It looks like you stopped the job and restarted it. Is that correct? If so, I think something might have gotten out of sync. If you did not make any edits (eg, to correct the defects), then can you start it from scratch?
On 5/12/2022 4:29 PM, Margot Wagner wrote:
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Hello FreeSurfer Developers,
I am attempting to run the HCPPipeline https://secure-web.cisco.com/1PrAyMCdNwWvmMb6-wd3cHZJPug7g4q9HEG-M9vN9SZYsjXT-XKY80ahU19Ui3uSE5SH6F8clsGzY3qbZJYTflApEWyryPDvtjrHNpGtahIY410hI7IB0G4o84lfZ3ISLzb0OcJ8zaX9UnMLXVyUAi8DxOkIueqJZurPNlnEUvMN1fKDqfbo_MWmu6DagUM7iqHOe5ga-3ONm9r4uzMVRBHbOT671eL5mZUqlXCY9N3Uyxb02xjQd6h291_yRztIHkC7CU5W8AMfEbLhVbpo-txTZfyn63rBokvJK0lJqmuq81UiXg1YIWmf--XbVt1ptC4SKOP3KOHxJHy_xVkx1LQ/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines using their provided example data according to their Installation and Usage Intructions https://secure-web.cisco.com/1Y9my6pk8D5YRbrVEZ1pMFY43_her0g021-eYiIxAcX3X1h6JAWWxWr7ZMJFM0vC8f4tzZQ9tQXpuLpRiPM-8QV7OAXcWVHwEtpVFROVeEY4z8MJa7BZQ5MET3VEnwoPpvG9kdGVR-t6U9GYK3uTl6uTJRBYoQTDNTp6Z6pD-vCgB_qP6TeXW0Thmla548L7BScrsc5abLNX2vSwX4TXrthZ2eKdhj7PcFbBUTNmtrKk0uaKb_Y7jVKQGzrJABhMFI0__O3qqHplMd8yEppSRU5FtuRuVXr97BC9lJw7stKpt7RJZU4Bl4BlfxVTVaqWnCXcY9icDRMg4Ppoce6-UeA/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fwiki%2FInstallation-and-Usage-Instructions%23getting-example-data.
Currently, I am trying to run FreeSurferPipelineBatch.sh and got an error message in FreeSurferPipeline.sh when it tries to run mri_surf2surf:
Reading source surface reg /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc No such file or directory mri_surf2surf: could not read surface /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc No such file or directory ERROR:
This occurs immediately after attempting to run mri_surf2surf --s 100307 --hemi lh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg
It appears no file lh.white.preaparc is made, nor any file matching "white" or "preaparc". I have been unable to find similar errors.
Attached is the output from the FreeSurferPipeline run as well as recon-all.log.
- FreeSurfer
version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 2) Platform: Debian GNU/Linux 10 (buster) 3) uname -a: Linux porter 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 GNU/Linux 4) recon-all.log: see attached
Thank you for your assistance.
-- Best Regards, Margot Wagner Graduate Student Researcher UCSD Bioengineering
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer