Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

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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.

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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/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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