Dear HCP team members, I am really sorry to bother you all again, but during running of recon-all command I am repeatedly getting this error: (standard_in) 2: Error: comparison in expression /home/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: line 80: 29951 Killed mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz "$SubjectDIR"/"$SubjectID"/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta
When I checked the output file no error was found (I have attached the output file with this mail) I saw Dr Matthew's post on freesurfer archives for the same problem (05/18/2012) and he said getopt (used in fsl-sub) doesn't work correctly when this flag is not set to 1 and it is better to set it to 0. Will you please let me know where do I make the change and what do I change it to? I am really sorry for putting up questions so many times but will greatly appreciate if I can get any answer regarding this. Much thanks for your patience and time... Regards, Sampada -- Sampada Sinha Post-Doctoral Associate University of Minnesota (East Bank) Molecular and neuroimaging laboratory Department of Psychiatry Minneapolis-55415 Phone number: 718-913-0636 email: [email protected] <email%[email protected]> [email protected] _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
FreeSurferPipeline.sh.o24550
Description: Binary data
