Hi again,
Still having the aforementioned R issue when running fix with a working copy of R and all it's libraries, my fault for posting late on a Friday. I've attached a log file of my issue generated by Adam Thomas, hopefully it's enlightening. Basically the R Batch command fails because it thinks it wants a file when it is given a directory, see my earlier post or the attachment for the exact error.
Thanks!
Jen
Script started on Mon Oct 27 15:34:57 2014
]0;evansjw@felix:/data/evansjw/fix1.06[?1034h[evansjw@felix fix1.06]$ /data/evansjw/fix1.06/fix -c /data/evansjw/ICA_fun/20pc
_e2/21Apr_gui.ica/ /data/evansjw/fix1.06/training_files/Standard.RData/ 20
+++ dirname /data/evansjw/fix1.06/fix
++ cd /data/evansjw/fix1.06
++ pwd
+ FSL_FIXDIR=/data/evansjw/fix1.06
+ export FSL_FIXDIR
+ . /data/evansjw/fix1.06/settings.sh
++ FIXVERSION=1.06
+++ uname -s
++ FSL_FIX_OS=Linux
+++ uname -m
++ FSL_FIX_ARCH=x86_64
++ '[' -z /data/evansjw/fix1.06 ']'
++ '[' -z '' ']'
++ FSL_FIX_MATLAB_ROOT=/usr/local/
++ FSL_FIX_MATLAB=/usr/local//bin/matlab
++ FSL_FIX_MCC=/usr/local//bin/mcc
++ FSL_FIX_MCRROOT=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime
++ '[' -f /data/evansjw/fix1.06/MCR.version ']'
+++ cat /data/evansjw/fix1.06/MCR.version
++ FSL_FIX_MCRV=v717
++ '[' '!' -z v717 ']'
++ FSL_FIX_MCR=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime/v717
++ FSL_FIX_MLCDIR=/data/evansjw/fix1.06/compiled/Linux/x86_64
++ FSL_FIX_MLOPTS='-nojvm -nodisplay -nodesktop -nosplash'
++ FSL_FIX_MLEVAL=-r
++ FSL_FIX_MLFILE='\<'
++ FSL_FIX_OCTAVE=/usr/bin/octave
++ FSL_FIX_OCOPTS='--traditional -q --no-window-system'
++ FSL_FIX_OCEVAL=--eval
++ FSL_FIX_OCFILE=
++ FSL_FIX_MATLAB_MODE=1
++ FSL_FIX_CIFTIRW=/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter
++ FSL_FIX_WBC=/vols/Data/HCP/workbench/bin_linux64/wb_command
++ export FSL_FIX_CIFTIRW FSL_FIX_WBC
++ '[' -z /data/evansjw/fsl ']'
++ FSL_FIX_FSLMATLAB=/data/evansjw/fsl/etc/matlab
+ '[' /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ = '' ']'
+ domot=0
+ loo=0
+ aggressive=0
+ '[' _-c '!=' _ ']'
+ '[' -c = -f ']'
+ '[' -c = -t ']'
+ '[' -c = -c ']'
+ fix_mode=3
+ '[' 20 = '' ']'
+ MELOUT=/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
++ dirname /data/evansjw/fix1.06/training_files/Standard.RData/
++ basename /data/evansjw/fix1.06/training_files/Standard.RData/ .RData
+ TRAIN=/data/evansjw/fix1.06/training_files/Standard.RData
+ THRESH=20
+ '[' '!' -d /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ ']'
+ '[' '!' -f /data/evansjw/fix1.06/training_files/Standard.RData ']'
+ shift 4
+ '[' _ '!=' _ ']'
+ case $fix_mode in
+ echo 'FIX Classifying components in Melodic directory: /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ using training file: /data/evansjw/fix1.06/training_files/Standard.RData and threshold 20'
FIX Classifying components in Melodic directory: /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ using training file: /data/evansjw/fix1.06/training_files/Standard.RData and threshold 20
+ CheckFeatures /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ '[' '!' -f /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/features.csv ']'
+ echo FIX features not already generated, so creating them now.
FIX features not already generated, so creating them now.
+ /data/evansjw/fix1.06/fix -f /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+++ dirname /data/evansjw/fix1.06/fix
++ cd /data/evansjw/fix1.06
++ pwd
+ FSL_FIXDIR=/data/evansjw/fix1.06
+ export FSL_FIXDIR
+ . /data/evansjw/fix1.06/settings.sh
++ FIXVERSION=1.06
+++ uname -s
++ FSL_FIX_OS=Linux
+++ uname -m
++ FSL_FIX_ARCH=x86_64
++ '[' -z /data/evansjw/fix1.06 ']'
++ '[' -z '' ']'
++ FSL_FIX_MATLAB_ROOT=/usr/local/
++ FSL_FIX_MATLAB=/usr/local//bin/matlab
++ FSL_FIX_MCC=/usr/local//bin/mcc
++ FSL_FIX_MCRROOT=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime
++ '[' -f /data/evansjw/fix1.06/MCR.version ']'
+++ cat /data/evansjw/fix1.06/MCR.version
++ FSL_FIX_MCRV=v717
++ '[' '!' -z v717 ']'
++ FSL_FIX_MCR=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime/v717
++ FSL_FIX_MLCDIR=/data/evansjw/fix1.06/compiled/Linux/x86_64
++ FSL_FIX_MLOPTS='-nojvm -nodisplay -nodesktop -nosplash'
++ FSL_FIX_MLEVAL=-r
++ FSL_FIX_MLFILE='\<'
++ FSL_FIX_OCTAVE=/usr/bin/octave
++ FSL_FIX_OCOPTS='--traditional -q --no-window-system'
++ FSL_FIX_OCEVAL=--eval
++ FSL_FIX_OCFILE=
++ FSL_FIX_MATLAB_MODE=1
++ FSL_FIX_CIFTIRW=/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter
++ FSL_FIX_WBC=/vols/Data/HCP/workbench/bin_linux64/wb_command
++ export FSL_FIX_CIFTIRW FSL_FIX_WBC
++ '[' -z /data/evansjw/fsl ']'
++ FSL_FIX_FSLMATLAB=/data/evansjw/fsl/etc/matlab
+ '[' /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ = '' ']'
+ domot=0
+ loo=0
+ aggressive=0
+ '[' _-f '!=' _ ']'
+ '[' -f = -f ']'
+ fix_mode=1
+ '[' /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ = '' ']'
+ MELOUT=/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ '[' '!' -d /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ ']'
+ shift 2
+ '[' _ '!=' _ ']'
+ case $fix_mode in
+ echo 'FIX Feature extraction for Melodic output directory: /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'
FIX Feature extraction for Melodic output directory: /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ mkdir -p /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix
+ echo 1.06
+ echo ' create edge masks'
create edge masks
+ /data/evansjw/fix1.06/fix_0a_create_edge_masks /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ echo ' run FAST'
run FAST
+ /data/evansjw/fix1.06/fix_0b_apply_fast /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ echo ' registration of standard space masks'
registration of standard space masks
+ /data/evansjw/fix1.06/fix_0c_reg_masks /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ /data/evansjw/fix1.06
+ echo ' extract features'
extract features
+ /data/evansjw/fix1.06/call_matlab.sh -l /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/logMatlab.txt -f fix_1a_extract_features /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ '[' -z /data/evansjw/fix1.06 ']'
+ . /data/evansjw/fix1.06/settings.sh
++ FIXVERSION=1.06
+++ uname -s
++ FSL_FIX_OS=Linux
+++ uname -m
++ FSL_FIX_ARCH=x86_64
++ '[' -z /data/evansjw/fix1.06 ']'
++ '[' -z '' ']'
++ FSL_FIX_MATLAB_ROOT=/usr/local/
++ FSL_FIX_MATLAB=/usr/local//bin/matlab
++ FSL_FIX_MCC=/usr/local//bin/mcc
++ FSL_FIX_MCRROOT=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime
++ '[' -f /data/evansjw/fix1.06/MCR.version ']'
+++ cat /data/evansjw/fix1.06/MCR.version
++ FSL_FIX_MCRV=v717
++ '[' '!' -z v717 ']'
++ FSL_FIX_MCR=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime/v717
++ FSL_FIX_MLCDIR=/data/evansjw/fix1.06/compiled/Linux/x86_64
++ FSL_FIX_MLOPTS='-nojvm -nodisplay -nodesktop -nosplash'
++ FSL_FIX_MLEVAL=-r
++ FSL_FIX_MLFILE='\<'
++ FSL_FIX_OCTAVE=/usr/bin/octave
++ FSL_FIX_OCOPTS='--traditional -q --no-window-system'
++ FSL_FIX_OCEVAL=--eval
++ FSL_FIX_OCFILE=
++ FSL_FIX_MATLAB_MODE=1
++ FSL_FIX_CIFTIRW=/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter
++ FSL_FIX_WBC=/vols/Data/HCP/workbench/bin_linux64/wb_command
++ export FSL_FIX_CIFTIRW FSL_FIX_WBC
++ '[' -z /data/evansjw/fsl ']'
++ FSL_FIX_FSLMATLAB=/data/evansjw/fsl/etc/matlab
+ opt_str=:z:o:p:h:c:b:l:r:m:f:d
+ NO_EXT=0
+ DEBUG=0
+ getopts :z:o:p:h:c:b:l:r:m:f:d opt
+ case $opt in
+ '[' -z '' ']'
+ LOGF=/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/logMatlab.txt
+ getopts :z:o:p:h:c:b:l:r:m:f:d opt
+ case $opt in
+ '[' -z '' ']'
+ FUNC=fix_1a_extract_features
+ getopts :z:o:p:h:c:b:l:r:m:f:d opt
+ '[' -z /data/evansjw/fsl ']'
+ '[' '!' -z '' -a '!' -z '' -a '!' -z fix_1a_extract_features ']'
+ '[' -z '' ']'
+ '[' -z 1 ']'
+ fmm=1
+ shift 4
+ '[' '!' -z '' -a 1 -eq 0 ']'
+ '[' '!' -z '' -a 1 -eq 0 ']'
+ '[' '!' -z fix_1a_extract_features ']'
+ F_ARGS=
+ for arg in '"$@"'
+ echo /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/
+ egrep '^[-+]?([0-9]+\.?|[0-9]*\.[0-9]+)$'
+ F_ARGS=' '\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'''
+ '[' -z '' ']'
+ MATLAB_BIN=/usr/local//bin/matlab
+ '[' -z '' ']'
+ OCTAVE_BIN=/usr/bin/octave
+ '[' -z '' ']'
+ CSUBDIR=/data/evansjw/fix1.06/compiled/Linux/x86_64
+ '[' -z '' ']'
+ MCR=/opt/fmrib/MATLAB/MATLAB_Compiler_Runtime/v717
+ '[' '!' -z /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/logMatlab.txt ']'
+ LOGGING=' >> /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/logMatlab.txt 2>&1 '
+ case ${fmm} in
+ :
+ '[' 1 -eq 0 ']'
+ '[' -z '' ']'
+ '[' 1 -eq 1 ']'
+ DOPTS='-nojvm -nodisplay -nodesktop -nosplash'
+ '[' 1 -eq 1 ']'
+ RUNTIME=/usr/local//bin/matlab
+ EVAL_CMD=-r
+ FILE_CMD='\<'
+ '[' '!' -x /usr/local//bin/matlab ']'
+ '[' -z '' ']'
+ FSL_MATLAB_PATH=/data/evansjw/fsl/etc/matlab
+ ML_PATHS='addpath('\''/data/evansjw/fix1.06'\''); addpath('\''/data/evansjw/fsl/etc/matlab'\'');'
+ '[' 1 -gt 0 -a 1 -lt 3 ']'
+ '[' '!' -z '' ']'
+ '[' '!' -z fix_1a_extract_features ']'
+ for arg in '${F_ARGS}'
++ echo ''\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'''
++ sed -e 's/^\(.* \)$/\"\1\"/'
+ arg=''\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'''
+ FUNC_ARGS=','\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'''
++ echo ','\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'''
++ sed -e 's/^.\(.*\)$/\1/'
+ FUNC_ARGS=''\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'''
+ cmd='/usr/local//bin/matlab -nojvm -nodisplay -nodesktop -nosplash -r "addpath('\''/data/evansjw/fix1.06'\''); addpath('\''/data/evansjw/fsl/etc/matlab'\''); fix_1a_extract_features('\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'')" >> /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/logMatlab.txt 2>&1 '
+ echo '/usr/local//bin/matlab -nojvm -nodisplay -nodesktop -nosplash -r "addpath('\''/data/evansjw/fix1.06'\''); addpath('\''/data/evansjw/fsl/etc/matlab'\''); fix_1a_extract_features('\''/data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/'\'')" >> /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//fix/logMatlab.txt 2>&1 '
+ sh
+ exit 1
+ R CMD BATCH '--no-restore --no-save --args /data/evansjw/fix1.06 /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/ /data/evansjw/fix1.06/training_files/Standard.RData 20' /data/evansjw/fix1.06/fix_2b_predict.R /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica//.fix_2b_predict.log
/usr/local/apps/R/3.1.0/lib64/R/bin/BATCH: line 60: /data/evansjw/ICA_fun/20pc_e2/21Apr_gui.ica/: Is a directory
]0;evansjw@felix:/data/evansjw/fix1.06[evansjw@felix fix1.06]$ exit
exit
Script done on Mon Oct 27 16:11:41 2014
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