Hello Bruce. Thank you for your reply. I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure.
Tanja. On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Tanja > > why is the wm too dark? Can you tell us something about your data > (population, coil, scanner, etc...)? > > cheers > Bruce > > On Wed, 28 Mar 2012, Tetiana Dadakova wrote: > >> Hi Louis, >> >> thank you very much for your reply. >> The problem with our data is that wm is too dark sometimes to use >> control points (intensity is too inhomogenious in some parts). That's >> why we would like to have the opportunity to just draw the wm where >> needed. But for some reason it doesn't correct the surfaces. >> >> Best wishes, >> Tanja. >> >> On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke >> <vi...@nmr.mgh.harvard.edu> wrote: >>> >>> Hi Tanja, >>> I would recommend you try using some control points. Place one or two >>> just >>> inside the wm surface near that wm finger which is not being included, >>> and >>> then possibly one or two control points carefully placed along the wm >>> finger >>> on voxels with the highest intensity (in the middle it looks like). Not >>> sure what the other coronal slices look like, but you may want to do >>> something similar on other slices. >>> -Louis >>> >>> >>> On Tue, 27 Mar 2012, Tetiana Dadakova wrote: >>> >>>> Dear FS list, >>>> >>>> After recon-all -all we had some wm missing in temporal part of the >>>> brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all >>>> -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. >>>> wm_missing2, but the surfaces still look as fig. wm_missing1. >>>> What can be the reason that wm.mgz edits didn't affect the surfaces? >>>> >>>> Thank you, >>>> Tanja. >>>> >>> >>> >>> 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
