Hi Anastasia,
I have been having difficulty running the trac-all -prep command on one subject (all of my other subjects have been fine), and it appears that the process gets stuck once processing for pathway 8 begins, and cannot find satisfactory control points. However, I was out of town and left the command running, and came back to find that "trac-preproc finished without error." Upon review of the log file, it appears that after 20786 tries, either control points for pathway 8 were established, or the preprocessing simply moved on to pathway 9, and was able to successfully complete. I am unable to attach the entire log file here, but have copied and pasted a small section with the errors below (from try 20784 - 20786). In try 20786, file writing begins, but then I see the following messages: INFO: Rejected 94 streamlines for straying off mask INFO: Rejected 6 streamlines for reversing direction INFO: Rejected 48 streamlines as length outliers I'm concerned that pathway 8 did not, in fact, process successfully, and I was wondering if you have any suggestions here. I am also wondering what this may mean for the other pathways for this subject, and how this may affect my data after bedpost and trac-all -path. Please advise on any suggestions you have. Thank you for your help, Michelle WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 105 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 13 INFO: Minimum allowable curvature at a dominant point is 0.0647175 INFO: Points where local peeks in curvature occur are 106 165 103 (curv = 0.136434) 109 156 97 (curv = 0.0996267) 89 142 87 (curv = 0.092719) 70 156 100 (curv = 0.112663) 74 166 104 (curv = 0.138384) INFO: Intermediate dominant points are 104 187 99 106 165 103 91 142 87 74 166 104 78 182 97 INFO: Final dominant points are 104 187 99 106 165 103 70 154 99 74 166 104 78 182 97 WARN: Defaulting to equidistant control points INFO: Selected control points are 104 187 99 107 162 102 91 142 87 70 158 101 78 182 97 INFO: Distances between consecutive points are 25 30 30 26 INFO: Selected control points in test subject's space are 139 191 42 142 167 42 128 150 35 109 162 41 115 185 41 INFO: Distances between consecutive points in test subject's space are 24 23 23 24 WARN: Could not find satisfactory control point fit - try 20785 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 12 INFO: Minimum allowable curvature at a dominant point is 0.0590185 INFO: Points where local peeks in curvature occur are 107 152 96 (curv = 0.0988129) 84 145 87 (curv = 0.0815938) 67 156 96 (curv = 0.128644) 73 168 108 (curv = 0.162002) INFO: Intermediate dominant points are 96 176 119 107 152 96 85 145 87 73 168 108 70 184 108 INFO: Final dominant points are 96 176 119 107 152 96 67 157 97 73 168 108 70 184 108 WARN: Defaulting to equidistant control points INFO: Selected control points are 96 176 119 107 157 100 87 144 87 68 159 98 70 184 108 INFO: Distances between consecutive points are 29 27 27 27 INFO: Selected control points in test subject's space are 132 177 50 142 163 41 125 152 35 107 163 40 108 185 45 INFO: Distances between consecutive points in test subject's space are 19 21 22 23 WARN: Could not find satisfactory control point fit - try 20786 Writing output files to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/mni/fminor_PP_avg33_mni_bbr_* Writing spline volume to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/mni/fminor_PP_avg33_mni_bbr_cpts_5.nii.gz Writing spline volume to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.nii.gz Done in 8115.17 sec. Loading streamline start ROI from /opt/freesurfer/trctrain/trc001/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc001/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc001/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc002/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc002/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc002/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc003/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc003/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc003/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc004/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc004/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc004/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc005/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc005/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc005/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc006/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc006/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc006/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc007/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc007/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc007/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc008/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc008/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc008/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc009/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc009/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc009/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc010/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc010/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc010/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc011/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc011/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc011/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc012/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc012/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc012/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc013/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc013/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc013/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc014/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc014/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc014/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc015/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc015/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc015/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc016/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc016/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc016/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc017/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc017/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc017/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc018/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc018/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc018/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc019/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc019/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc019/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc020/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc020/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc020/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc021/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc021/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc021/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc022/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc022/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc022/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc023/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc023/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc023/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc024/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc024/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc024/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc025/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc025/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc025/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc026/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc026/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc026/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc027/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc027/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc027/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc028/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc028/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc028/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc029/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc029/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc029/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc030/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc030/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc030/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc031/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc031/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc031/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc032/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc032/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc032/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc033/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc033/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc033/dlabel/mni/lh.atr_PP.bbr.trk INFO: Rejected 94 streamlines for straying off mask INFO: Rejected 6 streamlines for reversing direction INFO: Rejected 48 streamlines as length outliers INFO: Have 13431 total streamlines (min/mean/max length: 30/61/94) Processing pathway 9 of 18...
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