I think it may be the sagittal sinus that is labelled as grey matter. Best wishes Kasper
2015-05-04 14:26 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Sarah > > it's really hard to tell what's going on from a single slice. If you upload > the data and send us the specific coordinates you are talking about we will > take a look > > cheers > Bruce > > > On Mon, 4 May > 2015, Sarah Hirsiger wrote: > > > Dear FreeSurfer experts, > > > > > > > > I encounter some erroneous cortical surface models when running > recon-all with these additional flags: -talairach -nuintensitycor-3T > > > > (see picture 1) > > > > > > > > > > I thought this could be due to an unclean skull-stripping (such as the > residual skull parts maybe disturbing the segmentation). > > > > Thus, I used the command gcut to get a cleaner brain mask. > > > > However, running the following commands: > > > > > > > > > > recon-all -motioncor -talairach -nuintensitycor-3T -s subject > > > > recon-all -normalization -s subject > > > > recon-all -skullstrip -clean-bm -gcut -s subject > > > > recon-all -autorecon2 -autorecon3 -s subject > > > > > > > > did not really improve the cortical surface model (picture 2) > > > > > > > > > > > > > > > > Has anyone encountered similar difficulties? > > > > > > > > I really appreciate your help! > > > > > > > > Best wishes > > > > Sarah > > > > > > Ps: I run the recon-all command on Mac OS X Yosemite version 10.10.2 > using the FS version 5.3.0 > > > > > > > > *************************** > > > > Dr. phil. Sarah Hirsiger > > > > Experimental and Clinical Pharmacopsychology Group > > Department Psychiatry, Psychotherapy and Psychosomatics > > Psychiatric Hospital, University Zurich > > Lenggstrasse 31 > > 8032 Zurich, Switzerland > > > > Ph: +41 44 384 24 06 <tel:%2B41%2044%20384%2024%2006> > > Fax: +41 44 384 33 96 <tel:%2B41%2044%20384%2033%2096> > > sarah.hirsi...@bli.uzh.ch <mailto:sarah.hirsi...@bli.uzh.ch> > > > http://www.dppp.uzh.ch/research/psychiatric/neuropsychopharma/experimental.html > < > http://www.dppp.uzh.ch/research/psychiatric/neuropsychopharma/experimental.html > > > > > > > > > > > _______________________________________________ > 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. > > -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk
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