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Disabling root system integrity protection seems to have solved the problem.
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2442@gmail.com
443-254-6298


On Thu, Apr 18, 2019 at 6:12 PM Daniel Callow <ddcc2442@gmail.com> wrote:
Sorry, the beginning of the email seems to have been cut off. I was trying to run trac-all on one of my subjects to troubleshoot running the following command.

trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh

I posted the errors and attached the dmrirc file I used below. 

There seems to be an issue with  








writing to /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz...


Saving bvals and bvecs


mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs


mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Ex/image000001.dcm > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dcminfo.dat


mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvecs.tmp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs


mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvals.tmp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvals


orientLAS /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz


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



The error does not seem to be due to dwi_orig.nii.gz being missing as I see it in the folderr after it has been written there in a previous command.





What could be leading to these issues?
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298


On Thu, Apr 18, 2019 at 3:18 PM Daniel Callow <ddcc2442@gmail.com> wrote:
Hello,

trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the attached configuration file. 


I get the following error message



INFO: no Siemens slice order reversal detected (good!). 

TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00

i_ras = (-1, -0, 0)

j_ras = (-0, -1, 0)

k_ras = (-0, -0, 1)

writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz...

Saving bvals and bvecs

mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs

mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image000001.dcm > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat

mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs

mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals

orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz

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 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Thu Apr 18 15:16:47 EDT 2019



and after that I get


------------------------------

SUBJECT base_AES101

DATE Thu Apr 18 15:11:44 EDT 2019

USER amos

HOST 255a-280.umd.edu

PROCESSOR x86_64

OS Darwin

Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $

/Applications/freesurfer//bin/trac-preproc

PWD /Volumes/DANIEL/dti_freesurf

CMD cp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/mni2anatorig.mat /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/anatorig2mni.mat /Volumes/DANIEL/dti_freesurf/trac/base_AES101/dmri/xfms



Any idea what might be causing the issue?


Best,



Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298