Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

Path analysis
by Alan Francis 14 Aug '13

14 Aug '13

Hi Anastasia: One of my brains had a problem when doing trac-all -path analysis. Please see below the complete pathway. Thanks so much for your help. Alan csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -path -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-104 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-paths -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable5_3_0//bin/trac-paths #------------------------------------- #@# Path reconstruction Wed Aug 14 13:36:21 EDT 2013 rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni_bbr /usr/local/freesurfer/stable5_3_0//bin/dmri_paths --outdir /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt cwd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons cmdline /usr/local/freesurfer/stable5_3_0//bin/dmri_paths --outdir /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt sysname Linux hostname cerebro machine x86_64 user alanf Output directory: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni_bbr DWIs: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz Gradients: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs B-values: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals Mask: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_mask.bbr.nii.gz BEDPOST directory: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX Max number of tracts per voxel: 2 Tract volume fraction threshold: 0.05 Initial control point file: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt End ROI 1: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz End ROI 2: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all Neighbor aseg prior set: 14 Local aseg prior: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all Local aseg label ID list: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all Local aseg prior set: 15 Segmentation map: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/aparc+aseg.nii.gz DWI-to-atlas affine registration: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dmri/xfms/diff2mni.bbr.mat Number of burn-in samples: 200 Number of post-burn-in samples: 7500 Keep every: 5-th sample Update proposal every: 0-th sample Initial proposal SD file: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Loading DWIs from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz Loading mask from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX Loading b-values from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals Loading gradients from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs INFO: Found 10 baseline images (b = 0) out of a total of 70 frames INFO: Found 182362 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Wed Aug 14 13:37:20 EDT 2013

2 1

Tracula failed
by Alan Francis 14 Aug '13

14 Aug '13

Hi Anastasia: Thanks to your advice most of the data have been processed using Tracula. Two brains gave me error messages that are as follows: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 ERROR: must specify as many DWI dicoms as subjects csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #------------------------------------- #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_141102DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_141102DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_141102DIFFUSIONHighRess016a001.nii... TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997762, -0.0667414, -0.00403802) j_ras = (-0.0662713, 0.979101, 0.192276) k_ras = (0.00887916, -0.192114, 0.981333) writing to /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals flip4fsl /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -6.8719 fslswapdim /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz x y z /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvals eddy_correct /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz 0 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0000 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0001 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0002 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0003 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0004 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0005 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0006 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0007 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0008 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0009 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0010 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0011 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0012 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0013 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0014 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0015 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0016 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0017 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0018 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0019 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0020 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0021 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0022 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0023 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0024 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0025 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0026 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0027 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0028 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0029 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0030 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0031 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0032 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0033 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0034 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0035 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0036 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0037 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0038 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0039 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0040 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0041 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0042 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0043 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0044 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0045 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0046 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0047 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0048 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0049 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0050 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0051 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0052 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0053 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0054 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0055 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0056 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0057 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0058 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0059 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0060 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0061 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0062 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0063 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0064 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0065 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0066 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0067 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0068 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0069 mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot xfmrot /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.ecclog /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs ln -sf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/data.nii.gz awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz --mean --o /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/lowb.nii.gz niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Aug 12 17:30:05 EDT 2013 As always - thanks for your help, best, Alan Martinos Center.

2 5

Expert opts
by Victor Kovac 14 Aug '13

14 Aug '13

Dear Freesurfer experts, I am needing to manually re-set T1.mgz intensity ranges in recon-all, because, currently, only voxels under 80 are getting segmented as gray matter, which is generally outside of the brain. Additionally, all voxels with an intensity of 80 or more are segmented as wm. I have attached an image of what this looks like. I looked through this page ( http://ftp.nmr.mgh.harvard.edu/fswiki/recon-all#Arguments) but did not recognize a command that corresponds to what I need. Could any of you tell me how to use expert options to set intensity ranges for wm or gm? I need to re-set both, I think. Thank you so much! Victor

1 0

Fornix labelled as corpus callosum in patient with periventricular leukomalacia
by Corinna Bauer 14 Aug '13

14 Aug '13

Hello all, I am examining diffusion tracking in the corpus callosum of individuals with periventricular leukomalacia (PVL). The corpus callosum is particularly small and the anterior and mid-anterior labels are being applied to the fornix (see attached Fornix_labelled_as_CC.png). The midposterior and posterior look ok, while the central is very small, maybe one voxel in size. The wm segmentation, seen with ?l.white, also shows segmentation defaults with the anterior corpus callosum (see attached images). I tried to correct this using control points, which you can see did not fix the segmentation. Any suggestions? Corinna

2 1

MCSRCH ERROR
by Eli Fredman 14 Aug '13

14 Aug '13

I ran 10 cases through freesurfer5.3 last night and found that they all exited with the same error. This is the input that I used: recon-all -i /projects/schiz/NFL/case01409/strct/align-space/01409-t1w-realign-masked.nii.gz -autorecon1 -noskullstrip -subjid 01409 && cp subjects/01409/mri/T1.mgz subjects/01409/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01409 && recon-all -autorecon3 -subjid 01409 I've attached the recon-all.log file which shows the following error: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 (as a side note, the reason I don't simply run recon-all -all is because this doesn't seem to acknowledge the -noskullstrip tag). Thanks for the help! -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150

2 3

trac-all download
by ana ;osp 14 Aug '13

14 Aug '13

hi'm trying to download the trac-all file from the site in the tracula release notes, it is the download from 2012/1/09 recommended for all, but hen i click it open a page and gives me an error should i do something different than just click? thanks

2 1

FS version
by Cristian Paz 14 Aug '13

14 Aug '13

Dear experts! I have a question. I have run recon-all on a cluster , and I am editing on my local machine. I just checked the versions and I see that I have: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 at the computing cluster and freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on my local computer.... Is this a problem? Thank you very much for your help. Kind regards Cris

2 2

".thickness.fwhm15.fsaverage.mgh" missing
by Muhammad Naveed Iqbal Qureshi 14 Aug '13

14 Aug '13

Dear List Members, I converted my data from .dcm to .nii and than from .nii to .mgz volume, after that I have run the following command to calculate the cortical thickness; recon-all -s sub01 -all but I have not get ".thickness.fwhm15.fsaverage.mgh" files in the surf folder after recon-all get finished without errors. Please tell me the reason of the absence of these files. Previously I did not converted my data to .nii and I got all the files in surf folder. I used the following command earlier recon-all -i <path-to-dicom> -subject <name-of-the-subject> -all -qcache & waiting for reply Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

2 1

Prevent masking of activity outside of brain
by Cesar Echavarria 14 Aug '13

14 Aug '13

Hi Freesurfers, I want to look at activity in my subjects' retina for one of my experiments. I did volume-based analysis in freesurfer version 5.3 but I noticed that activity outside of the brain has been masked. Is there an option somewhere along the processing pipeline to prevent masking of activity outside the brain? I know that freesurfer version 4.5 does not do this masking, but was wondering if there was a way to stick to the current freesurfer version. Thanks you in advance for your help. Cesar

2 1

Fwd: Unsegmented ventricles
by Victor Kovac 13 Aug '13

13 Aug '13

Hi Bruce, I have never used expert options in Freesurfer. I googled "freesurfer expert options" and this link came up ( http://ftp.nmr.mgh.harvard.edu/fswiki/recon-all#Arguments) but I do not see how to specify ranges. Is it a flag after recon-all? Could you show me an example of how to set gm T1.mgz values? Thank you very much! Victor On Tue, Aug 13, 2013 at 3:55 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Victor > > yes, look at the expert options. You can set the range of allowable wm and > gm values (and csf for that matter). > > cheers > Bruce > > On Tue, 13 Aug 2013, Victor Kovac wrote: > > Hi Bruce, >> I was using v5.1 but switched to v5.3 for these troublesome cases. The >> biggest issue is that this is a longitudinal study and these scans are >> from >> patients' 4th visits. Looking in the asegstats tables from all 4 visits, >> it >> would appear that the patients having this issue have had a ~20% increase >> in >> cortical WM since their 3rd visit last year, after showing a steady >> decline >> previously. >> >> There isn't great GM/WM contrast, so I added control points to this >> subject. >> That reset the T1.mgz value of voxels that I would consider to be WM to >> 109 >> or higher, yet I still see nearly all GM with T1.mgz values in the 80's >> and >> 90's segmented as WM, which is why I am confused. >> >> From what I can see, for this brain (MPS3008-4) only voxels with a T1.mgz >> of >> less than 80 are being segmented as GM. Is there a way for me to manually >> plug in the voxel intensity ranges for GM and WM and re-create the >> surfaces? >> >> Thank you very much for your help with this! >> >> Victor >> >> On Tue, Aug 13, 2013 at 3:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> never mind, I see the problem. I think this is due to the lack >> of gray/white contrast in this subject. I'll try some control >> points, but it may be that it will need some expert opts to >> specify the white and pial intensity ranges >> On Mon, 12 Aug 2013, Victor Kovac wrote: >> >> Dear Bruce, >> I have uploaded the subject with unsegmented >> ventricles (MPS3025-4) via File >> Drop. This subject has an artifact from a >> ventricular shunt in his left >> hemisphere, and we are only using data from his >> right hemisphere. >> >> I have also uploaded a subject (image attached) >> whose cortical GM is being >> segmented as WM, and whose pial boundary is extended >> past the cortex. This >> is a recurrent issue with the atrophied brains I am >> working with. I added >> control points to bright white matter voxels in >> order to re-threshold WM >> voxel intensity and hoped that re-running >> autorecon-cp -autorecon3 would fix >> the issue, but it seems to have done nothing. >> >> Could you take a look at this subject and tell me if >> you know there is a way >> to get FreeSurfer to take my re-thresholding >> attempts and recreate the pial >> and white matter boundaries? >> >> Please let me know if there was an issue with my >> upload, and, again, thank >> you for your help! >> >> Victor >> >> On Fri, Aug 9, 2013 at 2:28 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> hmmm, you could manually correct it but if you >> upload that >> dataset I'll take a look as well >> >> >> On Fri, 9 Aug 2013, Victor Kovac wrote: >> >> Dear Bruce, >> As I have been looking through brains I >> have run >> recon-all on with v5.3, I'm >> noticing that there are many cases of >> lateral >> ventricles being left >> unsegmented in subjects with dilated >> ventricles. >> >> An image of one case of unsegmented >> ventricles is >> attached, where a subject >> has an artifact from his shunt which may >> be causing >> the error. I have >> manually adjusted this subject's >> talairach to fix >> its talairach failure. >> Should I be using the attached script >> "tkmedit-lv.sh" to fill the >> ventricles, or is there a better method? >> >> Thank you very much for your help. >> >> Victor >> >> On Fri, Aug 2, 2013 at 1:13 PM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Victor, >> >> yes, 5.3 is most of what you need. >> I think I >> added a couple of >> control points as well, but they >> should be in >> the subject dir i >> sent you. >> >> cheers >> Bruce >> On Fri, 2 Aug 2013, Victor Kovac >> wrote: >> >> Bruce, >> Thank you so much for >> analyzing this >> subject -- the >> segmentation looks much >> better! Was it simply >> running the >> subject with v5.3, >> or did you add any >> flags to the recon? >> >> As you mentioned, the pial >> and white >> matter surfaces >> extend further than >> they should, but I have >> found adding >> control points >> to white matter near the >> cortical surface has helped >> a lot in >> similar cases. >> >> I have two other subjects >> whose >> ventricles were left >> unsegmented, but have >> less atrophy than the >> subject I sent >> you. I tried >> filling the ventricles >> using the attached script, >> then ran >> recon with >> -autorecon2-wm -autorecon3 >> flags, but it did not have >> any effect. >> Would you >> recommend just running the >> subject with v5.3? >> >> Thank you! >> >> Victor >> >> On Thu, Aug 1, 2013 at 10:32 >> AM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Victor >> >> the 5.3 recon finished >> and you can >> grab the >> subject from: >> >> >> >> >> http://gate.nmr.mgh.harvard.**edu/filedrop2/?p=if8d3r4<http://gate.nmr.mgh.harvard.edu/filedrop2/?p=if8d3r4> >> >> I think the ventricles >> are *much* >> better. The >> white surface was >> incorrect in anterior >> temporal >> regions due to >> lack of >> myelination, but that >> is expected. >> You might >> be able to improve >> them, but there is >> little enough >> contrast that >> I'm not sure how >> good they will be >> >> cheers >> Bruce >> >> >> >> On Tue, 30 Jul 2013, >> Victor Kovac >> wrote: >> >> Dear Freesurfer >> experts, >> I am running recon-all >> on very >> atrophied >> brains with mixed >> results. Attached >> is an image of a brain >> where >> segmentation has >> gone awry. >> There is no message >> indicating talairach >> failure, and >> the >> segmentation appears >> to need WM and >> pial edits as well as >> the >> ventricles to be >> filled, so I am >> not sure how to >> proceed. >> >> If you have any >> recommendations as >> to how to >> fix these >> errors, I would very >> much appreciate it -- >> these data >> are past >> their deadline, >> and I am at a >> loss. >> >> Thank you! >> >> Sincerely, >> Victor >> >> >> >> >> 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<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. >> >> >> >> >> >> >> >> >> >>

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