New subject: recon-all -long error (the third step of the longitudinal pipeline)

3 May 2022


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Hello Experts,
I'm attempting to run the longitudinal pipeline, as described in this tutorial page (https://secure-web.cisco.com/1Ixk7gG7cuuWHkljgthBFn12YPhnTaeVaFK7XUh0r8RABWO...). I've tried the pipeline on 13 subjects (from the Alzheimer Disease Neuroimaging Initiative), each with varying number of time points. For all of them, I succeeded in the first two steps ( [CROSS] & [BASE] ), but recon-all threw an error for all subjects & for all time-points midway through the third step ( [LONG] ).
For example, for the subject 128_S_4832, I've run the cross-sectional step for all time points, resulting in corresponding folders called $SUBJECTS_DIR/128_S_4832_Ses01 and so on, and a template in the folder $SUBJECTS_DIR/128_S_4832 (from the [BASE] step). The exact command that exited with ERRORS was:
recon-all -long 128_S_4832_Ses01 128_S_4832 -all -parallel -openmp 16
Like in the first two step, I was using parallel computing with 16 cores. From recon-all.log in the folder $SUBJECTS_DIR/128_S_4832_Ses01.long.128_S_4832/scripts, it appears that the last command that reported no issue was:
mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
After this step, recon-all threw an error. The last four lines in my log file are:
Usage: reconbatchjobs logfile cmdfile1 [cmdfile2 ...]
See recon-all script for examples.
Linux ubda-d050 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 128_S_4832_Ses01.long.128_S_4832 exited with ERRORS at Sat Apr 30 22:10:07 HKT 2022
I've searched the list and no similar errors have been reported.
1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) Platform: CentOS Linux 7 (Core)
3) recon-all.log & recon-all.error: see attached
Many thanks for your advice in advance!
Best regards,
Manson Fong
[https://secure-web.cisco.com/1RCpfhD31IvrvhPAqouiPEccsev2Meg7QPUJ7MSltmEQqz4...]
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