Is this perhaps the same issue that I reported in this thread?: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38258.html
If so, it is due to a "bug" of sort in the recon-all in v5.3 It appears that some of our followup conversation occurred off list, so for others benefit, I'm pasting in the key exchange below (and to remind Bruce): --- from Bruce --- ok, I see what's going on. Here is the sequence of calls: 1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs L408_base lh Makes the white surface *without* using the aparc. Because there are a string of "hypointensity" labels in the aseg, the white surface is frozen in these locations. 2. mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base lh internally recreates the white surface but doesn't save it. The frozen vertices are allowed to move since the aparc *is* used in this call, and the vertices are deemed to be in real cortical regions. The pial surface then starts from the (inwards deformed but not written to disk) white surface, and then settles inside the white surface that is on disk. I'm not sure how we settled on this logic. Why recreate the white surface? Why not run with -nowhite -orig_pial white? That way the algorithm uses the white surface that the user can see and things should be consistent Bruce -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu On 4/24/15 7:42 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: no, I don't think it would. If you upload a case with crossing surfaces I'll take a look cheers Bruce On Fri, 24 Apr 2015, Clara Kuehn wrote: > Dear Bruce, > thanks for the reply. I often have the case that the aseg.mgz is already >correct, however the surfaces cross because the aparc+aseg.mgz >incorrectly classified the hemispheres. If running autorecon2-cp uses the >aseg.mgz, which is already correct, would that make any changes to the >aparc+aseg.mgz? > > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Gesendet: Freitag, 24. April 2015 03:12:55 > Betreff: Re: [Freesurfer] crossing medial surfaces > > I don't think you want noaseg. Why not try autorecon2-cp so it starts > after the aseg but uses it? > > cheers > Bruce > On Thu, 23 Apr 2015, Clara Kuehn wrote: > >> Hi Paul, >> >> thanks for your reply. I think the problem is that after editing the >>aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the >>aparc+aseg.mgz, so the surfaces still cross. >> >> Cheers, Clara >> >> ----- Ursprüngliche Mail ----- >> Von: silve...@gmx.com >> An: freesurfer@nmr.mgh.harvard.edu >> Gesendet: Donnerstag, 23. April 2015 03:24:51 >> Betreff: Re: [Freesurfer] crossing medial surfaces >> >> Hi Clara, >> The method for dealing with the crossing medial surfaces that works for >>me is decribed in the email below. Though, I'm not sure if there are any >>issues or concerns with this approach particularly in regard to >>thickness or the segmentations. >> Paul >> Sent: Tuesday, October 22, 2013 at 9:49 AM >> From: "silve...@gmx.com" <silve...@gmx.com> >> To: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] medial wall crossing the surface: repost >> Thanks Bruce for your response, I'll fix aseg where it is incorrect, >>but what about the instances where the aseg is correct and the pial >>surfaces cross? Other than needing to update aseg.stats, are there any >>other concerns with the 'hemisphere' approach I described below? >> >> Thanks again, >> Paul >> >> >> >>> ----- Original Message ----- >>> From: Bruce Fischl >>> Sent: 10/22/13 09:46 AM >>> To: silve...@gmx.com >>> Subject: Re: [Freesurfer] medial wall crossing the surface: repost >>> >>> Try fixing the aseg and rerunning >>> Cheers >>> Bruce >>> >>>> On Oct 21, 2013, at 6:23 PM, "silve...@gmx.com" <silve...@gmx.com> >>>>wrote: >>>> >>>> Not always, but yes, in some instances the aseg crosses. >>>> >>>> >>>>> ----- Original Message ----- >>>>> From: Bruce Fischl >>>>> Sent: 10/18/13 01:22 PM >>>>> To: silve...@gmx.com >>>>> Subject: Re: [Freesurfer] medial wall crossing the surface >>>>> >>>>> Does the aseg cross as well? >>>>> >>>>> >>>>> >>>>>> On Oct 17, 2013, at 10:07 PM, "silve...@gmx.com" <silve...@gmx.com> >>>>>>wrote: >>>>>> >>>>>> Dear All, >>>>>> >>>>>> I too am seeing the medial pial surfaces crossing hemispheres in >>>>>>some subjects. >>>>>> >>>>>> The approach that appears to be working for me involves making >>>>>>copies of brainmask.mgz and aseg.mgz >>>>>> For the left hemisphere crossing into the right, edit brainmask.mgz >>>>>>and aseg.mgz to delete voxels at the crossing belonging to the right >>>>>>hemisphere. >>>>>> I then run recon-all -autorecon-pial -hemi lh -subjid subject >>>>>> followed by returning the brainmask.mgz and aseg.mgz back to their >>>>>>original copy. >>>>>> >>>>>> This is similarly repeated for the right hemisphere crossing into >>>>>>the left. >>>>>> >>>>>> Are there any issues or concerns with this approach particularly in >>>>>>regard to thickness or the segmentations? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Paul >>>>>> _______________________________________________ >>>>>> 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. >>>> >>>> >> >> >> _______________________________________________ >> 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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
