External Email - Use Caution
Could you point me towards the correct log file? I am unable to locate it at
the moment. Also, here are the results of running tree on that directory:
INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/
├── antsdn.brain.mgz
├── aparc.a2009s+aseg.mgz
├── aparc+aseg.mgz
├── aparc.DKTatlas+aseg.mgz
├── aseg.auto.mgz
├── aseg.auto_noCCseg.label_intensities.txt
├── aseg.auto_noCCseg.mgz
├── aseg.mgz
├── aseg.presurf.hypos.mgz
├── aseg.presurf.mgz
├── brain.finalsurfs.mgz
├── brainmask.auto.mgz
├── brainmask.mgz
├── brain.mgz
├── ctrl_pts.mgz
├── filled.auto.mgz
├── filled.mgz
├── lh.ribbon.mgz
├── mri_nu_correct.mni.log
├── mri_nu_correct.mni.log.bak
├── norm.mgz
├── nu.mgz
├── orig
│ └── 001.mgz
├── orig.mgz
├── orig_nu.mgz
├── rawavg.mgz
├── rh.ribbon.mgz
├── ribbon.mgz
├── segment.dat
├── surface.defects.mgz
├── T1.mgz
├── talairach.label_intensities.txt
├── talairach.log
├── talairach_with_skull.log
├── transforms
│ ├── bak
│ ├── cc_up.lta
│ ├── talairach.auto.xfm
│ ├── talairach.auto.xfm.lta
│ ├── talairach_avi.log
│ ├── talairach_avi_QA.log
│ ├── talairach.lta
│ ├── talairach.m3z
│ ├── talairach_with_skull.lta
│ ├── talairach.xfm
│ ├── talairach.xfm.lta
│ └── talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
├── wm.asegedit.mgz
├── wm.mgz
├── wmparc.mgz
└── wm.seg.mgz
3 directories, 49 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 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.
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: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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.
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Tuesday, October 10, 2023 9:23 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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/1vPkbEAK5bMDGqCFPm2XbnT4LY6OU1C0wiLgdqP58DKdTza7_Z9slAIjVMbkcLqhnuKISWU3urLZ7EDHuLl56yllUndw9mYe75A2plvzmNvVTiSe4LXNgsON7N4_yyVBfmVsS4sp-tKxBUX-WrTk-haZAjmlxuIiAIG_WGoH9QvbU67g1WdszoZ5ENkrr2rdOqiLmbxcrj0xhAIMlG6NyEbeEM8VR7mf02_zJrc6dnvfKvXqN0o1rFL7X8ODQ81V6GU92I93-AwRwX18sscUhjDLnd01L6Jj6fzieGfgGhdIebQoBgJNo3RpL4t_ZFjx7pdNifW_RogD7-DbT5Ye4AQ/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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