External Email - Use Caution
I ran standard recon-all on a single subject and then trac-all -prep.
The process ran for approximately 1 hour and exited with errors: Segmentation fault.
This is my first time testing Tracula, so user error likely.
Here are the final lines from the console and trac-all.log attached:
INFO: Distances between consecutive points in test subject's space are 9 13 13 12
WARN: Could not find satisfactory control point fit - try 912
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 114 voxels
Selecting 5 points on center streamline
INFO: Minimum allowable distance between dominant points is 15
INFO: Minimum allowable curvature at a dominant point is 0.0447089
INFO: Points where local peeks in curvature occur are
67 116 39 (curv = 0.0963721)
77 75 87 (curv = 0.114559)
75 76 95 (curv = 0.0564307)
69 74 105 (curv = 0.126918)
74 67 115 (curv = 0.0809615)
INFO: Intermediate dominant points are
67 135 33
67 116 39
75 82 76
69 74 105
74 49 116
INFO: Final dominant points are
67 135 33
67 116 39
77 75 88
69 74 105
74 49 116
WARN: Defaulting to equidistant control points
INFO: Selected control points are
67 135 33
68 108 46
75 83 75
69 74 105
74 49 116
INFO: Distances between consecutive points are 30 39 32 28
INFO: Selected control points in test subject's space are
56 58 -8
56 46 -3
58 35 9
55 30 22
57 19 26
INFO: Distances between consecutive points in test subject's space are 13 16 14 12
WARN: Could not find satisfactory control point fit - try 913
Writing output files to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_*
Writing spline volume to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz
Segmentation fault
Darwin Matthews-MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Sep 17 16:26:23 EDT 2018
Thanks,
-Matt
Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks!
a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.commailto:matt@grecsek.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, September 18, 2018 at 11:50 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
External Email - Use Caution
I ran standard recon-all on a single subject and then trac-all -prep.
The process ran for approximately 1 hour and exited with errors: Segmentation fault.
This is my first time testing Tracula, so user error likely.
Here are the final lines from the console and trac-all.log attached:
INFO: Distances between consecutive points in test subject's space are 9 13 13 12
WARN: Could not find satisfactory control point fit - try 912
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 114 voxels
Selecting 5 points on center streamline
INFO: Minimum allowable distance between dominant points is 15
INFO: Minimum allowable curvature at a dominant point is 0.0447089
INFO: Points where local peeks in curvature occur are
67 116 39 (curv = 0.0963721)
77 75 87 (curv = 0.114559)
75 76 95 (curv = 0.0564307)
69 74 105 (curv = 0.126918)
74 67 115 (curv = 0.0809615)
INFO: Intermediate dominant points are
67 135 33
67 116 39
75 82 76
69 74 105
74 49 116
INFO: Final dominant points are
67 135 33
67 116 39
77 75 88
69 74 105
74 49 116
WARN: Defaulting to equidistant control points
INFO: Selected control points are
67 135 33
68 108 46
75 83 75
69 74 105
74 49 116
INFO: Distances between consecutive points are 30 39 32 28
INFO: Selected control points in test subject's space are
56 58 -8
56 46 -3
58 35 9
55 30 22
57 19 26
INFO: Distances between consecutive points in test subject's space are 13 16 14 12
WARN: Could not find satisfactory control point fit - try 913
Writing output files to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_*
Writing spline volume to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz
Segmentation fault
Darwin Matthews-MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Sep 17 16:26:23 EDT 2018
Thanks,
-Matt
freesurfer@nmr.mgh.harvard.edu
-
Matthew Grecsek -
Yendiki, Anastasia