Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

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Thanks, but the issue isn't that graphics aren't displaying, it's that freeview won't load because qt can't be initialized.

Abeoseh Flemister ________________________________ From: fsbuild fsbuild@contbay.com Sent: Friday, January 5, 2024 8:27 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Flemister, Abeoseh B. flemistera@missouri.edu Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "Re: [Freesurfer] Freeview not showing output",

https://secure-web.cisco.com/1MhQHLfqOsV0yN00hyLvm-y1m7NI9NP7S-GpPfeIKcao9Gu...

In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL above, that link is,

https://secure-web.cisco.com/1D77XANVVrjdkYfjYWX5qP542z7Dn3Frt2Qvbz-sr_9p66h...

- R.

On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. flemistera@missouri.edu wrote:

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Hi Yujing,

Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve unfortunately run into another error: This application failed to start because no Qt platform plugin could be initialized.

I saw an emailhttps://secure-web.cisco.com/1sex5BbjwVm7Vqn3F18BjMh4cio7IL8BUJJSNfISgMRjE97tPF6susbOp_EibTi_Rib1-3fWMGSEj8zGWHPxLR2GefWAJO6hAMhWk3ljFTJNt8UzJJ7g64luToLn5QhJsNduB0adfJnSocWm3Sr6UXIQTw_VG14v1_iXsFwciWl3tqZKsyg4XY7Bj1YRW5OCyZ_QQM_SNARfbprfL44uGWj3HS0vRM0ajIPDdJjRJEdjU_dtmR8Y7hdnowdnjN8MA7dH5ev7ZR64zoszVrlcknlcTe1L7BwLGzdSTIMvQRymZDCdDaTO7Ed60jgqgQZjr/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66231.html on this topic but I don't think it was ever answered.. Apologies if I'm reading the thread wrong. Any help would be greatly appreciated!

Abeoseh Flemister ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Friday, January 5, 2024 3:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. This is from your recon-all.log “ mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz") “

There is a space in your path to nii.gz. Can you remove the space by renaming the directory?

Also, your SUBJECTS_DIR points to your Freesurfer install directory - /usr/local/freesurfer/subjects. You might run into permission or symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Flemister, Abeoseh B. Sent: Friday, January 5, 2024 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

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Hi FreeSurfer Team,

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread https://secure-web.cisco.com/1dNYuQ5feZYQ6hNc76goinSvD-Ypnc3onN5YQA8IZaGD9ZMsgPU8h02eq6smQW_JlVSoe2pmWi9i4IcVcvgPNAErLGWflT-2DHnEGZhHuYuSO7uagH4fed_iEleZMZ8fgVidAMFlNu_V6xq1SiHRk7nBL5_vNP6s-l8W5JP5TtFTlM7qsiZb0cfyjC0beae7q8RstHZ1a7H1bThMO8tUOdBPq6h2mtRu15a6hLnBK4v7YbPIeyWQj1PNy1poAzCsu_PpjvCs0OTiVKjJIHv6obmHjItvr-tP8RedoW0g4wzOQSCgST1rQnUsemz7IcLPP/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg62253.html where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains.

I attached my recon-all.logs.. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions!

Thanks, Abeoseh Flemister _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1PFNTyeGz0gtw1JvlbsnH4k_ZWiaBRnQzBHuh8e3Nfaf2po...