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.edu> on behalf of Matthew Grecsek <matt@grecsek.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, September 18, 2018 at 11:50 AM
To: Freesurfer support list <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