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_...

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/1TEXQ5EYB9LOX23P4f0QsCWsgDayARXAUE94TZk30GfILIEm...

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