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Hello,
I was runnning reconall in one of my images and it got stucked fixing surface defects, since i run it on a cluster it stopped when it runned out from cpu time. As you will see in the log the command started in SUNday 16 14:59:32 CEST 2019 and ended in Mon Jun 17 05:10:16 CEST 2019 which is more than usual for a recon-all duration. I have checked some of the previous images and there is clearly an alignment problem as you can check in this image:
How can I solve this error? freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c OP:ubuntu 18 command: recon-all -all -s $SUBJ$session -i $T1 -sd $SUBJECTS_DIR \ -hippocampal-subfields-T1 -brainstem-structures -3T -openmp 1 thank you, Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu
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