Thank you, Sita, for your reply. 1. The skull strip was good, the cortex disappeared after we added cp. I removed control points and put new ones that are surely in wm, now re-running.
2. I have one more question: I did previous analysis with FS5.0 on 1.5T data with non-isotropic voxels. Now for FS5.1 we use 3T images with 1x1x1mm voxels. For previous analysis the error, when a part of occipital cortex is excluded, appeared in around 1 per 40 cases. Now with better data and newer version we have this problem in around 1 per 5 cases. The only idea I can think of is increased inhomogeniety in field due to increased static field of scanner. Can it be true? Can you suggest other possible reasons? Thank you, Tanja. On Wed, Mar 7, 2012 at 4:29 PM, Sita Kakunoori <s...@nmr.mgh.harvard.edu> wrote: > > Hi Tanja, > > Sorry if I missed something but was the cortex stripped off even > before you made any edits. If so, it's probably skull strip error. Please > refer to this wiki for instructions to correct the error. > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix > > But if part of the brain is missing only after you added control points > and ran -autorecon2-cp -autorecon3, then please check if any of the > control points were placed in GM or really close to GM. > > Sita. > > > > On Wed, 7 Mar 2012, Tetiana Dadakova wrote: > >> Dear FS list, >> >> We started using FS 5.1 and encountered a problem with control points. >> After first recon-all some of the cortex (in occipital part) was >> missing, so we added control points and re-ran -autorecon2-cp >> -atorecon3. >> After that, the part of the brain with control points was removed from >> brainmask.mgz (Fig1). >> >> I never had this problem in 5.0, therefore I assume that something has >> been changed in 5.1 regarding cp. Could you please suggest what can be >> the problem and if it is described somewhere? >> >> Thank you, >> Tanja. >> > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
