Hello,<div><br></div><div>I recently upgraded from Ubuntu 13.10 to 14.04, and I started getting a new error message while running "recon-all" with .nii  file inputs (details below). From the error message I believe the problem might be that Ubuntu 14.04 ships with perl version 5.18 (as opposed to 5.14 for previous versions), and the Ubuntu 14.04 Perl manpage (<a href="http://manpages.ubuntu.com/manpages/trusty/man1/perl5120delta.1.html">http://manpages.ubuntu.com/manpages/trusty/man1/perl5120delta.1.html</a>), specifically lists "shellwords.pl" as a newly deprecated library.&nbsp;</div><div><br></div><div>My naive instinct was to install perl version 5.14 using perlbrew, and switch to it whenever a new shell is launched by editing my .bashrc file, by adding the lines&nbsp;</div><div>"source ~/perl5/perlbrew/etc/bashrc"</div><div>"perlbrew switch perl-5.14.4"</div><div><br></div><div>When I do this my shell recognizes perl-5.14.4 as the active version, but freesurfer does not. This makes me worry it won't be such a simple fix. Any Ideas as to the best way to handle this? Am I on the right track?</div><div><br></div><div>Many Thanks!</div><div>-Samuel Thorpe</div><div><br></div><div><br></div><div>bugr related info:</div><div>---------------------------------------------------------------------</div><div>FREESURFER_HOME: /usr/local/freesurfer</div><div>SUBJECTS_DIR: /usr/local/freesurfer/subjects</div><div>"which recon-all" gives "/usr/local/freesurfer/bin/recon-all"</div><div>Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0</div><div>Debian version: jessie/sid</div><div>Kernel info: Linux 3.8.0-32-generic x86_64</div><div>Linux OS: Ubuntu 14.04 LTS "Trusty Tahr"</div><div><br></div><div><br></div><div>example commands executed:</div><div>---------------------------------------------------------------------</div><div>subject: "bert", "bert_nii"</div><div>after converting "/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz"</div><div>to .nii using "mri_convert" (operation successful), I attempt,&nbsp;</div><div>"recon-all -i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s bert_nii -all"</div><div><br></div><div><br></div><div>error message:</div><div>---------------------------------------------------------------------</div><div>"Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line 460."</div><div><br></div><div><br></div><div>/usr/local/freesurfer/subjects/bert_nii/script/recon-all.log attached</div>