External Email - Use Caution On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote:
> > > On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote: > > External Email - Use Caution > Would providing better manual segmentations of those structures of > interest help you in building better solutions? > I can work with the segmentation that is produced now, but I am interested > in improving the results for extracerebral tissues using multimodal imaging > and better manual segmentations. > > The samseg authors used 20 subjects and did not find that increasing that > helped all that much (at least on dice scores) > That is promising - if the list of those subjects is public and they are part of the oasis dataset as indicated by the paper there is a way to subdivide the segmentation of already existing labels > Can you shed some light on the steps required for creating the current > atlas? > > Unfortunately not. The atlas creation software was the lowest priority of > the samseg authors, so it is not easy to run. I myself find it extremely > challenging to create new atlases, so I can't support helping others do > that. We're trying to get it more streamlined (for you and for us:) > I see. If the process can be automated like in multi-atlas label fusion it would be a great way to gain more information about both cerebral and extracerebral tissues. Is building an atlas for T2-weighted images somewhere on the priority list? thanks, Mikolaj > > > thanks, > > Mikolaj > > On Wed, Sep 21, 2022 at 4:01 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> by template I'm assuming you mean the atlas. There is not an easy way to >> create a new atlas or modify the existing one (though we are developing >> methods to do both). For the eyes, you could probably just write something >> to look at the column index in the eyes. If it is less than 128, then set >> it to left otherwise right. >> >> On 9/21/2022 6:01 AM, Mikolaj Pawlak wrote: >> >> External Email - Use Caution >> Dear Freesurfers, >> I have been using samseg for a while and like it a lot. Thank you for >> this tool. How do you modify the template for this tool? Is there a >> guideline for this? >> I would like to divide Fluid_Inside_Eyes label to left and right and >> improve the bone information in the template. What is the procedure? >> thanks, >> Mikolaj Pawlak >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1GWqfB7tG8HCWZgCRPEm38jICApGGWm5W-V-EFWXyg-Z1BO2HS6hxlAH54e4RKZTyNZi4WjBT4IVWiNXMD2ewgIWWN8PpR-q7XlBJzOFFZx3_i4Wua9bqHZfLSnyuGYQBzCAyAZI026nAiRa55L2gLZvYtMPzkVr9Mo7pTRs1IjB8Zw1atcbjBQVLdNvuRyN4hUw8aPIl_gKP-6ibwZc8S49_Y0RuLrtuIOqdFah-64-E_wkVHjbutKrvLtHz2bu1c1vP9QoOmVyDz-d8H1RRZp0DwE9T68zs74kQJPFbxINExf235wse4OfmZcWDMsFF/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1VDEmNgD-Jh72tJ-8lvFADFo1kr1vPAaJGg-5CTE2Uk4WU0tmHR89g8ypT168s19PJruOO8OqNjAnzS1uSve4dXblLJgzJ4iCauHDfmF2EkU7D4yTQ3fRgxwaqhNQ-0OhtShgIUsliE21QHncJXqOHVC5gH1bSoRVzPG8zKIvQPmgqZ42vpDLJ_ZEyrOk-xmIhXK2zKM0mPoWRnty5vi_e8Sq8-SsFHmvtO-3s0ywk1h3A2GN4qkcfkB7t9oFNCPLNl_5E7nZVvPd8CoLNU-gHGSmeGGh2o6MYnx7L6br1KuAn4XS5REToMpR4unW0Bip/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1GWqfB7tG8HCWZgCRPEm38jICApGGWm5W-V-EFWXyg-Z1BO2HS6hxlAH54e4RKZTyNZi4WjBT4IVWiNXMD2ewgIWWN8PpR-q7XlBJzOFFZx3_i4Wua9bqHZfLSnyuGYQBzCAyAZI026nAiRa55L2gLZvYtMPzkVr9Mo7pTRs1IjB8Zw1atcbjBQVLdNvuRyN4hUw8aPIl_gKP-6ibwZc8S49_Y0RuLrtuIOqdFah-64-E_wkVHjbutKrvLtHz2bu1c1vP9QoOmVyDz-d8H1RRZp0DwE9T68zs74kQJPFbxINExf235wse4OfmZcWDMsFF/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1VDEmNgD-Jh72tJ-8lvFADFo1kr1vPAaJGg-5CTE2Uk4WU0tmHR89g8ypT168s19PJruOO8OqNjAnzS1uSve4dXblLJgzJ4iCauHDfmF2EkU7D4yTQ3fRgxwaqhNQ-0OhtShgIUsliE21QHncJXqOHVC5gH1bSoRVzPG8zKIvQPmgqZ42vpDLJ_ZEyrOk-xmIhXK2zKM0mPoWRnty5vi_e8Sq8-SsFHmvtO-3s0ywk1h3A2GN4qkcfkB7t9oFNCPLNl_5E7nZVvPd8CoLNU-gHGSmeGGh2o6MYnx7L6br1KuAn4XS5REToMpR4unW0Bip/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> The information in this e-mail is intended only for the person to whom it >> is addressed. 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