Hi Las can you send us a couple of images of the problems you are seeing?
cheers Bruce On Mon, 7 Jul 2014, Las Blawimo wrote: > Dear FreeSurfer Experts, > > > We are collecting a 0.9mm isotropic FSPGR sequence on a GE MR750 3T scanner. > We're observing, in many subjects, a problem mentioned in previous posts to > the list where the pial surface does not follow the cortex properly in the > anterior temporal lobe region (and also in some frontal regions). The white > matter surface generally looks very good. This is with the default options > from recon-all in v5.3. > > We've also tried running the following options, based on previous posts > (expert options) and the release notes for version 5.2: > > -norm2-b 20 -norm2-n 5 > > and > > -norm2-b 20 -norm2-n 5 -3T > > In general, there is a modest improvement in the medial temporal lobe pial > surface in most subjects. A substantial/desired improvement is observed in > only a few subjects. In general, there was no detrimental effect to either > the white matter or pial surface when using these flags. > > Based on older posts to the list, we've also tried using the following > flags: > > -mprage > > and > > -washu_mprage > > The improvement to the pial surface is much more substantial in almost all > subjects, to some extent with the -mprage flag, mostly with the > -washu_mprage flag. However, this dramatic improvement in pial surface > accuracy was accompanied by many major issues with the white surface in > widespread areas across the brain. Also, some subjects fail to reconstruct > fully due to large defects in the surfaces with this option in place (also > something I've read about happening to people using the -washu otpion on the > list). > > A few questions: > > Would you suggest we also try the options "-norm1-b" and "-norm1-n" in > addition to the norm2 options? If so, any suggested starting values to try? > > Alternatively, would it be sensible to try to use the white surface from the > default pipeline and combine it with (or perhaps initialize) the pial > surface from the -washu_mprage flag? > > Do you have other suggestions for us to try? > > Thank you for your time and help! > > Sincerely, > > Las > > _______________________________________________ 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.
