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: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@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.
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/1h1dmf0-BrrfML5cAsE2Uzp1ye7QoPfGoMVzDhbpG8_jta7BCO42Vr3qk0aOU_qAIOx1SmpVOiqUr88H02Uanb7xuvWrhrfix4kezK70NqAOhAIz6veYxgNtF3f88HpZS1k5zBsOMXe8el3Vvf7IMfwqSMFItnT5m2DVvUOy0HHi3dfvT3dspMyLs-V8IhSWPoGXh0svdDE5ucrdNMxUzbSN-U7lcM6agaKCz_K0e_pM_INeL7lsRAEcnv-Z0Hj_rv7NlJgpiBVV71zLdd4T8-YcZi9BUdFQL7GocL7RkIpJge_gMQ5u1BobSvRKsFBPV/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.]
Logfile for bbregister
Tue Oct 10 10:25:38 EDT 2023
setenv SUBJECTS_DIR /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer
cd /opt/freesurfer-7.2.0/subjects
/opt/freesurfer-7.2.0/bin/bbregister --s sub-01 --init-fsl --dti --6 --mov /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/lowb.nii.gz --reg /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/diff2anatorig.bbr.lta
bbregister 7.2.0
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
FREESURFER_HOME /opt/freesurfer-7.2.0
mri_convert /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/lowb.nii.gz /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/template.nii
mri_convert /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/lowb.nii.gz /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/template.nii
reading from /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/lowb.nii.gz...
TR=6525.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999127, 0.0416454, -0.00341054)
j_ras = (0.0415005, 0.998523, 0.0350694)
k_ras = (-0.00486598, -0.0348972, 0.999379)
writing to /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/template.nii...
fslregister --s sub-01 --mov /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/template.nii --reg /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/reg.init.dat --niters 1 --maxangle 90 --tmp /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
Log file is /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/reg.init.dat.fslregister.log
Tue Oct 10 10:25:38 EDT 2023
--s sub-01 --mov /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/template.nii --reg /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/reg.init.dat --niters 1 --maxangle 90 --tmp /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/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
Logfile for fslregister
Tue Oct 10 10:25:38 EDT 2023
--s sub-01 --mov /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/template.nii --reg /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/reg.init.dat --niters 1 --maxangle 90 --tmp /home/dylan/Documents/TRACULA/OUTPUTS/sub-01/dmri/xfms/tmp.bbregister.473930/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
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