Hi Marie hmmm, it's hard to see without seeing why it is happening. Maybe you can attach some images? Alternatively you can upload a subject dir and give us the coordinates of the regions that are not as accurate as you would wish, and we will take a look.
cheers Bruce On Wed, 7 Mar 2018, Marie Sigmund wrote: > > Hello FreeSurfer Developers, > > I am trouble-shooting some FreeSurfer Data and there are two errors which > occur frequently. > > 1. The pial surface does not include all of the graymatter. I read that you > should in this case corr > ect the WM so it adjusts the GM automatically. I tried this out a couple of > times and there is still > some GM left over which is not included. > > 2. Gyri or sulci are sometimes labeled as wm-hypointensities. I thought about > correcting it on the a > seg.presurf volume (on the website it is stated that using a FreeSurfer > version of 6.0 or higher you > should make corrections to the ASEG there). The problem is that on this > volume the segmentation is > different to the final one and not necessarily wrong. > > I've searched the list and no similar errors have been reported. Does anyone > have any thoughts on ho > w to trouble-shoot this one? Thanks a lot! > > 1) FreeSurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > 2) uname -a: Linux R0223 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 > 17:43:14 UTC 2015 x86_6 > 4 x86_64 x86_64 GNU/Linux > > _______________________________________________ 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.