External Email - Use Caution Dear Bram,
Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag. Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and statistics and not have an impact on surfaces computed ? Best, Matthieu Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder < brdiam...@mgh.harvard.edu> a écrit : > If you haven't already, you may want to run the subject through recon-all > with the -bigventricles flag since it looks like the lateral ventricle was > significantly mislabeled in the aseg. If using the -bigventricles flag > doesn't fix your problem, you can edit the aseg.mgz manually by following > the directions in this tutorial > <https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations>. > Then run the following command (again, substituting <subj_id> for your > subject's id): > > recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id> > > I would try this before doing the wm.mgz edits I suggested in my previous > email. > > Best, > Bram > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder < > brdiam...@mgh.harvard.edu> > *Sent:* Friday, September 14, 2018 11:07:42 AM > *To:* matthieuvanhou...@gmail.com > *Cc:* freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Troubles to determine the type of recon editing > needed > > > Hi Matthieu, > > > I've taken a look through the files you shared with us and I see the poor > surfaces in the posterior right hemisphere you were referring to in your > message. It looks like your subject has a combination of abnormally large > ventricles and significant wm abnormalities, so I'm surprised FreeSurfer > did as well as it did. > > > As for the recon editing - I would recommend editing the wm.mgz to more > accurately represent the wm from slice 84 to 39. You can take a look at the > white > matter edits tutorial > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0> > for details on how to do that. Then run the following command (substituting > <subj_id> for your subject's id): > > > recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> > > > The surface reconstruction may also benefit from labeling the right > lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not > certain since you didn't send us the surfaces for the left hemisphere. > Before you do that, edit the wm.mgz as explained in the tutorial and tell > us how that goes. > > > All the best, > > Bram > > > *Bram R. Diamond, BSc* > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > 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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