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Sorry, that fix did not infact fix the problem. I am still getting the following error.
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
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 15:12:04 EDT 2019
Any help you can provide with debugging would be greatly appreciated. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Fri, Apr 19, 2019 at 8:04 AM Daniel Callow ddcc2442@gmail.com wrote:
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 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 *ddcc2442@gmail.com ddcc2442@gmail.com* 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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298