Hi Bruce, For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and down can get it out of the minimum and make it work, so there might be a bug.
Peace, Matt. From: "Emil H.J. Nijhuis" <emil.nijh...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, May 9, 2014 at 4:53 AM To: <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images Dear Bruce, thank you for your help. attached I have put an fslview, tkmedit screen-shot of the T2 image and a tksurfer image of lh.woT2.pial. It appears that without consideration of the T2 this effect does not happen. What would be your recommendation if I would like to keep using the T2 weighted image? Yours, Emil Hi Emil how do the surfaces look before you apply the T2 deformation? And how do they look visualized over the T2 instead of the T1? cheers Bruce On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: > Hi, > > I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm > isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio > scanner with a 32-channel head coil. Unfortunately for half of my subjects I > receive an rather odd pial surface artefact, while the 'white' surfaces do > not suffer from the same issue. > > The command line I have used was: > > recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial > -3T > > Are you familiar with this issue and do you have some advice for me? > > Thank you very much for your help. > > Yours sincerely, > > Emil > > -- > ---------------------------------------------- > Emil H.J. Nijhuis, PhD > Researcher - Division of Diagnostic and Interventional Neuroradiology > University Hospital Basel > Petersgraben 4 > CH 4031 Basel Switzerland > > > _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi nfo/freesurfer _______________________________________________ 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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