you do not need the white or pial surfaces, just the orig.nofix.
On 6/19/2022 5:17 PM, Wang, Yu wrote:
External Email - Use Caution
Hi freesurfer expects,
I have tried to use this way to solve the problem, but it did not work because I don’t have the files like lh.pial. But I tried to use the command “recon-all -s c1NT816 -I smwrc1NT816_screen_mpr.nii -no-ants-n4 -all ”. It seems this command can solve the problems and it shows “finished without error” . But the segmentation looks very strange on the freeview and I did not know what is going wrong. And I will attach the strange figure with this email.
Thank you for answering my previous questions and looking forward to your reply.
Thanks in advanced,
Yu
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Sunday, June 19, 2022 at 9:50 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] recon-all -s exited with ERRORS
It looks like there are a lot of defects as I see a lot of these messages
An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... https://secure-web.cisco.com/1ZQofRODLaENfz_F8BjYcuwTkgaJ_geo9_wYOUwBzvQbXeHuqpJ_K59H1xaLDzsghyZ0z172R9pUKRnuDqFw8Io0LPaEnDxuiol9LC1SsSgw72ZV3cAyfHFVv-VWNmsq2PfdnUxDZGvyKQpBt62X2y18fORQ7aRA1F95OqtdQfzmGox2qdqgDTcoCESQFKDyakRsi-LDGflsy5o9rEV3e-Rfq2BUOWLP3k9MSCsao5IdAwYJNejoxV6alb8lzeYOzjwfu9zL17LLXkHaIZgB-HZYx10IZO6rliDu0zLQ93ddcPUxICWPHdkAuupoauQJd20x22j7E5F7vSjilFdIlp8-6T6Y__icToIgjAadfJj8/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FTopologicalDefect_freeview%26data%3D05%257C01%257Cw.yu1%2540wustl.edu%257Ce6db721793b143e5b35208da520310b4%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C637912470361937470%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DS%252BJcM0fPfTK3noKeAnSvAWOTBK3QsS0zTg5GCHPrIuI%253D%26reserved%3D0
Try following those instructions
On 6/14/2022 5:37 PM, Wang, Yu wrote:
* External Email - Use Caution * Hi, FreeSurfer Developers, I am attempting to use the recon-all to reconstruction, I successfully run this command in some subjects, but it also failed in around 1/3 of subjects. And after running the recon-all of this 1/3 subjects. It will show “mri_watershed error:GLOBAL region of the brain empty” and I already solve this with the command “recon-all -skullstrip -no-wsgcaatlas -s smwrc1NT816”. And after working with this, I tried to use the command “recon-all -autorecon2 -autorecon3 -s smwrc1NT816” and it shows the output as without given some detailed reasons: *recon-all -s smwrc1NT816 exited with ERRORS at Mon Jun 13 13:54:10 CDT 2022* ** *For more details, see the log file /Applications/freesurfer/7.2.0/subjects/smwrc1NT816/scripts/recon-all.log* *To report a problem, see****MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <https://secure-web.cisco.com/1v_YsxsDMyibcPMlMZUDfbXgymjfxHh90qh38K0_TWrGGD9551SzY6sBg5FFlJwSHv8pbv0i0MO2hB6uNbjVr6eMOzXhPDU6Mti288pMLtI8Tl4BFKIoeyYZ293Dp7mK9R9UwgKS2PzcPuWLB4NdWAjNgmRicKVtJ5SALiz_geJ34DRuMUocim0_TaMG22u6QE5VF3V4WOCRTjAUE1UNQRglgWwINlJ0rh77lwxEgyNNiPk5b8288GmI-FfI9J4ZtS01B3GNopUMVlIlE9JNNWklB9ymmPlhDwPXnsDstTOQ2jX6-mH836ThkbEM-LpzIVblkMoQTi_7ODQ9p3_ZCBgxdZLfSNTJkO_4dAiv0qo8/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1iPjG6_yDpeRBXccjdFdxifv54y1GvmJtNQuC-KaFzx3NzAM79VncTDzeOsHzRjZXnNBtfoaUmJp-iqE4rmlb_37cgVnP3yoki6Hp6iDUWG3J7O_20a1Pt0eBKm4QhifNMlGWguI5yCIPrx5roSppTd3PlAL7k5JfTjaFrGD1Ogx4sy6MWpeqn3cWM2ox5FY9fPhWkCMZnY4RcShAJveekgUswk3t5qqqGNBK9kILalsHRBCIKK35oVStKCn7nAaCv0gXMdgLUdoM1OJyAI6Aa6OkZIfE6MM8BVu5_1htGYbtk48IVxo1d8kVfjrOGsnqdjvbyuTBrBrM_T-Y7zKIZA%252Fhttp%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FBugReporting%26data%3D05%257C01%257Cw.yu1%2540wustl.edu%257Ce6db721793b143e5b35208da520310b4%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C637912470361937470%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DMx66dknkFcPaPNtKZAlg%252FTEQtW7UYDTyNs%252Fd%252Fx%252BSbL4%253D%26reserved%3D0>* I’ve searched over the internet and did not find the reasons and solutions of my problems. And I will attached the recon-all.log in case it's of any use. I try to work out on two machine, and they show the same problems : 1. FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b and freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2. Platform: MacOs 11.4 and ubantu 20.04.4 3. uname -a:Darwin WANGs-MBP.attlocal.net 20.5.0 Darwin Kernel Version 20.5.0: Sat May8 05:10:31 PDT 2021; root:xnu-7195.121.3~9/RELEASE_ARM64_T8101 arm64 or:Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 1. recon-all.log: see attached (this one is run by macOS) I will be appreciated if you can give me a hand with these problems. And looking forward to your reply. Sincerely, Yu _______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/1gQpzsN6AGRajuAzQuu_M2vlHFxxngtg5qRy2s1e_Njc___P3-keBH40L7dPnLJbNP6Qx_sCuVRrHV0MYYLQCaDq_xu3ICk3Sr5c2WdciurtSj4qhOM7p6ItOWOpc3GT9-ub3l-AHr0Y1F-pEFZbaue8qOzUVtFisSSIPR8mZdBEPWJ85tEjZ-bcX1x6Hr9APvfJSzxV1IGD0YtGBQXzGjKkLwv3RcBhGZcO-uGlOVqLwkOc4x4vzPrLvsvp64ax3EgjD7JOwoACbhyBmn_FDrL7DCLOMO5LbdibE3zZJAPqnCru7A9BAqBGbYCuKkzS-bWA2OdAxpW3UoNhLy_EVCupR2zlcr6jjPcWHaNQq8po/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D05%257C01%257Cw.yu1%2540wustl.edu%257Ce6db721793b143e5b35208da520310b4%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C637912470361937470%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252FBlFwZuuRdeZgy7CBJ3d70HXJoz5axEj8HIenw3RjpA%253D%26reserved%3D0>
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