Re: [Freesurfer] Pial Surfaces Cutting off Gyri
Thank you Bruce. I've had this prob randomly before - but recently it's been each of the last 10 datasets - so I think its a process issue that I introduced - but would love help from any direction. If I use the upload site - which files to you need? will send wm.mgz, ?h.orig surface - any others? Thank you - Sherri -Original Message- >From: Bruce Fischl >Sent: Apr 7, 2010 1:15 PM >To: Sherri Novis >Cc: Sita Kakunoori , freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > >Hi Sherri, > >you may also have a topological defect near those control points, which >is causing the surfaces to lose the wm (and hence the gm also). What does >the wm.mgz look like there? Is the wm segmented correctly but not >included in the ?h.orig surface? If you upload this data we can take a >look, if you want. >Bruce > > >On Wed, 7 Apr 2010, Sherri Novis wrote: > >> Thanks Sita. I have struggled with how to capture very ghostly gray matter. >> Sometimes throwing a CP in it works (I understand now this may be hosing it >> sometimes) - if AR2-cp w/CPs in white matter is not driving the pial >> surfaces to capture all the gray - is the only way to capture the ghostly >> gray matter to directly edit the pial surface? >> >> I was trying to avoid that. I was told don't ever edit the pial surfaces - >> not sure why though. Will manual edits of the pial surfaces cause other >> problems in getting surface segmentation stats? >> >> Thank you - >> Sherri >> >> -Original Message- >>> From: Sita Kakunoori >>> Sent: Apr 7, 2010 12:55 PM >>> To: Sherri Novis >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri >>> >>> >>> Hi Sherri, >>> >>> one of the control points seems to be in gray matter, which is probably >>> causing this. Please try deleting it and rerunning autorecon2-cp. >>> >>> Sita. >>> >>> >>> On Tue, 6 Apr 2010, Sherri Novis wrote: >>> >>>> Hello brilliant and generous FS people, >>>> >>>> I have introduced a problem I cannot solve. I am simply trying to >>>> capture as much gray matter as possible. We have some very bad constrast >>>> images (ghostly edeges where the gray matter should be). I'm adding >>>> control points to try to capture - however, now when I run AR2-cp, the >>>> pial surfaces go haywire on the superior borders of the slices. >>>> >>>> Attached are two images displaying the problem. >>>> >>>> I have edited wm.mgz to fill in the ventricles because I was getting >>>> islands, and I manually edited the brainmask to remove some vasculature >>>> that was being included in the pial surfaces. >>>> >>>> Can you tell me where I introduced this instability? >>>> >>>> Best Regards, >>>> Sherri >>> >>> >>> 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
Re: [Freesurfer] Pial Surfaces Cutting off Gyri
Thanks Sita. I have struggled with how to capture very ghostly gray matter. Sometimes throwing a CP in it works (I understand now this may be hosing it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces to capture all the gray - is the only way to capture the ghostly gray matter to directly edit the pial surface? I was trying to avoid that. I was told don't ever edit the pial surfaces - not sure why though. Will manual edits of the pial surfaces cause other problems in getting surface segmentation stats? Thank you - Sherri -Original Message- >From: Sita Kakunoori >Sent: Apr 7, 2010 12:55 PM >To: Sherri Novis >Cc: freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > > >Hi Sherri, > >one of the control points seems to be in gray matter, which is probably >causing this. Please try deleting it and rerunning autorecon2-cp. > >Sita. > > >On Tue, 6 Apr 2010, Sherri Novis wrote: > >> Hello brilliant and generous FS people, >> >> I have introduced a problem I cannot solve. I am simply trying to capture >> as much gray matter as possible. We have some very bad constrast images >> (ghostly edeges where the gray matter should be). I'm adding control points >> to try to capture - however, now when I run AR2-cp, the pial surfaces go >> haywire on the superior borders of the slices. >> >> Attached are two images displaying the problem. >> >> I have edited wm.mgz to fill in the ventricles because I was getting >> islands, and I manually edited the brainmask to remove some vasculature that >> was being included in the pial surfaces. >> >> Can you tell me where I introduced this instability? >> >> Best Regards, >> Sherri > > >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
Re: [Freesurfer] Skull Stripping extra dura & vasculature
Thanks Bruce. Is there anyway to address it in the intensity normalization phase? -Original Message- >From: Bruce Fischl >Sent: Feb 9, 2010 12:29 PM >To: Sherri Novis >Cc: freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Skull Stripping extra dura & vasculature > >Hi Sherry, > >that's pretty tough. The dura is very bright and quite close to the gm. >You may need to erase more of the dura > >Bruce > >On Tue, 9 Feb 2010, Sherri Novis >wrote: > >> Hello, >> >> I have a series of datasets with skull stripping issues - namely left over >> dura/vasculature in the occipital cortex, and some in frontal >> areas.(Attached is a jpeg of the type of issue. It's pervasive throughout >> the slices, across a handful of subject data.) >> >> I have rerun skull stripping changing the watershed value, however it's not >> making the distinction between dura and gray matter. (recon-all -skullstrip >> -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS >> version: freesurfer-Linux-centos4-stable-pub-v4.3.0) >> >> I also attempted to edit 50% of the slices by erasing voxels to make a clear >> boundary between the dura and cortex and then re-ran autorecon2 to see if it >> would at least adjust the pial surfaces - however that did not work (pial >> surfaces still crossed the one pixel boundary I made into the dura). >> >> Can you recommend any other flags or things to try before I edit/erase the >> excess by hand? >> >> Thanks for your time - >> Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Skull Stripping extra dura & vasculature
Hello, I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.) I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0) I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura). Can you recommend any other flags or things to try before I edit/erase the excess by hand? Thanks for your time - Sherri<>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] WM.mgz corrections in the ventricles & Individual Normalization
Hello - I have two questions: 1) I noticed on wm.mgz volumes that were segmented properly, that even when the ventricles were automatically filled in, on some slices they are somewhat patchy (partially filled in with white, with some black/blank voxels). Do these patchy wm fill-ins require manual fill-ins to make them entirely opaque? I went through the tutorial, and it was not clear whether a patchy fill-in required a correction or not. 2) What is the best automated measurement that can be used to normalize an individual's cortical segmentation volumes for between subject comparison? We have been using gray+white volumes (why we need the ventrical volume processing to be consistent) - but not sure if ICV would be better individual normalizer. Thank you for your time - Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How do Control Points and Pial Surfaces Interact?
Hello - I am trying to compare normalized segmentation stats across groups. We are adding control points to the white matter in an attempt to push out the pial surfaces when it appears grey matter has been clipped or cut short.I am loading the following: tkmedit [SubjectID] brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white. The CPs are being saved, and after running autorecon-all the CPs are referenced in the recon-all.log file - however the pial surfaces are not redrawn around the control points. Should the white matter CPs force new pial surfaces? Am I missing a step in here? I checked the archive for the last year without luck - so I apologize if this is a repeat question. Thanks much for your help - Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Aparc Stats & Different versions of Freesurfer
Hello - I am comparing aparc stats across several groups of data, and just noticed that recently processed groups do not have corpus callosum values... which made me wonder if different versions of freesurfer will produce different aparc data... Can aparc stats from an older version of freesurfer be compared to aparc stats from a more recent version? Or do they all have to be processed with the same version? Also - we noticed that the aparc areas do not extract in the same order... is this also because of the different version used to process the data? Thanks much, Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Details about aseg Stats
Hello - can anyone tell me where I can find details on what aseg stats include and exclude from each measurement? The ones I need in particular are: Left-Cerebral-White-Matter Left-Cerebral-Cortex and IntraCranialVol. I'd like to understand if L-Cereb-Cortex means just gray matter, and/or if it includes ventricles & subcortical structures. I'm also trying to find out if IntraCanial Volume means the space of the skull cavity, or if it means something different. Thanks much in advance - Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
