Hi List,

We just upgraded our Linux Box to Fedora 23 and installed csh so recon-all would run, yet we’re still getting crashed analyses.

Here is the error from my recon-all.error file:

------------------------------

SUBJECT 2_03T_N12_12_18441

DATE Thu Jan 21 16:20:16 GMT 2016

USER dsbarron

HOST psyws26.psych.ox.ac.uk

PROCESSOR x86_64

OS Linux

Linux psyws26.psych.ox.ac.uk 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $

/home/freesurfer/bin/recon-all

PWD /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri

CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Here is the error when I try to call just the mrinucorrect.mni function:

bash-4.3$ mri_nu_correct.mni

mri_nu_correct.mni:1: parser error : Start tag expected, '<' not found

#! /bin/tcsh -f

^

Document not parsed successfully. 

Any suggestions/ideas? Please help! Thanks!

Cheers,

Daniel

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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu