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INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/
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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: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Lawless, Dylan
Sent: Tuesday, October 10, 2023 10:29 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
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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:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Tuesday, October 10, 2023 9:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
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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:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Lawless, Dylan
Sent: Tuesday, October 10, 2023 9:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
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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://github.com/lawlessrd/TRACULA_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.
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