Hello,

I am continuously getting a “Segmentation fault” error during –autorecon1 when it’s running mri_binarize. I have been running Freesurfer on a Mac, but now I am trying to implement it using Linux. I am running this version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on Linux 2.6.9-89.0.20.ELsmp x86_64.

I this a memory issue, or can there be another explanation? I’ve tried multiple times and with different subjects.

Here is my log output:

home/harshad/data5/Freesurfer/PATHD/process/P2608/mri/] [2011-09-13 16:08:43] running:

/usr/local/freesurfer//mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.31037/nu1.mnc ./tmp.mri_nu_correct.mni.31037/1//template.mnc

Transforming slices:......................................................................................Done

mri_binarize --i ./tmp.mri_nu_correct.mni.31037/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31037/ones.mgz

Segmentation fault

Linux vhasfcapp21 2.6.9-89.0.20.ELsmp #1 SMP Mon Jan 18 12:19:33 EST 2010 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P2608 exited with ERRORS at Tue Sep 13 16:10:11 PDT 2011

Any help would be greatly appreciated.

Thanks,

Vanessa Palzes

Research Assistant

Brain Imaging & EEG Lab

San Francisco VA Medical Center

4150 Clement Street

San Francisco, CA 94121

Tel: 415-221-4810 ext. 6155