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I am running trac-all preproc with the following code setenv FREESURFER_HOME /Applications/freesurfer_dev source $FREESURFER_HOME/SetUpFreeSurfer.csh *#Must set SUBJECTS_DIR to where data is or else uses what was set up when installing freesurfer* setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons *#Must set up configuration file - see trac-all-config-file in dti_analysis compository* *#In configuration file can change number of subject to perform analysis on each cluster* *#RUN FIRST* trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh *and the attached configuration file. * *However, I get the following error.* #@# Intra-subject registration Tue Jul 2 18:21:42 EDT 2019 mri_convert /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz mri_convert /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz... TR=9.62, TE=3.90, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... orientLAS /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -6.32147 -1.97853 6.55573 -rt nearest /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -6.32147 -1.97853 6.55573 -rt nearest /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... TR=9.62, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Reslicing using nearest writing to /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz... tkregister2 --mov /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz --targ /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat --reg /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jul 2 18:21:47 EDT 2019 #------------------------------------- /Applications/freesurfer_dev/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Tue Jul 2 18:21:49 EDT 2019 cp /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat /Volumes/DANIEL/dti_freesurf_MCIP/trac/base_MCIP0006/dmri/xfms cp: /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat: No such file or directory cp: /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat: No such file or directory Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jul 2 18:21:49 EDT 2019 *What might be causing the issue? Does it seem like tkregister2 isn't working?* *Thank you for help or assistance you can provide.* *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_MCIP/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/DANIEL/dti_freesurf_MCIP/trac # Subject IDs (one per time point per subject) # set subjlist = (MCIP0001_pre MCIP0001_post\ MCIP0002_pre\ MCIP0002_post\ MCIP0003_pre\ MCIP0003_post\ MCIP0004_pre\ MCIP0004_post\ MCIP0006_pre\ MCIP0006_post\ MCIP0007_pre\ MCIP0007_post\ MCIP0008_pre\ MCIP0008_post\ MCIP0009_pre\ MCIP0009_post\ MCIP0010_pre\ MCIP0010_post\ MCIP0011_pre\ MCIP0011_post\ MCIP0012_pre\ MCIP0012_post\ MCIP0017_pre\ MCIP0017_post\ MCIP0019_pre\ MCIP0019_post\ MCIP0023_pre\ MCIP0023_post\ MCIP0024_pre\ MCIP0024_post\ MCIP0026_pre\ MCIP0026_post\ MCIP0027_pre\ MCIP0027_post\ MCIP0028_pre\ MCIP0028_post\ MCIP0030_pre\ MCIP0030_post\ MCIP0031_pre\ MCIP0031_post\ MCIP0032_pre\ MCIP0032_post\ MCIP0033_pre\ MCIP0033_post\ MCIP0035_pre\ MCIP0035_post\ MCIP0036_pre\ MCIP0036_post\ MCIP0041_pre\ MCIP0041_post\ MCIP0048_pre\ MCIP0048_post\ MCIP0052_pre\ MCIP0052_post\ MCIP0053_pre\ MCIP0053_post\ MCIP0054_pre\ MCIP0054_post\ MCIP0055_pre\ MCIP0055_post\ MCIP0058_pre\ MCIP0058_post\ MCIP0061_pre MCIP0061_post) # Longitudinal base template subject IDs (one for each time point above) set baselist = (base_MCIP0001 base_MCIP0001 base_MCIP0002 base_MCIP0002\ base_MCIP0003 base_MCIP0003\ base_MCIP0004 base_MCIP0004\ base_MCIP0006 base_MCIP0006\ base_MCIP0007 base_MCIP0007\ base_MCIP0008 base_MCIP0008\ base_MCIP0009 base_MCIP0009\ base_MCIP0010 base_MCIP0010\ base_MCIP0011 base_MCIP0011\ base_MCIP0012 base_MCIP0012\ base_MCIP0017 base_MCIP0017\ base_MCIP0019 base_MCIP0019\ base_MCIP0023 base_MCIP0023\ base_MCIP0024 base_MCIP0024\ base_MCIP0026 base_MCIP0026\ base_MCIP0027 base_MCIP0027\ base_MCIP0028 base_MCIP0028\ base_MCIP0030 base_MCIP0030\ base_MCIP0031 base_MCIP0031\ base_MCIP0032 base_MCIP0032\ base_MCIP0033 base_MCIP0033\ base_MCIP0035 base_MCIP0035\ base_MCIP0036 base_MCIP0036\ base_MCIP0041 base_MCIP0041\ base_MCIP0048 base_MCIP0048\ base_MCIP0052 base_MCIP0052\ base_MCIP0053 base_MCIP0053\ base_MCIP0054 base_MCIP0054\ base_MCIP0055 base_MCIP0055\ base_MCIP0058 base_MCIP0058\ base_MCIP0061 base_MCIP0061) # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects #1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 set runlist = (57 58 59 60 61 62) # 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_MCIP/diffusion_recons/ set dcmlist = ( MCIP0001.pre/MRDC.1.dcm MCIP0001.post/MRDC.1.dcm\ MCIP0002.pre/MRDC.1.dcm\ MCIP0002.post/MRDC.1.dcm\ MCIP0003.pre/MRDC.1.dcm\ MCIP0003.post/MRDC.1.dcm\ MCIP0004.pre/MRDC.1.dcm\ MCIP0004.post/MRDC.1.dcm\ MCIP0006.pre/MRDC.1.dcm\ MCIP0006.post/MRDC.1.dcm\ MCIP0007.pre/MRDC.1.dcm\ MCIP0007.post/MRDC.1.dcm\ MCIP0008.pre/MRDC.1.dcm\ MCIP0008.post/MRDC.1.dcm\ MCIP0009.pre/MRDC.1.dcm\ MCIP0009.post/MRDC.1.dcm\ MCIP0010.pre/MRDC.1.dcm\ MCIP0010.post/MRDC.1.dcm\ MCIP0011.pre/MRDC.1.dcm\ MCIP0011.post/MRDC.1.dcm\ MCIP0012.pre/MRDC.1.dcm\ MCIP0012.post/MRDC.1.dcm\ MCIP0017.pre/MRDC.1.dcm\ MCIP0017.post/MRDC.1.dcm\ MCIP0019.pre/MRDC.1.dcm\ MCIP0019.post/MRDC.1.dcm\ MCIP0023.pre/MRDC.1.dcm\ MCIP0023.post/MRDC.1.dcm\ MCIP0024.pre/MRDC.1.dcm\ MCIP0024.post/MRDC.1.dcm\ MCIP0026.pre/MRDC.1.dcm\ MCIP0026.post/MRDC.1.dcm\ MCIP0027.pre/MRDC.1.dcm\ MCIP0027.post/MRDC.1.dcm\ MCIP0028.pre/MRDC.1.dcm\ MCIP0028.post/MRDC.1.dcm\ MCIP0030.pre/MRDC.1.dcm\ MCIP0030.post/MRDC.1.dcm\ MCIP0031.pre/MRDC.1.dcm\ MCIP0031.post/MRDC.1.dcm\ MCIP0032.pre/MRDC.1.dcm\ MCIP0032.post/MRDC.1.dcm\ MCIP0033.pre/MRDC.1.dcm\ MCIP0033.post/MRDC.1.dcm\ MCIP0035.pre/MRDC.1.dcm\ MCIP0035.post/MRDC.1.dcm\ MCIP0036.pre/MRDC.1.dcm\ MCIP0036.post/MRDC.1.dcm\ MCIP0041.pre/MRDC.1.dcm\ MCIP0041.post/MRDC.1.dcm\ MCIP0048.pre/MRDC.1.dcm\ MCIP0048.post/MRDC.1.dcm\ MCIP0052.pre/MRDC.1.dcm\ MCIP0052.post/MRDC.1.dcm\ MCIP0053.pre/MRDC.1.dcm\ MCIP0053.post/MRDC.1.dcm\ MCIP0054.pre/MRDC.1.dcm\ MCIP0054.post/MRDC.1.dcm\ MCIP0055.pre/MRDC.1.dcm\ MCIP0055.post/MRDC.1.dcm\ MCIP0058.pre/MRDC.1.dcm\ MCIP0058.post/MRDC.1.dcm\ MCIP0061.pre/MRDC.1.dcm\ MCIP0061.post/MRDC.1.dcm) # 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 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 = () 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 = 0 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0mlist = () # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # set echospacing = 0 # 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 = 0.3 # 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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