External Email - Use Caution        


Hey Freesurfer team,

  I'm working on running Tracula, and have been running into segmentation fault issues.  We have consistently been running into segmentation fault issues.  The data we are working with comes from children, and I'm concerned that differences in MRI image brightness and mapping between adult and children's brains may be throwing Tracula off.  In many cases the typical pathlist of files ( lh.cst_AS, rh.cst_AS, etc) are not fully populated in the bedp step.  We have therefore started submitting the job with the set pathlist and set ncpts to only point to files which are generated during the bedp step.  Nonetheless, we are still getting segmentation fault errors during the final path step.  I'm using freesurfer version 6.0.0-2beb96c, but I'm not sure what version of Tracula I'm using.  This is a log of the error:

Initial proposal SD file: /data/Abeona/W4WUM/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/Abeona/W4WUM/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Loading DWIs from /data/Abeona/W4WUM/dmri/dwi.nii.gz
Loading mask from /data/Abeona/W4WUM/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from /data/Abeona/W4WUM/dmri.bedpostX
Loading b-values from /data/Abeona/W4WUM/dmri/bvals
Loading gradients from /data/Abeona/W4WUM/dmri/bvecs
INFO: Found 1 baseline images (b = 0) out of a total of 31 frames
Segmentation fault (core dumped)
Linux ip-10-0-0-222 4.4.0-137-generic #163-Ubuntu SMP Mon Sep 24 13:14:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Oct 24 01:22:16 UTC 2018

The Freesurfer help I've looked at previous suggested that it could be a memory error, but we're using a remote drive that has lots of disk space and 26 GB RAM, so I doubt that's it.  Checked the LANG, we are using en_US.UTF-8.  I've run this on at least 8 different patients so far, and only one of them has not had this kind of error.  Some of the different patients have different numbers of the normal path files exported into /dlabel/diff/, so it seems like there is patient-to-patient variability in how well the bedp phase is able to map things out. 

Thanks for your help!
-Jon



Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.