Dear mailing list

I am encountering an error at the trac-all –path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error “Segmentation fault” (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help?

I am using freesurfer 5.2 and FSL 5.0.2.1 (linux)
Regards
Nawaf
ATTACHED: ERROR MESSAGE + config file below

=========================================================

[nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject
Too many )'s.
INFO: SUBJECTS_DIR is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer
INFO: Diffusion root is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer5.2
trac-paths -c /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/dmrirc.local -log /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/trac-all.log -cmd /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer5.2/bin/trac-paths
#-------------------------------------
#@# Path reconstruction Thu Mar 28 10:01:34 EST 2013
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.cst_AS_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.cst_AS_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.ilf_AS_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.ilf_AS_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.unc_AS_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.unc_AS_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fmajor_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fminor_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.atr_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.atr_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.ccg_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.ccg_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.cab_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.cab_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.slfp_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.slfp_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.slft_PP_avg33_mni_bbr
rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.slft_PP_avg33_mni_bbr
/usr/local/freesurfer5.2/bin/dmri_paths --outdir /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.cst_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.cst_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.ilf_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.ilf_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.unc_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.unc_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fmajor_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fminor_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.atr_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.atr_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.ccg_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.ccg_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.cab_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.cab_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.slfp_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.slfp_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh.slft_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh.slft_PP_avg33_mni_bbr --dwi /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri/dwi.nii.gz --grad /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri/bvecs --bval /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri/bvals --mask /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lowb_brain_mask.nii.gz --bpdir /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri/xfms/diff2mni.bbr.mat --init /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Segmentation fault (core dumped)
foreach: No match.

=====================================================================================================================================

[nyassi@bee1 scripts]$ cat dmrirc_single_subject
#
# dmrirc.example
#
# 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 /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#

# Subject IDs
#
set subjlist = (C01)

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#

# 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 dcmroot = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/DICOMS/raw_dti/HURLE_LISA
set dcmlist = (IM-0001-0001.dcm)

# 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 bvecfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvecs.txt

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# Single-column format, one value for each volume in the diffusion data set
# Default: Read from DICOM header
#
# set bvalfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvals.txt

# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 0

# 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 = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.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 = 0.3

# 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 = /path/to/mni_template.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 = donald

# Parent directory of the CVS template subject
# Only used if doregcvs = 1
# Default: $FREESURFER_HOME/subjects
#
# set cvstempdir = /path/to/cvs/atlases/of/ducks

# 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: 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