The error message in your log file ("dyld: Symbol not found...") has been addressed here:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61247.html

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <nayanw775@gmail.com>
Sent: Tuesday, October 22, 2019 2:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all error

 

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I have attached the log-file from the trac-all command

Thanks and Regards

Nayan Wadhwani

On Mon, Oct 21, 2019 at 10:26 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

Please attach your log file from scripts/trac-all.log.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <nayanw775@gmail.com>
Sent: Tuesday, October 22, 2019 1:13 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all error

 

        External Email - Use Caution        

Hello Freesurfer,

I did changes asked by you but still error persists.

While i am using dicom images why it is asking for NIFTI format.

I checked the lib folder also and checked and all the files mention above are there in the folder.

Do i need to check something else.

Sent from my iPhone

On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, the config file seems to be in rich text format - not sure how that'll work. Try converting it to plain text (if you use mac, from the Format menu of the text editor).

Best,

Anastasia.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <nayanw775@gmail.com>
Sent: Saturday, October 19, 2019 1:36 AM
To: Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] trac-all error

 

        External Email - Use Caution        

Hello Freesurfer,

After running recon all script which completed successfully, I ran trac-all command which exited with error and tried running it with dicom files.

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

Abort  

ERROR: input file must be in NIfTI format

Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019

And please help me the correct config the one I created, I am attaching it below to try it with .nii files

Thanks and Regards

Nayan Wadhwani

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