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: https://secure-web.cisco.com/1p9u2_NBbOAc0qnjlGxSllp_ZZuxw7-lwoxYpC_WEQDib2n... 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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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.
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...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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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.
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-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.
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_jta7...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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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.
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: freesurfer@nmr.mgh.harvard.edumailto: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/1ayDCnUttV5vXr7HvXq-NJ7-Abn6k527bQrCAJ-GjAglany...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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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-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 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-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.
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: freesurfer@nmr.mgh.harvard.edumailto: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/1vPkbEAK5bMDGqCFPm2XbnT4LY6OU1C0wiLgdqP58DKdTza...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.]
[ WARNING : This email came from an external source. Please treat this message with additional caution.]
External Email - Use Caution
I don’t understand how the error could happen, and where ‘if: Expression Syntax.’ comes from. The error was reported from this sections code in fslregister:
set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol` if(! -e "$refvol") then echo "ERROR: cannot find $SUBJECTS_DIR/$subjid/mri/$fsvol" exit 1; endif
Can you ‘stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask’ from your command line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:01 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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: freesurfer@nmr.mgh.harvard.edumailto: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://secure-web.cisco.com/11de1w2dcQF74TDU571d6c_IPpqChXvZ4C9LySAlxcsl-It...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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I ran this command and received the same error:
Singularity> stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask if: Expression Syntax.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Wednesday, October 11, 2023 9:32 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Maffei, Chiara, PHD CMAFFEI@mgh.harvard.edu; Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
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I don’t understand how the error could happen, and where ‘if: Expression Syntax.’ comes from. The error was reported from this sections code in fslregister:
set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
if(! -e "$refvol") then
echo "ERROR: cannot find $SUBJECTS_DIR/$subjid/mri/$fsvol"
exit 1;
endif
Can you ‘stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask’ from your command line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:01 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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: freesurfer@nmr.mgh.harvard.edumailto: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/1LMTzVLcPAicgJi1fUYAb73NuZQ6EmtGFx1EUEvl4E-QwKi...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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External Email - Use Caution
Ok, now we know stem2fname is the problem. I can’t reproduce the error on my end.
If you do ‘which stem2fname’, it returns the location of the script. Can you change the first line from “#! /bin/csh -f” to “#! /bin/tcsh -f”?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:39 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 I ran this command and received the same error:
Singularity> stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask if: Expression Syntax.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Wednesday, October 11, 2023 9:32 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Maffei, Chiara, PHD <CMAFFEI@mgh.harvard.edumailto:CMAFFEI@mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
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I don’t understand how the error could happen, and where ‘if: Expression Syntax.’ comes from. The error was reported from this sections code in fslregister:
set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
if(! -e "$refvol") then
echo "ERROR: cannot find $SUBJECTS_DIR/$subjid/mri/$fsvol"
exit 1;
endif
Can you ‘stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask’ from your command line?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: freesurfer@nmr.mgh.harvard.edumailto: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://secure-web.cisco.com/1V_D2AJpmryI5mwXyys2apcnzIVLHcF04ujKvW9ZRBOKJCf...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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I made the change you suggested but it didn’t appear to have any effect. I still get the same if: Syntax error with trac-all.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, October 11, 2023 10:12 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Maffei, Chiara, PHD CMAFFEI@mgh.harvard.edu; Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
External Email - Use Caution Ok, now we know stem2fname is the problem. I can’t reproduce the error on my end.
If you do ‘which stem2fname’, it returns the location of the script. Can you change the first line from “#! /bin/csh -f” to “#! /bin/tcsh -f”?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:39 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 I ran this command and received the same error:
Singularity> stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask if: Expression Syntax.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Wednesday, October 11, 2023 9:32 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Maffei, Chiara, PHD <CMAFFEI@mgh.harvard.edumailto:CMAFFEI@mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.
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I don’t understand how the error could happen, and where ‘if: Expression Syntax.’ comes from. The error was reported from this sections code in fslregister:
set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
if(! -e "$refvol") then
echo "ERROR: cannot find $SUBJECTS_DIR/$subjid/mri/$fsvol"
exit 1;
endif
Can you ‘stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask’ from your command line?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 9:52 AM To: freesurfer@nmr.mgh.harvard.edumailto: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/1bEPmp1R804ZxfhwsjHiVSTO1JVBgjiXMqvSunCWFKlEBWf...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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freesurfer@nmr.mgh.harvard.edu
-
Huang, Yujing -
Lawless, Dylan