External Email - Use Caution There should be a log for the command you ran.
I’m wondering what your FREESURFER_HOME and SUBJECTS_DIR are. What are the files in /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/? From: [email protected] <[email protected]> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list <[email protected]> Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Sure thing, I have attached the two log files i could find at OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930. Please let me know if these aren't the correct log files. ________________________________ From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of Huang, Yujing <[email protected]<mailto:[email protected]>> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <[email protected]<mailto:[email protected]>> Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution The error that you cut and paste here doesn’t show which command it was running. Can you attach the log file? Best, Yujing From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: [email protected]<mailto:[email protected]> Subject: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Hello, I am attempting to create a freesurfer v7.2.0 docker container that can run tracula on the freesurfer outputs, however, I am unable to get past the intra-subject registration step without receiving the following error: --s sub-01 --mov /home/dylan/Documents/TRACULA /OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.464939/template.nii --reg /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.464939/reg.init.dat --niters 1 --maxangle 90 --tmp /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.464939/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov fslregister 7.2.0 dylan-virtual-machine Linux dylan-virtual-machine 6.2.0-32-generic #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2 x86_64 GNU/Linux nIters 1 if: Expression Syntax. ERROR: cannot find /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask Linux dylan-virtual-machine 6.2.0-32-generic #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Oct 6 09:08:11 EDT 2023 Here is a link to the github page I am using for my custom dockerfile: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ayDCnUttV5vXr7HvXq-NJ7-Abn6k527bQrCAJ-GjAglanyLP4uA5h9wSsb35_w8-NWAmXbAwaks_-iBZzi5evHpYgP7fU_IDIDLw7rZoLPMIkO2lWZithWyoz7GQJckLNPsFCEC4tBc-SDBFC6aJngIDXF8WwKtzNfTolxomRsWYDTkd9ARtq92eplzykfURf7A0svCrluS-j7QQNODjtBhXG7-zLwfGDHUAotgJD1CHyLXjYWADSqF7ope-5_05tDwOT4NlG0CVeaDzHaJyEw/https%3A%2F%2Fgithub.com%2Flawlessrd%2FTRACULA_VUIIS.git<https://secure-web.cisco.com/1p9u2_NBbOAc0qnjlGxSllp_ZZuxw7-lwoxYpC_WEQDib2nh-SHR4OWAycQlippKySYkI6oYPh48-9YEKyeU4uhUYZwiIkFGX4MWaWyKOFe9JL54EKe4hlaD1Tb0six-bEDDimHm9Ns1w2oH3-Fymqiei_fWV31CTJMQ6PJVq4hNDteG1M3YHxrHZwPlkKXId1326fBdqNWBtMhpePKtxkRDz65eGtSmSxGoZBjSEPLPYg6wz6-YQnn5LJ7M-q7tn5f7JUiN2I6oqGJAuJqRXyue2JYubQxqUcqSPVkA9oRrRqmhtlqMnid33PhuzeISf8Xi1D6xATlgJnBU4kbgTcw/https%3A%2F%2Fgithub.com%2Flawlessrd%2FTRACULA_VUIIS.git>. I used neurodocker to combine installations for FSL and Freesurfer. I am using FSL v6.0.0 and Freesurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b. The log output contains the same information as the code linked above. Machine info: uname -a Linux dylan-virtual-machine 6.2.0-32-generic #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2 x86_64 GNU/Linux I have also attached the config file I have created for this test dataset. [ WARNING : This email came from an external source. Please treat this message with additional caution.]
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