon2-wm in repeated iterations. It helped a little but I still am missing a large chunk of both gray and white temporal matter. I'm not sure how many iterations it will take to get a complete tracing but it doesn't seem to be helping as much as the initial few runs.

Ammar Moiyadi, BS Professional Research Assistant Psychiatry, School of Medicine 303-724-5490 ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 10, 2011 6:01 PM To: Moiyadi, Ammar Subject: RE: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points

can you send us the recon-all.log file for that subject? And make sure to cc the list on your replies so others can help!

Bruce On Tue, 10 May 2011, Moiyadi, Ammar wrote:

...

Hi Bruce - The image is of the brainmask.mgz file. I have attached another image showing the wm.mgz file - you're right, the wm regions where I placed the control groups is very dark if not absent. I still don't understand why the proper gray matter boundaries were not obtained however. I did run autorecon2-wm after adding the control points but I will run it again just in case.

Thanks for your help,

Ammar ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 10, 2011 2:34 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points

what image are you displaying in this png? If it is one of the brain*.mgz then your control points aren't working as the wm is still very dark where you place them. Did you run autorecon2-wm after putting the control points in?

On Tue, 10 May 2011, Moiyadi, Ammar wrote:

...

Dear Freesurfers,

Freesurfer's autorecon is having trouble tracing both gray and white matter boundaries in the temporal region of one of my subjects (even after I added control points for the white matter). I have attached a png screen shot of this abnormality and was wondering if anyone has any ideas to correct this since I have never seen such a large tracing error before.

Your input is much appreciated!

Ammar

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