Hi Bruce, I just noticed this reply. Looks like you came to save the day!
I am using a Mac OSX - Snow Leopard 10.6.8 (2 x 3 GHz Quad-Core Intel Xeon) Thanks, Vy On Mon, Apr 1, 2013 at 4:17 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Vy and Martin > > there was a bug in mri_mask that I just fixed that caused the > brain.finalsurfs.mgz to be empty when the brain.finalsurfs.manedit.mgz > existed. Vy: if you tell us what hardware/software platform you are using > we can get you an updated version. Not sure if this will fix your problem, > but it might. I also modified mris_make_surfaces in a way that could help > and you can try a new version of that if mri_mask doesn't fix things for > you > > cheers > Bruce > On Mon, 1 Apr 2013, Martin Reuter wrote: > > > > > Also: brain.finalsurfs.manedit is mainly for correcting situations where > the > > pial surface extends into the cerebellum. Did that happen in your case > > without editing? For other edits (e.g. pial including dura) you should > fix > > the brainmask.mgz . > > > > Best, Martin > > > > > > > > On 04/01/2013 04:39 PM, Martin Reuter wrote: > > Hi Vy, > > > > not sure what it going on in your data. Surfaces are copied from > > the base and if they are not accurate there you need to fix it > > there. It seems you did that and you worked the edits in the > > right order. > > > > What exactly happened? You fixed cross and base and everything > > look fine. When you run long it looks fine, but when you edit > > long and run it again it messes up? > > > > Did you edit only the brain.finalsurfs or also other things at > > the same time? Also, if you edited long, these edits will be > > kept and not replaced with new edits from base or cross. So if > > cross or base get edited it may be good to rename or remove the > > edit file in the long and run long without edits again. This way > > the cross and base edits get transferred to long automatically. > > Only if that is not sufficient you need to do edits in the long. > > > > Sorry I cannot say more right now without knowing what you did. > > > > Best, Martin > > > > > > > > On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh > > <vy_d...@rush.edu> wrote: > > BTW, we are using Freesurfer 5.1: > > freesurfer-i686-apple-darwin9.8.0-stable5-20110525 > > > > On Fri, Mar 29, 2013 at 10:08 AM, Vy > > Dinh <vy_d...@rush.edu> wrote: > > Dear Developers, > > I have a significant problem when rerunning the pial > > edits for the longitudinal data. Our dataset > > consists of subjects & a followup scan (for each > > sub). To be thorough, we edited > > brain.finalsurfs.manedit.mgz (as it was further in > > the processing stream) for the cross-sectional > > scans, the base scans, and the longitudinal scans. > > The longitudinal data were created only after the > > base has been edited and rerun. Likewise, the base > > was only created and rerun after the > > cross-sectionals were finalized. > > > > We work with a clinical population so minor edits do > > show up on the longitudinal scans. However, after > > editing and recreating the surfaces from these > > longitudinal scans, the pial surfaces has extended > > to include dura & other voxels that were not > > previously included within the pial surface (during > > the initial creation of the longitudinal data). We > > tried both commands (listed below) and get this same > > problem: > > > > recon-all -autorecon2-pial -autorecon3 -long tpN > > tp_base > > (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) > > or recon-all -autorecon3-pial -long tpN tp_base ( > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) > > > > Could you please help us figure out why the pial > > surface extends to include nonbrain regions when > > recreating the surfaces? > > > > What solutions would you suggest in resolving this > > problem? > > > > Thank you, > > > > Vy Dinh > > Research Associate > > Department of Neurological Sciences > > Rush University Medical Center > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > 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. 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. >
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