External Email - Use Caution Hi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ? Best, Matthieu 2018-09-18 15:56 GMT+00:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Matthieu > > yes, you will want to run all of your subjects with it > > cheers > Bruce > On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: > > >> External Email - Use Caution >> >> Dear Bram, >> >> It looks like the -bigventricles flag fixed my problem with my specific >> subject. Not only, this took >> into account large ventricles but also corrected grey matter segmentation >> from extra Dura tissue >> that was erroneously segmented in GM. >> >> I understand the first point of amelioration allowed by the flag but >> don't understand where the >> second point come from ? >> >> If I used the -bigventricles flag for all my atrophied and large >> ventricles patients and not for my >> healthy patients, wouldn't it introduce a bias when further statistically >> comparing groups between >> them ? >> >> Best, >> Matthieu >> >> 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <brdiam...@mgh.harvard.edu >> >: >> 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. 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 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. >> >> >> >> > _______________________________________________ > 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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