External Email - Use Caution Ok I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ? Best, Matthieu Le mar. 18 sept. 2018 à 18:03, Bruce Fischl <fis...@nmr.mgh.harvard.edu> a écrit : > I think it should be ok. It will be a bit slower, but shouldn't reduce > accuracy I don't think. Try it and see > Bruce > On Tue, 18 Sep 2018, Matthieu > Vanhoutte wrote: > > > > > 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 . 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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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