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.
