Hi Bruce,
Thank you very much for your mail. I am going to specify my question. In fact, we saw a problem after the recon-all step. The dura was included in the lh.pial and rh.pial. Indeed, the red demarcation included the meninges. I send you an attachment Cheers Marine 2017-06-21 18:51 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Marine > > the brainmask is just a rough estimate of what is brain and what is not. > You don't need to worry if it is not accurate *unless* the lh.pial and/or > rh.pial surfaces end up not being accurate because of dura left in the > brainmask. > > cheers > Bruce > > On Wed, 21 Jun 2017, Lisa Delalande wrote: > > >> Hi, >> >> >> >> I am a PhD student and faced a problem with Freesurfer, more specially >> with >> segmentation. First of all, I did a typical qsub command. However, when I >> cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are >> often considered as grey matter. >> >> I tried these different commands : >> >> >> 1.) setenv SUBJECTS_DIR /path/to/your/data >> >> setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50' >> >> recon-all -multistrip -clean-bm -s <subjid> -no-isrunning >> >> >> 2.) recon-all -skullstrip -clean-bm -gcut -subjid <subjid> >> >> cd $SUBJECTS_DIR/yoursubj/mri/transforms >> >> cp talairach_with_skull.lta bak >> >> cp talairach_with_skull_2.lta talairach_with_skull.lta >> >> recon-all -s yoursubj -skullstrip -clean-bm -clean-lta" >> >> >> >> without success I finally used a manual method : >> >> >> >> 3.) tkmedit skullstrip3_before brainmask.mgz -aux T1.mgz >> >> >> >> but the latter is source of error and time-consuming. I've got 105 MRI >> scans >> to rectify. Do you have a council to improve le first step of the >> reconn-all >> ? >> >> >> Sincerely >> Marine Moyon >> >> >> > _______________________________________________ > 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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