External Email - Use Caution Or, are you saying that I do not need to turn it off for NHP?
Get Outlook for iOS<https://secure-web.cisco.com/1dONy4vR-n6Y0a9Bp50DjAYEcab4XFWNYEp12Bg12m_cvRNSc_qJGeaJVW6sP25kGw-PeSPgjoIaMpSg5Eilgf0CTGogwucNX_MvODoK-ntWBQIlY8z3gZZEo_aEQagsOr7STbtigUfaQvhNOgC5cFcSYKv9RVE8z1fTN_0bLnWOZaSQ59jS9F8sAsTFxVukQKh7rpeYhybgrqbVtoNBde_-F48f8d1L3d-58wF2DvbKfLy-J_M5FJHKFZQv_FF1p-xHplxEHNxPf7kK1H9zLaQ/https%3A%2F%2Faka.ms%2Fo0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Koch, Erin M. <er...@caltech.edu> Sent: Monday, January 25, 2021 10:47:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation External Email - Use Caution Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem? Thanks, Erin Get Outlook for iOS<https://secure-web.cisco.com/1DmYXz9AvDs-8SzQ0hBvO0ciJ2KHeyjiheztEzwGHZ-eGDy03rJ8WleExBnEpox-gBx3Ssa0i_H6MCTY3EgMW-U4BzTyCSUkc5dTaNnLsHRux6UyYQdVMYOSmznSH1OAq1gsHihjOXeao-bJyLvt-uZyKU3wAMr18UT-UhnMTafbK9PU_qJQ1WwH7Pf0Ay1Nz3ylb-1O9evs7EpGe4echU9Rdknkx20O2pm_pdSN4_rwh4tLyok4bDwBp5kx1UXLhWrBtYA0YPWv8sV74P7cVVQ/https%3A%2F%2Faka.ms%2Fo0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, January 25, 2021 8:01:12 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP? On 1/15/2021 5:40 PM, Koch, Erin M. wrote: External Email - Use Caution Hi Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else. Erin ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation There have been some changes that are breaking your stream. Try this cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion On 12/14/2020 5:35 PM, Koch, Erin M. wrote: External Email - Use Caution Hi all, The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug\" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log. This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 . As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now. Thank you for your help. Best, Erin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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/1lpTEsIS7hfF765PsSmOY0KBnX0qFmnLNjmdNOgxm8D8O0th4MH_05w1Bg3DrEyCm3frTd9tZe5BJ0FjcHjbb18jUWpSwVa3Vx9jZUPknSFpdy-tjtcwGgnOgshBZTxK4tD2uVkI38MBIGqCTtggqeFu0T-ulBT5jJLFS_ndMkQbAzIvvKlHIcImpUIYnjm48OZBr075SP2TJBXdp8kAuSON-1qn7MY1Ud5oAuT_L2y8GGSRYo9n03MbuzKs0idhfG3hua8VMGoATW67r2NsT8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1_hNONTW7W5-OaDObXh6c_1aitbnlbI9-XJ6saE9Bghs0LyK-mDnSULttW89oQb38CkKoqGXcGoExhXC_PXo-5aqo3nGhKVNY2ABAENCVvjhyCeyt3NVeMHHT-WH7lHlcX3hyr9gVBrs1EJSfVlvTggckNssK7A_7fZY_-qzoKx2w1UQIk0ppXzYZBUBKBZIwobSHHRPcMXiG27nhQ9We5VoUF9iRk3Mvee8JEv2tKpIwGbmnc_nIBMZQO497bulhtNcmlejLCnzu79oXblsg6w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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/1lpTEsIS7hfF765PsSmOY0KBnX0qFmnLNjmdNOgxm8D8O0th4MH_05w1Bg3DrEyCm3frTd9tZe5BJ0FjcHjbb18jUWpSwVa3Vx9jZUPknSFpdy-tjtcwGgnOgshBZTxK4tD2uVkI38MBIGqCTtggqeFu0T-ulBT5jJLFS_ndMkQbAzIvvKlHIcImpUIYnjm48OZBr075SP2TJBXdp8kAuSON-1qn7MY1Ud5oAuT_L2y8GGSRYo9n03MbuzKs0idhfG3hua8VMGoATW67r2NsT8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1ti0YqeboWO4wmYzCGnRbvZ3P1wiehVYQ8e4iqb1fcWS-Di3tRyIzjA-B3dy979Y7ro8_U7PgG7dmMf7g1DYDfMXouQMMSBX-30iEJ1niwmyW-ajjGBnQZptjBbhr5uZtvar_Nbk_jz4CQPxInNTgcbWE7iNfAeIuFNvJMRZuH7VwKLVM1h1_BnHyu0pvMG2yZAFWwx8n54HQlqeGSvghXAa-SzBK-pkhBUhsxgvm1glR9dm8vOsHCu90ovKEaxBbA-9JTRRHOvM8hbHnC_yQHQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
