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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
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://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD...
cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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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 BFISCHL@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_vv8nxE1dIIEqQkXLPn02gYzyNgEqNHyVZ6TFg52b...
cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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/1becugLiqcOpUqQNIegkkN2yDAafYNqSQqfkb3eJYG4qU3v... 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/1zEFFeYHHOGdpaI64aGDbuS5WeByRWhOoSZe6Nf4zwao9e8... < https://secure-web.cisco.com/1zEFFeYHHOGdpaI64aGDbuS5WeByRWhOoSZe6Nf4zwao9e8... .
HI Chemda
The “nofix” files are surfaces prior to topology correction, so they will have defects in them. The defect_labels files are *not* surfaces, they are scalar fields over the surface (like curvature files), so load them that way
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of chemda wiener Sent: Monday, December 2, 2024 4:19 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: recon-all command stuck before creating pial files
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 <BFISCHL@mgh.harvard.edumailto:BFISCHL@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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD...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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of chemda wiener Sent: Sunday, December 1, 2024 5:41 AM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1zEFFeYHHOGdpaI64aGDbuS5WeByRWhOoSZe6Nf4zwao9e8r85BwFAWJNCxkA62IG93p2g5JpdenKBAkF87RqLQb1aFytq_sNSmZ9sCl7Tyh0odb8FgmQt6O3d2Uc7jhpVBW3-M97X28c4HbnxZuF8p9ulrVD4WXDeHdST-dbJGcLJHQh7RwFyz3vrQX8YnYmgYVN3f-nZaIjJin02bty48qk5H6QP8wiMnH5t2WCvYP3q59zT3lXKsfY6GQYyWuV2x6YX6jyL783BprEk7xdPa09VVUUWpw3j2x9a9qzkrcWDYe_JUS_YVkMpVhx673rYBYjOXQ-TAoWdiTURQDFTg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1zEFFeYHHOGdpaI64aGDbuS5WeByRWhOoSZe6Nf4zwao9e8r85BwFAWJNCxkA62IG93p2g5JpdenKBAkF87RqLQb1aFytq_sNSmZ9sCl7Tyh0odb8FgmQt6O3d2Uc7jhpVBW3-M97X28c4HbnxZuF8p9ulrVD4WXDeHdST-dbJGcLJHQh7RwFyz3vrQX8YnYmgYVN3f-nZaIjJin02bty48qk5H6QP8wiMnH5t2WCvYP3q59zT3lXKsfY6GQYyWuV2x6YX6jyL783BprEk7xdPa09VVUUWpw3j2x9a9qzkrcWDYe_JUS_YVkMpVhx673rYBYjOXQ-TAoWdiTURQDFTg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
freesurfer@nmr.mgh.harvard.edu
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chemda wiener -
Fischl, Bruce R.,PHD