I think it does not include both, so yes you should add them. On Fri, 13 Nov 2009, Matt Clarkson wrote:
> Hi Bruce, > > in general, the vents look good. So, just one more question, if I may. I > notice that the segmentation labels have ventricles and choroid-plexus. > So, in the wmparc.stats, and aseg.stats, does the volume of the left lateral > ventricle include the left choroid plexus, or should I add both numbers > together? > > Many thanks > > 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 3:09:58 PM GMT +00:00 GMT Britain, Ireland, > Portugal > Subject: Re: [Freesurfer] Filling Big Ventricles > > Hi Matt, > > are the ventricles labeled properly in the aseg? If so, then you probably > don't need to do anything. If not, then you'll need to manually edit > them, and run from there forward (-make all should do it). > > cheers, > Bruce > On Fri, 13 Nov > 2009, Matt Clarkson wrote: > >> Hi Bruce, >> >> Thanks. So it sounds like FreeSurfer 4.5 should now be adequately filling >> ventricles in the general case, and that -bigventricles offers didn't reach >> a level of robustness you were happy with, so best to avoid that? What about >> the flag -fillven on mri_edit_wm_with_aseg? Any use? >> >> In terms of the fix mentioned below, the fix literally is: >> >> 1. recon-all -all >> 2. mri_binarize --i $SUBJECTS_DIR/$PD/mri/aparc+aseg.mgz --match 4 --match >> 43 --match 5 --match 44 --o $SUBJECTS_DIR/$PD/mri/vents.mgz --binval 255 >> 3. Add vents.mgz to wm.mgz >> 4. recon-all -autorecon2-wm >> >> so, it could well be affecting the results more by virtue of the fact that >> we essentially perform a re-run? >> >> Thanks ever so much. >> >> 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 2:44:03 PM GMT +00:00 GMT Britain, Ireland, >> Portugal >> Subject: Re: [Freesurfer] Filling Big Ventricles >> >> 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
