Zheng,

Can you send me the file 'brain.mgz' via our file-drop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

This looks like a problem we'll have to re-create locally.

Nick

On Fri, 2009-10-02 at 15:48 +0800, Hui Zheng wrote:

Hi Nick,

For one of our subjects, during the processing of base subject, I encountered this segmentation fault error at the stage of WM segmentation. Here's the output from the pipeline.

#@# WM Segmentation Thu Oct 1 15:08:16 SGT 2009

mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (102.0): 101.3 +- 7.3 [80.0 --> 125.0] GM (74.0) : 72.5 +- 10.2 [30.0 --> 96.0] setting bottom of white matter range to 82.7 setting top of gray matter range to 92.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 1078 sparsely connected voxels removed... thickening thin strands.... Segmentation fault (core dumped) Linux neuron02 2.6.9-42.ELsmp #1 SMP Tue Aug 15 10:35:26 BST 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Thu Oct 1 15:09:04 SGT 2009

I have restarted the processing several times, every time it stopped with same error. I can upload the data if needed.

Cheers, Zheng Hui

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