Dear Martin and FreeSurfer experts, Thanks for your response.
I have just finished re-running some subjects from scratch in 5.3 and it appears that the edits from brain.finalsurfs.manedit.mgz are not being applied to the longitudinal subject directories. Just to clarify, I have been doing ALL of the pial surface edits in the brain.finalsurfs.manedit.mgz, not just the pial surface edits that have extended into the cerebellum. The rationale for doing this is mainly continuity, as the previous research assistant made all pial surface edits in this way because of a response she had received from the FS forum saying that there shouldn't be any problem with performing all the pial surface edits in the brain.finalsurfs.manedit.mgz file. Is there something in the FreeSurfer longitudinal processing code that would treat edits near the cerebellum of the brain.finalsurfs.manedit.mgz file differently from those made in other parts of the brain (e.g. lateralorbitofrontal, dura, etc.,)? Can you think of anything else that would be causing this or anything that I could try to get the longitudinal processing stream to incorporate the edits from the brain.finalsurfs.manedit.mgz file? Thanks for your help! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> Begin forwarded message: From: Martin Reuter <mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Date: May 2, 2014 4:20:17 PM CDT To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits) and then in the long, the surface looks not good? Edits should automatically be copied from cross->long (if the manedit file exist). Surfaces are taken from the base to initialize longitudinal processing. That is why both step1 and step2 above are important. Step3 is a good idea to make sure that the longs are not polluted by some earlier edits. For example edits from cross are only copied over if the long has no manedit file, else only the edits in the long will be used. (I think this also answers some of the questions in the archive mail 1 you cite below, the archive mail 2 is a question about cross sectional processing, but I think there the problem is that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so edits probably get overwritten). I also have the feeling that we fixed something about the editing in longitudinal processing after 5.1, but cannot find it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu<mailto:reu...@mit.edu> Web : http://reuter.mit.edu<http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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