External Email - Use Caution Thanks Bruce! Unfortunately when I try to open the lh.defect_labels it quits freeview. The lh.orig.nofix loads okay, but I was wondering if it was a problem that this file is even called "nofix", does that mean it was not able to correct for defects?
On Sun, Dec 1, 2024 at 5:49 PM Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu> wrote: > Hi Chemda > > > > Usually that means something big has gone wrong in the segmentation or > skull stripping (like the cerebellum is still attached to a cortical > hemisphere in the wm.mgz or the skull is or something like that). More > generally this happens when there is a topological defect that is too big > to automatically correct in a reasonable amount of time. You can visualize > the defects following the instructions here: > > > > > https://secure-web.cisco.com/1yn9Tu_vv8nxE1dIIEqQkXLPn02gYzyNgEqNHyVZ6TFg52bt7__RfTaqyQSf09Ik1xyNYk1tmdRnrL3y1-MSqUex2YxvdFoiqHH0BbLxvLWaJNXZ_uMv5zYpX66YhFoe23pBJ_SVy0jfFmpU1579VwEIX7HVV7s45zhWfOuAeqeCDL8WhT8vq4ZPJL2DPRx61-kBDbwksonysLqcgHBTUIChZpK3lZ4LdIGEvCeaq9GX2-2yf3D8C8gYdXS6inTn0fqOiRpRQBQ3W7ErX09XGodaHU6gj9KHwQhCzFbc1G7SA8Z8cd2xzSnvfuUHZ9FAAB07tOQUSlmZNrPFx6r3VEQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewWorkingWithData%2FFreeviewSurfaces%3Fhighlight%3D%2528defect%255C_labels%2529 > > > > cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *chemda wiener > *Sent:* Sunday, December 1, 2024 5:41 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Fwd: recon-all command stuck before creating pial > files > > > > * External Email - Use Caution * > > > > Hi, > > > > My name is Chemda Wiener. I am a PhD student in a Neuro-Engineering lab. > We are working with MRI scans of patients with epilepsy and I am attempting > to use freesurfer to create the mesh .pial files. When I run the freesurfer > recon-all command, the command gets stuck at "correcting defects" with the > last file it creates being the "lh.defect_chull". It has been stuck for a > few days on this part until I finally killed the process. I tried running > autorecon2 afterwards on this patient to see if it can pick up from where > it stopped but it gets stuck again at the same place. > > > > I would appreciate any help in the matter. > > > > Thank you in advance for your time and your software! > > Chemda > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1becugLiqcOpUqQNIegkkN2yDAafYNqSQqfkb3eJYG4qU3v47wJ2RldqLob9cik3U8X3p1IcbN13fc-Zd9Hx7COnlmCjryVqvM3Ye2JaPbhEOJJW4L2ExUKT7D09gqaZ8X9D2BZZjBqUGlos7VQyYUli24zvdVt84avaHNmgxfHAbA0JJ8plfyD5mo1PwnRABtSIyTbGsmxg_llJNbQLjUgfwCqHMAR_nqKo-0ccObThBI1740AQAQwX8IlOOJ6h6ZwdbiZ5vkwu6cQ47ublNS7HtMC9IgOHL5qdltff5HCsoSfham6EE4a5P2duxaAD8r6KoJguCqfGmzeAHYWjUYg/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. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1zEFFeYHHOGdpaI64aGDbuS5WeByRWhOoSZe6Nf4zwao9e8r85BwFAWJNCxkA62IG93p2g5JpdenKBAkF87RqLQb1aFytq_sNSmZ9sCl7Tyh0odb8FgmQt6O3d2Uc7jhpVBW3-M97X28c4HbnxZuF8p9ulrVD4WXDeHdST-dbJGcLJHQh7RwFyz3vrQX8YnYmgYVN3f-nZaIjJin02bty48qk5H6QP8wiMnH5t2WCvYP3q59zT3lXKsfY6GQYyWuV2x6YX6jyL783BprEk7xdPa09VVUUWpw3j2x9a9qzkrcWDYe_JUS_YVkMpVhx673rYBYjOXQ-TAoWdiTURQDFTg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1zEFFeYHHOGdpaI64aGDbuS5WeByRWhOoSZe6Nf4zwao9e8r85BwFAWJNCxkA62IG93p2g5JpdenKBAkF87RqLQb1aFytq_sNSmZ9sCl7Tyh0odb8FgmQt6O3d2Uc7jhpVBW3-M97X28c4HbnxZuF8p9ulrVD4WXDeHdST-dbJGcLJHQh7RwFyz3vrQX8YnYmgYVN3f-nZaIjJin02bty48qk5H6QP8wiMnH5t2WCvYP3q59zT3lXKsfY6GQYyWuV2x6YX6jyL783BprEk7xdPa09VVUUWpw3j2x9a9qzkrcWDYe_JUS_YVkMpVhx673rYBYjOXQ-TAoWdiTURQDFTg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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