I edited the wm.mgz according to the guide, but it didn't change anything when I ran the reconstruction.
What is the brush value supposed to be when editing? 255? On Tue, 2017-02-28 at 08:33 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=93lv6rMeBtNdchspc1YZuOz4_prdsA0bBMzpiAfbfFA&e= > > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Manual edit to include missing cortex? (Rockers, Elijah D.) > 2. Re: Manual edit to include missing cortex? (Lee Tirrell) > 3. How to output particular area from stats subdir (Jing Gu) > 4. Re: chose between 5.3 and 6.0 (Bruce Fischl) > 5. Ct file (yusif Al-kheder) > 6. Re: Ct file (Douglas N Greve) > 7. Different segmentation atlas (Julie Hall) > 8. Re: gzip: stdin: unexpected end of file (Kambiz Tavabi) > 9. Re: gzip: stdin: unexpected end of file > (zkauf...@nmr.mgh.harvard.edu) > 10. Building Freesurfer dev with GPU support/CUDA enabled > (Francis Tyson Thomas) > 11. ACPC alignment before or after running on Freesurfer? > (Lee Subin Kristine) > 12. Re: ACPC alignment before or after running on Freesurfer? > (Antonin Skoch) > 13. Re: Strange wm error (Melanie Ganz) > 14. Re: Building Freesurfer dev with GPU support/CUDA enabled > (R Edgar) > 15. Re: XL defect detected (Shane S) > 16. Re: editing topological defect (Shane S) > 17. Re: chose between 5.3 and 6.0 (Shane S) > 18. mri_convert error: 'GetDICOMInfo(): dcmGetDWIParams() 7' in > FS6.0 (Gustav M?rtensson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 27 Feb 2017 21:45:39 +0000 > From: "Rockers, Elijah D." <edrock...@houstonmethodist.org> > Subject: [Freesurfer] Manual edit to include missing cortex? > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1488231939.3484.60.ca...@houstonmethodist.org> > Content-Type: text/plain; charset="utf-8" > > Is there something I can do to extend the pial surface to include cortex > that it ignored? In some places there are rather large chunks of cortex > not included in the pial surface. > > https://urldefense.proofpoint.com/v2/url?u=http-3A__imgur.com_a_FnAgj&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=bUoYvwIUVPBh2GqxxJBmM5PPMRasPMoCnG44Zr233L8&e= > > > Link is to a screenshot, notice the top of the brain. It's fairly > pronounced, visible in 12 adjacent sagittal slices. > > I tried using the "Reposition Surface" tool, but I'm not exactly how it > works, and I ended up just making the surface look crazy there. > > I also tried adding control points in the white matter near the edges of > the WM surface by the problem and ran the reconstruction, as someone in > the archives suggested, but it didn't change the surface. > > Thanks for your help, > Eli > > Houston Methodist. Leading Medicine. > > U.S. News & World Report has recognized Houston Methodist as one of the > nation?s top 20 hospitals, placing it for the second time on the magazine?s > prestigious Honor Roll. It is also designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=tdm1uCFp1Qa-cqbw-ETWTqnNcjd9OmsdyD2Fx1Z7tzQ&e= > and > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_HoustonMethodist&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=7GrzKHkkWqTKw3HTTh9lCXDMVPdu9qlbNLMf4MiQXz4&e= > . > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist > Hospital and/or its relevant affiliates and may contain restricted and > privileged material for the sole use of the intended recipient(s). Any > review, use, distribution or disclosure by others is strictly prohibited. If > you are not the intended recipient (or authorized to receive for the > recipient), please contact the sender and delete all copies of the message. > Thank you. > > > > ------------------------------ > > Message: 2 > Date: Mon, 27 Feb 2017 17:51:06 -0500 (EST) > From: Lee Tirrell <ltirr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Manual edit to include missing cortex? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1702271738330.8245-40vermis.nmr.mgh.harvard.edu&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=naQQzgxoBngRWZD46h5B99J89tVXNq2bEjUkR6WHjsc&e= > > > Content-Type: text/plain; charset="iso-8859-7" > > Dear Eli, > > You may have to draw in voxels in the wm.mgz volume if it doesn't extend out > far > enough. After rerunning, this will push out the white surface, which causes > the > pial surface to be positioned further out. You can refer to our tutorial page > for more information: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FsTutorial_TroubleshootingData&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=OkiD5uf2YKeGm89ewMOieqZGQI8ZRrmpPoKRjKbfdqE&e= > > > Specifically, the "Edits to the wm volume (segmentation error)" section > explains the types of changes you may have to make: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FsTutorial_WhiteMatterEdits-5Ffreeview&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=NwOL2oDm1qJq2MK7XxV74WL1RKAyJFnC6DsR6dHfZtY&e= > > > After making the changes, re-run with this command: > recon-all -autorecon2-wm -autorecon3 -s subject_name > > Let me know if you have further questions. > > Best, > Lee > > > > > On Mon, 27 Feb 2017, Rockers, Elijah D. wrote: > > > Is there something I can do to extend the pial surface to include cortex > > that it ignored? In some places there are rather large chunks of cortex > > not included in the pial surface. > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__imgur.com_a_FnAgj&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU&s=bUoYvwIUVPBh2GqxxJBmM5PPMRasPMoCnG44Zr233L8&e= > > > > > > Link is to a screenshot, notice the top of the brain. It's fairly > > pronounced, visible in 12 adjacent sagittal slices. > > > > I tried using the "Reposition Surface" tool, but I'm not exactly how it > > works, and I ended up just making the surface look crazy there. > > > > I also tried adding control points in the white matter near the edges of > > the WM surface by the problem and ran the reconstruction, as someone in > > the archives suggested, but it didn't change the surface. > > > > Thanks for your help, > > Eli > > > > Houston Methodist. Leading Medicine. > > > > U.S. News & World Report has recognized Houston Methodist as one of the > > nation?s top 20 hospitals, placing it for the second time on the magazine?s > > prestigious Honor Roll. It is also designated as a Magnet hospital for > > excellence in nursing. Visit us at houstonmethodist.org. 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