Dear Freesurfers, I am trying to run trac-all with many subjects through a configuration file. The first subject gets processed without error, but after that I keep getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found.
This is my command with the output (below configuration file and the log file) trac-all -prep -c dmrirc_bonn_running2only.txt -no-isrunning INFO: SUBJECTS_DIR is /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients INFO: Diffusion root is /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/dmrirc.local -log /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.log -cmd /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.cmd -no-isrunning #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue 26 Aug 2014 10:34:54 BST mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999333, -0.0350092, 0.0104045) j_ras = (-0.0349891, 0.999385, 0.00210945) k_ras = (0.010472, -0.001744, 0.999944) writing to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz... flip4fsl /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.02198 fslswapdim /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz x y z /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz mv -f /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs mv: rename /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs: No such file or directory Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 Thanks in advance for all your help! All the best, Barbara My configuration file looks like this: # # 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: ayendiki $ # $Date: 2013/02/16 22:49:06 $ # $Revision: 1.3.2.4 $ # # 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 /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients # Subject IDs # set subjlist = ( 3258 3734^20100714^5 3790^20071127^6 3854 4099 4130^20081031^8 4279^20080519^8 4335^20080607^5 449^20070514^4 4585 4594^20081017^4 4597^20081110^5 4695 4928^20090226^12 4969 5018 5040 5125 5141 5236^20100706^12 5239 5346 5351 5377^20100615^14 5658 5948 5968 6091 6116 6189 6369 6541 6671 6770 7064 7174^20110828^5 7220 7231 7241 923^20080410^5 c0039 c0056 c0067 c0132 c0136 c0137 c0187 c0306 c0324 c0337 c0349 c0359 c0389 c0442 c0443 c0474 c0542 c0627 c0660 c0688 c0773 c1088 c3422 c3667 c3728 c3768 c3789 c3826 c4932 c5279 c5511 L4974 L4995 L5041 L5222 L5242 L5302 L5303 L5309 L5416 L5424 L5433 L5436 L5438 L5447 L5480 L5777 L6017 L6023 L6077 L6078 L6126 L6178 L6300 L6522 L6549 L6794 R1087 R4523 R4700 R4858 R5208 R5219 R5412 R5844 R5973 R5974 R6058 R6081 R6297 R6596 R6774 R7192 ) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects set runlist = (5) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile, bvalfile, and nb0 must be specified (see below) set dcmlist = ( /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3258/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3734^20100714^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3790^20071127^6/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3854/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4130^20081031^8/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4279^20080519^8/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4335^20080607^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/449^20070514^4/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4585/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4594^20081017^4/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4597^20081110^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4695/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4928^20090226^12/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4969/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5018/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5040/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5125/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5141/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5236^20100706^12/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5239/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5346/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5351/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5377^20100615^14/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5658/data.nii.gz 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/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5041/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5222/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5242/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5302/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5303/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5309/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5416/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5424/data.nii.gz 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/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6077/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6078/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6126/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6178/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6300/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6522/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6549/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6794/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R1087/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4523/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4700/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4858/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5208/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5219/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5412/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5844/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5973/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5974/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6058/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6081/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6297/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6596/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6774/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R7192/data.nii.gz ) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bveclist = ( /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3258/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3734^20100714^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3790^20071127^6/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3854/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4130^20081031^8/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4279^20080519^8/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4335^20080607^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/449^20070514^4/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4585/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4594^20081017^4/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4597^20081110^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4695/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4928^20090226^12/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4969/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5018/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5040/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5125/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5141/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5236^20100706^12/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5239/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5346/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5351/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5377^20100615^14/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5658/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5948/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5968/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6091/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6116/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6189/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6369/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6541/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6671/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6770/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7064/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7174^20110828^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7220/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7231/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7241/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/923^20080410^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0039/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0056/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0067/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0132/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0136/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0137/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0187/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0306/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0324/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0337/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0349/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0359/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0389/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0442/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0443/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0474/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0542/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0627/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0660/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0688/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0773/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c1088/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3422/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3667/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3728/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3768/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3789/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3826/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c4932/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5279/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5511/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4974/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4995/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5041/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5222/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5242/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5302/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5303/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5309/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5416/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5424/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5433/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5436/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5438/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5447/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5480/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5777/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6017/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6023/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6077/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6078/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6126/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6178/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6300/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6522/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6549/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6794/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R1087/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4523/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4700/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4858/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5208/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5219/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5412/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5844/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5973/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5974/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6058/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6081/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6297/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6596/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6774/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R7192/data.bvec ) # set bvallist = ( /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3258/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3734^20100714^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3790^20071127^6/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3854/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4130^20081031^8/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4279^20080519^8/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4335^20080607^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/449^20070514^4/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4585/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4594^20081017^4/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4597^20081110^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4695/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4928^20090226^12/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4969/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5018/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5040/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5125/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5141/data.bval 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/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5242/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5302/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5303/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5309/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5416/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5424/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5433/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5436/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5438/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5447/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5480/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5777/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6017/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6023/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6077/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6078/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6126/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6178/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6300/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6522/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6549/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6794/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R1087/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4523/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4700/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4858/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5208/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5219/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5412/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5844/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5973/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5974/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6058/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6081/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6297/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6596/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6774/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R7192/data.bval ) # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 6 # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # 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 = 0.2 # 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 # # 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 # # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # 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 # # 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 # # 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: 5000 # set nsample = 7500 # 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 My trac-all log is this Tue 26 Aug 2014 10:34:51 BST /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients /Applications/freesurfer/bin/trac-all -prep -c dmrirc_bonn_running2only.txt -no-isrunning Subject 4099 SUBJECTS_DIR /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 NEURO-220 NEURO-220.local Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 16G used (3274M wired), 48G unused. ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 New invocation of trac-preproc NEURO-220 NEURO-220.local Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 16G used (3275M wired), 48G unused. #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue 26 Aug 2014 10:34:54 BST mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999333, -0.0350092, 0.0104045) j_ras = (-0.0349891, 0.999385, 0.00210945) k_ras = (0.010472, -0.001744, 0.999944) writing to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz... flip4fsl /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.02198 fslswapdim /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz x y z /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz mv -f /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs mv: rename /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs: No such file or directory Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue 26 Aug 2014 10:36:26 BST
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