External Email - Use Caution 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 *ddcc2...@gmail.com <ddcc2...@gmail.com>* 443-254-6298
On Thu, Apr 18, 2019 at 6:12 PM Daniel Callow <ddcc2...@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 > *ddcc2...@gmail.com <ddcc2...@gmail.com>* > 443-254-6298 > > > On Thu, Apr 18, 2019 at 3:18 PM Daniel Callow <ddcc2...@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 >> *ddcc2...@gmail.com <ddcc2...@gmail.com>* >> 443-254-6298 >> >
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