External Email - Use Caution Dear FreeSurfer Developers,
I hope this email finds you well. I'm an MRes student from Imperial College London. I'm attempting to run recon-all in parallel, as described in the FreeSurfer tutorial of Andy's brain book: https://secure-web.cisco.com/1f8N_u253wnYss7NsLFujqzigTyBNU3U_hugHrybuTHK9C_Sf3BWtmSIBfxyKZ5t_Xe0OMDi53roE3DYCbdyCpXGTJNusKkD3C1AX2PJ_lubSB7XtTe-Bo0_QcZV6sDyiNhlBt6QFIqzeas-CidAMJVgwkAKsFiyz2KMJ2OoY2hhBiIv5qCubyyPEeuU3LjD0gzRWClmy3Bxpeao_SacJjLAmiGGP7dmg9OOFGoWxQeG5Du1d3LcrdkhhyIj9hWJiL63oFvTtEtzthwMjp54-g7HeS6uiS9LE8mAnkexzizCKgP0-4HOf8n8A1_sHu9QTMzkYCbSY58AM33_21_rdjg/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_04_ReconAllParallel.html The appropriate way would be: ls .. | grep sub- > subjList.txt # here I deleted the special character of subject number manually, the right format would be `sub-101` for sub in `cat subjList.txt`; do cp ../${sub}/ses-BL/anat/*.gz . done gunzip *.gz SUBJECTS_DIR=`pwd` ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache # the last step However, when running the last step, I've got the following error: ERROR: cannot find sub-101_ses-BL_T1w.nii Linux nhp-System-Product-Name 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-101_ses-BL_T1w exited with ERRORS at 2022 02 18 Friday 10:49:24 CST For more details, see the log file To report a problem, see http://secure-web.cisco.com/1TEXQ5EYB9LOX23P4f0QsCWsgDayARXAUE94TZk30GfILIEmrLkX205hI385WF8KsYMldy7cb12muDTSO7GCHPyBlgzjZFLwcs_mK44KGZXsLd3xP7OexgAuBukVFvJFWj-1pP4ZKfOs946IA9iJOHKDIAJOL3InRYN7iRVgD7qMmInijZM1I-bTRqUq9ZVE0MjNaam3IX-sh-6FnohulVsEVBDtiUMA4phnVdT5aNOsrthHmVJqnOtfyZydkiyvn0U_bzIRaoUCGd4p6pIqz_6zgMoPyFnj5izN8i3sUY5oUG2eXK-bkK4oKSzgi7NNwqRJlLfQjncJpFpXU7dKUDA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting In addition, I have attached the dataset that has been processed except for the last step in my last email, the recon-all.log weren't generated in this case. Does anyone have any thoughts on how to trouble-shoot this issue? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.7 (Final) 3) uname -a: Linux nhp-System-Product-Name 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: were not generated Many thanks in advance! Best regards, Ye
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