Re: [Freesurfer] issue running trac-all longitudinal
External Email - Use Caution 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/image01.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 *ddcc2...@gmail.com * 443-254-6298 On Fri, Apr 19, 2019 at 8:04 AM Daniel Callow 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 > *ddcc2...@gmail.com * > 443-254-6298 > > > On Thu, Apr 18, 2019 at 6:12 PM Daniel Callow 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/image01.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 * >> 443-254-6298 >> >> >> On Thu, Apr 18, 2019 at 3:18 PM Daniel Callow 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=6
Re: [Freesurfer] issue running trac-all longitudinal
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 * 443-254-6298 On Thu, Apr 18, 2019 at 6:12 PM Daniel Callow 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/image01.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 * > 443-254-6298 > > > On Thu, Apr 18, 2019 at 3:18 PM Daniel Callow 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/image01.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
Re: [Freesurfer] issue running trac-all longitudinal
External Email - Use Caution 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/image01.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 * 443-254-6298 On Thu, Apr 18, 2019 at 3:18 PM Daniel Callow 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/image01.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_
[Freesurfer] issue running trac-all longitudinal
External Email - Use Caution 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/image01.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 * 443-254-6298 # # dmrirc.long.example # # This example is applicable to longitudinal studies, where DWI data from # multiple time points are available for each subject. For a simple example # with a single DWI data set per subject, see dmrirc.example instead. # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: #$Author: zkaufman $ #$Date: 2016/12/20 17:04:05 $ #$Revision: 1.3.2.1 $ # # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" # # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer@nmr.mgh.harvard.edu # # # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/DANIEL/dti_freesurf/trac # Subject IDs (one per time point per subject) # set subjlist = (Ex.AES101 Rest.AES101) # Longitudinal base template subject IDs (one for each time point above) # set baselist = (base_AES101 base_AES101) # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # set runlist = () # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) # set dcmroot = /Volumes/DANIEL/dti_freesurf/diffusion_recons/ set dcmlist
