Hi Matt, yes, the filling procedure has evolved and is better in current versions than previous ones.
cheers, Bruce On Fri, 13 Nov 2009, Matt Clarkson wrote: > Hi Bruce, > > I agree with your point, however this method was instigated by a previous > person at our institution, so I'm looking at it afresh. Also, the addition > of regions 4, 43, 5 and 44 does do "something". I agree though that when I > look at wm.mgz using tkmedit on a vanilla FreeSurfer run, it appears that the > white matter is a grey colour, and that the vents have been filled with white > (colour 255). > > So, is it possible that a previous version of FreeSurfer did not by default > try and fill the vents in, and now version 4.5 does by default attempt to > fill the vents in? > > Cheers > > Matt > > > ----- Original Message ----- > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "Matt Clarkson" <clark...@drc.ion.ucl.ac.uk> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, November 13, 2009 2:25:16 PM GMT +00:00 GMT Britain, Ireland, > Portugal > Subject: Re: [Freesurfer] Filling Big Ventricles > > Hi Matt, > > the -bigventricles stuff is something I messed with for a while, but didn't > get to work robustly and haven't gotten back to it. I'm not sure I > understand your fix though. If the aseg properly labels the ventricles, > then they should be filled in the wm.mgz, and if the aseg doesn't, then > your fix doesn't help. Do you manually correct before doing this? > > cheers, > Bruce > > > On Fri, 13 Nov 2009, Matt Clarkson wrote: > >> Hi there, >> >> we have various Alzheimer cases, where the FreeSurfer pipeline can >> occasionally struggle to correctly segment the ventricles, which results in >> white matter and pial surfaces "leaking" into the ventricles. >> >> I have tried using -bigventricles passed into the autorecon2 stage, but I >> can't tell if its doing much. I checked the log files, and you can see >> -bigventricles passed to several binaries such as mri_ca_register and >> mri_ca_label, so the flag is definitely being passed from the command line. >> >> Is the -bigventricles meant to be used in this way, and what should it be >> doing? >> >> Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, >> but I can't find the documentation to say what it does and if I should be >> using it. >> >> So, we have previously used a technique whereby we run freesurfer once then >> create a vents image like: >> mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 >> --o vents.mgz --binval 255 >> >> and then add this into the wm.mgz to fill some holes in. I have attached two >> .png files to illustrate the effect. In this example, I have chosen the >> slice where the surfaces just start to leak into the ventricles. So, on >> these snapshots, the problem looks quite small, but on other subsequent >> slices, you can get fairly large leakage into the ventricles. >> >> So, with these options, what would be the best way to cope with very >> abnormal ventricles? >> >> Many thanks in advance. >> >> Matt Clarkson >> >> Senior Research Associate >> Dementia Research Centre >> UCL >> Institute Of Neurology >> Queen Square >> London WC1N 3BG >> >> m.clark...@ucl.ac.uk >> Tel: 08451 555 000 ext. 723653 >> Fax: 020 7676 2066 >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
