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: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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.
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/1K4dLmAe94DFQUgZKSZ8ekWe1UQrA7ejSPcM7n1PG1fTK-L_PnspJVpyy9kZjqdaGgUVfLJMZiKLHtFDq1RbXDLp2EmHflSPKY4oD1uPHPnRpqdn2BiDXiNCmUwGEbXMXTEmwBJHAkHX8FN53MRbrK_Lb3FruyhsuOOST3RLEyv3w2Dh-FxsbfyQly9C4FQZEJscE7nmiK0FcqU0BQSgztwRfE42-7duWajxuc9JqlDlVS7crmdsHr_mJXkf5swQB/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.
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