Re: [Freesurfer] recon-all -long error (the third step of the longitudinal pipeline)

What happens if you remove -parallel? That flag does not do much any more but cause trouble (we have removed it in recent versions)

On 5/3/2022 2:58 PM, FONG, manson CM [CBS] wrote:

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Hello Experts,

I'm attempting to run the longitudinal pipeline, as described in this tutorial page (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial https://secure-web.cisco.com/1Ixk7gG7cuuWHkljgthBFn12YPhnTaeVaFK7XUh0r8RABWOczLFEHenETdpjMXuBvtHTYhkyQHUY_jcSnOm3F4ioC4XITBqfSUk3TszuSu5O5sJoqBytSbe7R-iRpQYcpcZu9VrtyyO2-NRsKeVIGOHKAsBzJA0ZfyJQOp7OEBqrMXdtFG2So7d_P9RmGzsr98M_Ddd72CSDjT1na4EJKG0f2Uy0KhLR-nVRT09EXf3yvbP2zZs6SnrycNJaPd-DBwFHHJqxiIjoVScybOZFgUt-uvE41YIFGWMdFMEQwXsjI6ibzxClVoCEkqc6zKAJD/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial). 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

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