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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
# # 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 = ( AES101.Ex/image000001.dcm AES101.Rest/image000001.dcm) # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = () # Diffusion gradient table (if using the same one for all scans) # Must be specified if it cannot be read from the DICOM headers # The table must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bvecfile = () # Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = () # Diffusion b-value table # Must be specified if it cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvalfile = () # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0mlist = (AES101.Ex/field/TE4.92_image000001.dcm AES101.Rest/field/TE4.92_image000001.dcm ) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0plist = ( AES101.Ex/phase/TE4.92_image000001.dcm AES101.Rest/phase/TE4.92_image000001.dcm ) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # set cvstemp = # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # set cvstempdir = # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 10000 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0
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