Hi Nawaf - Can you please send your trac-all.log? It's possible that the problem started at an earlier step.
Thanks, a.y On Thu, 28 Mar 2013, Nawaf Yassi wrote:
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/fm ajor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm inor_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/fm ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm inor_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/bve cs --bval/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri/bva ls --mask/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lowb_brain_mask.nii.gz --bpdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dmri.bed postX --ntr 2 --fmin 0.05 --roi1/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m 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--roi2/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m 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iff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/fmajor_PP_avg33_mni_bbr_cpts_7.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/fminor_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cst_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cst_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.unc_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.unc_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fmajor_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fmajor_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fminor_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fminor_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slft_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fmajor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fmajor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fminor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/fminor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/lh.slft_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m ni/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/d iff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d iff/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
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