Hi Tanja, yes, 3T will have more dielectric/RF penetration inhomogeneity than 1.5T. There was also a change to recon-all that caused the control points to be applied to the subcortical normalize as well as cortical (previously it was just cortical) that a number of people have now reported messes things up, so we are going to back it out. We will distribute a new recon-all that reverts to the previous behavior sometime soon (right Nick?).
sorry for the problems. Bruce On Thu, 8 Mar 2012, Tetiana Dadakova wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
