Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] trac-all -path error
by Anastasia Yendiki 29 Mar '13

29 Mar '13

Hi Nawaf - The first error occured much earlier in the log file. Your gradient table file could not be found. Did you set the bvecfile variable in your configuration file? a.y On Fri, 29 Mar 2013, Nawaf Yassi wrote: > Hi Anastasia > Thanks for your reply > Here is the file attached (I have replaced the subject's name with 'AAAAA' > for anonymity) > Regards > Nawaf > > > On 29/03/13 2:17 AM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> > 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 >> ³Segmentation fault² (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/C >> 01/scripts/ >> trac-all.log >> -cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C >> 01/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/C0 >> 1/dpath/lh >> .cst_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .cst_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .ilf_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .ilf_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .unc_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .unc_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/fm >> ajor_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/fm >> inor_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .atr_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .atr_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .ccg_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .ccg_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .cab_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .cab_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .slfp_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .slfp_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .slft_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .slft_PP_avg33_mni_bbr >> /usr/local/freesurfer5.2/bin/dmri_paths >> --outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf >> er/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/Analysi >> s/C01_freesurfer/C01/dpath/rh >> >> .slfp_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysi >> s/C01_freesurfer/C01/dpath/lh >> >> .slft_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysi >> s/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_freesurfe >> r/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 >> >> ni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz >> --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 >> >> ni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz >> --reg/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ >> C01/dmri/xfm >> s/diff2mni.bbr.mat >> --init/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dlabel/d >> >> iff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/fmajor_PP_avg33_mni_bbr_cpts_7.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/fminor_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/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_freesurf >> er/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/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_freesurf >> er/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov >> ery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov >> ery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov >> ery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/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(a)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 >> >> >> >> > > > The >> information in this e-mail is intended only for the person to whom it >> is > addressed. If you believe this e-mail was sent to you in error and the >> e-mail > contains patient information, please contact the Partners Compliance >> HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to >> you in error > but does not contain patient information, please contact the >> sender and properly > dispose of the e-mail. > > >

1 0

Multiple skull strip problems--too much skull left AND cerebellum removed
by Hayley Dorfman 29 Mar '13

29 Mar '13

Hi everyone, With Bruce's extraordinary help, I've been able to get a formerly impossible subject through recon-all without error. However, the only remaining issue is that the skull strip is very strange, and is leaving too much skull at the top while simultaneously cutting off the entire cerebellum. As a result, it is also having some trouble segmenting, so I'd prefer to fix the skull strip in a way that will hopefully also fix the segmentation (see attached screenshots). I don't have any experience editing a bad skull strip that needs to have both brain added back in, and skull removed, so I'm not sure of the best order of operations. Does anyone have any suggestions? Would the best option be to use gcut for the skull and then go back in and clone the cerebellum afterwards? Thanks! Hayley

1 0

Download problem wih freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg
by Leila Reddy 29 Mar '13

29 Mar '13

Hi, I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I click on the download link I get an error: 550 Failed to change directory. I can't find a file with this filename in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version not yet available (and when will it be available)? Thanks, Leila

2 1

odd tkregister
by Borzello, Mia 29 Mar '13

29 Mar '13

Hi freesurfers, In using tkregister, I generated an odd (see attached): the image not only looks sheered but there is an old white box showing up. I'm not sure how to resolve this. Thanks a lot, Mia

1 0

contrast matrix
by xiangbo_2010 28 Mar '13

28 Mar '13

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang

6 18

Linear Mixed modal
by xiangbo_2010 28 Mar '13

28 Mar '13

Dear experts Whether can the design of contrast in freesurfer 5.2 the same as SPM? it is difficult to make the contrast in freesurfer if the categorical variables were much more, specifically compute the interaction or F-test in study. Thanks！ Bo Xiang

2 1

coregistering- ideal CT type
by Borzello, Mia 28 Mar '13

28 Mar '13

Hi freesurfers, I working on a coregistration right now with a few different CT scans. None of them have looked that good with tkregister (for example when I used one CT scan, the electrodes didn't even show up). Is there an certain CT I need to be using? Thanks, m

1 0

Correlation with cortical thickness
by Martijn Steenwijk 28 Mar '13

28 Mar '13

Dear all, I've a question regarding computing correlations with cortical thicknesses on the surface; Suppose I have two variables for each subject: (age and weight) and I want to compute the correlation between cortical thickness and weight, corrected for age. Option 1: Fsgd contains: Variables weight Contrast file contains: 0 1 Option 2: Fsgd contains: Variables age weight Contrast file contains: 0 0 1 Is it true that the effect of age is regressed out in the second option; and it computes the correlation between CT and weight after correcting for age? Best, Martijn

3 3

aseg.mgz altered after auto-recon2?
by Joshua Lee 28 Mar '13

28 Mar '13

Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge.

3 5

FSFAST and octave error dfor fast_selxavg3.m
by Mario Ortega 28 Mar '13

28 Mar '13

Hi Freesurfer group, Im attempting to use FS-FAST with resting BOLD data, and I have come across the following error. I tried changing files to non .gz extension, and still have this error.. $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ `fast_selxavg3' is a script from the file /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m `fast_ldanaflac' is a function from the file /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m ------------------------- outtop = /media/GOLDIN/FSFAST Extension format = nii.gz error: `MRIread' undefined near line 87 column 7 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/flac_customize.m at line 87, column 5 error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 65, column 7 ------------------------------------------ When I attempt to use fast_selxavg3 standalone in octave, I get this error. octave:1> fast_selxavg3; error: `sess' undefined near line 26 column 19 error: evaluating argument list element number 1 error: evaluating argument list element number 1 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 26, column 8 thanks, Mario Ortega GS4 Washington University in St. Louis, Dept. of Neurology

2 1

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Freesurfer March 2013