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 [fis...@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 [fis...@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 >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
