External Email - Use Caution Dear Freesurfer Team,
Thank you for this update. How can I replace the current recon-all script with this new script? Do I just replace the recon-all script located in the “bin” folder with this new script? Additionally, I was wondering if you knew when these changes might formally be incorporated in a later version of freesurfer. Thank you again for your help in advance. Sincerely, James Park From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, September 8, 2020 at 6:42 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all Try using this version of recon-all https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel On 9/8/2020 12:09 PM, Park, James wrote: External Email - Use Caution Hello, Thank you for such a prompt response. This has happened consistently and across multiple mac laptops that we utilize in our laboratory. Below is the freesurfer version that we are utilizing as noted in the build-stamp.txt file: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 That would be great thank you so much. Sincerely, James Park From: <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, September 8, 2020 at 12:06 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all The issue with the ribbon is something we recently became aware of. does it happen consistently for you? I can send you a recon-all that will fix this for you, just tell me which version you are running. On 9/8/2020 11:49 AM, Park, James wrote: External Email - Use Caution Sincerely, James Park From: "Park, James" <james.kunwoo.p...@emory.edu><mailto:james.kunwoo.p...@emory.edu> Date: Tuesday, September 8, 2020 at 11:48 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: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all Dear FreeSurfer Developers, We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag. We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed). recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel When the same code was run without the -parallel flag, the recon-all line ran successfully. This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551. The recon-all.log file has been attached here as a reference. Thank you for your help in advance. Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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