Hi Jee Won and Priyanka, I created a bit of a hack that I'd like y'all to test out. Go to https://gate.nmr.mgh.harvard.edu/safelinks/greve/ (user guest, pwd collab) and download dngtester and ventfix (you may need to chmod a+x both of them). Run ventfix with --help to see how to run it. I've run it on a bunch of cases, and it seems to work, but I'd like to see how it runs on your data before I fully incorporate it into FS.
doug On 1/10/2022 8:49 AM, Kang, Jee Won wrote: > External Email - Use Caution > > Hello all, > > Apologies for the delay in response! > > For the applications in my group's work, we are looking at ventricular > volume, as well as white matter volume. To that degree, we are interested in > whether there are any processing steps earlier in the pipeline that we can > implement just to minimize the manual editing required - just anecdotally, > there have been cases where lateral ventricle volume increases over 5% after > making manual edits, and I was unable to identify if there was a common > element to the subjects with ventricle problems. > > Thank you for your work on this! We really appreciate it. > > Thank you, > Jee Won > ________________________________________ > > > Message: 2 > Date: Tue, 4 Jan 2022 22:11:53 +0000 > From: "Nadar, Priyanka (NIH/CC/OCRTME) [F]" <priyanka.na...@nih.gov> > Subject: Re: [Freesurfer] [EXTERNAL] Re: Ventricle segmentation issue > - ventricle mislabeled as white matter > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <mn2pr09mb5210a46f62e837624f830d5184...@mn2pr09mb5210.namprd09.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > I am not part of Jee Won's team: just generally interested. For my work, I am > looking at ventricular volume and so it would be good to not have to manually > correct a large number of my scans. > ________________________________ > From: Douglas N. Greve <dgr...@mgh.harvard.edu> > Sent: Tuesday, January 4, 2022 1:19 PM > To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > Subject: [EXTERNAL] Re: [Freesurfer] Ventricle segmentation issue - ventricle > mislabeled as white matter > > > CAUTION: This email originated from outside of the organization. Do not click > links or open attachments unless you recognize the sender and are confident > the content is safe. > > > Hi Jee Won and Priyanka, there are several things going on here. First, the > original aseg (aseg.presurf.mgz) has these areas labeled as nothing (0); they > show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it would be good to > have them properly labeled, but is this critical to your applications? Eg, > are you looking at ventricular volume? > > On 12/21/2021 9:19 AM, Kang, Jee Won wrote: > > External Email - Use Caution > > Hello all, > > > I found a very common error in our data while I was correcting recons. The > lateral ventricles (usually the horns) are being misclassified as white > matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. > > > We were able to fix this issue by manually filling in the ventricles in > aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg > -autorecon3, but this is obviously quite a labor-intensive fix for a > substantial portion of our data. This was also the only way to fix the > segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not > fix the problem. I'm not sure why Freesurfer is having issues here, as the > areas it is mislabeling have very distinct intensity boundaries - the T1 > intensity is usually between 20 and 45 in the areas that are being > mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who > had this ventricle segmentation issue, and you can see that a large portion > of the right ventricle has just not been segmented properly; the intensity of > the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 > (R cerebral white matter) in aseg.mgz. > > > Would you be able to provide some insight into why this might have been > happening, and what we could do in the future to prevent such extensive > manual editing in the future? I can also say that this data was processed > with a T2 image as well, and supplying that flag didn't help with the > segmentation issue. > > > Thank you, > > Jee Won > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1ZGRySYd-5iOMX55uEC_0An1dt-wqdEh2tYIkVApSE6ZYz5vgCOhjM3YCIEraQI_yeq-f2LVImXeqaaoq02BGetl2OuNR0310S0nQ-icV2Z6kJOU_eMoItd70EyNI3_bFVlchyLjila_nbuiyQ_JMj09HBn9XgmDiOuoC28CQMUEG25sb2-CgIy3mNn_1jTIhKRD7g5lDXMIKgIOJqf0WNy6Mf2S-70lFFQst6-UzHazXMlcBKGEUBqf8pXxC0-jp-GPOtOsa5OBIDVxeIHm3uuNv-QIBhaUJu4QhaZ9sNUJV-DqMP9h5Rb03I89PLbbh/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1ZqS8cWsEssRz42XvJjlhsimqJ1nYH5mixwDzGDjtILm4E-MRySPi216RGkLtrz1NZkUkOSe27kxUIwGsfIYA6oqFsKZHo5ljQA2UYFhbiFoVnHZVNl9_AGRJGd0Sf_L67KNrPqMNrYbs-4e1S-LhMzDjn-1ehljNsZv3fH_TTBaV9tSuDLXApnk6O5LYuu8NupYT2_papPAOD-Y7bxLROvrolkJwSQ8DVkXApbS06JMF-gpsuf8djNXmfQwbOjE5lCGfXJbIeiVZEPzN3O_VixRUkrwFUIVEMEGNpC6e40dRwCjvbhOiNj0o9eIvgUT6%2Fhttps%2A3A%2A2F%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%3BJSUlJSUl%21%21NZvER7FxgEiBAiR_%21-9fJB3wbHHpQyDaKhT96fwzzCWMB6HSE9HWgXUWLFfYC-NUT-vCLhsvf9P9M1mEC6BaVoYdFl9OP%24 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > https://secure-web.cisco.com/1gVqme6sA9cPGfgCDQ6Fpp2n5Lj5J53gAjbriKQ1P52rXgwdMif13ai5XdO_3tpccVicA1W5ZCGL8OHI4gSzG-8bLE9t5tMnHRMWDH1HBKrBYhNXhBfTGDTZneoaG_IIvJPzhTgIMf8NTm_qSX3-vTodjqG2oHccq3kSjRVI3POVu9z3x-aXUomcj5aFF9jfHi9bx-t0x6CxKWzhcsrmULCdTpD01nx2WlM9sTMsF_jVeO4mbIy4Nu9ruGRPKLwTS_GVIZ49if6PcR134hfq89FqCt6cD3bNK1SNydIgJFXeDZwQolEhhrAhtTUA8ldfZ/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20220104%2F5b6bf39e%2Fattachment-0001.html__%3B%21%21NZvER7FxgEiBAiR_%21-9fJB3wbHHpQyDaKhT96fwzzCWMB6HSE9HWgXUWLFfYC-NUT-vCLhsvf9P9M1mEC6BaVoZNjvxh9%24 > > ------------------------------ > > > _______________________________________________ > 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
