Hello freesurfers,

I installed freesurfer in a linux machine without problems, but when I am trying to install it on a Windows computer within a virtualmachine I keep getting the same error. I’ve tried the instructions in the tutorial and also tried to set an entirely new virtual machine with the same steps I did in my linux set up, to no avail.

When I run:

recon-all -s SUBJECT -all -i FILE.img

I get:

INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Dec 22 18:00:14 EST 2015 /tmp/000002_1_4/mri

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

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

recon-all -s 000002_1_4 exited with ERRORS at Tue Dec 22 18:00:18 EST 2015

For more details, see the log file /tmp/000002_1_4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The log file is too long to put in the body of the e-mail, so here is the pastebin for recon-all.log http://pastebin.com/3FxHTz3J.

Looking at it, it seems that the problem happens after

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

So I cd’ed into the mri directory and run it, which gave me the error:

/media/sf_Desktop/Patients/A.o/000003_1_4/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux Tue Dec 22 17:52:00 EST 2015 Can't locate MNI/Startup.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. tmpdir is ./tmp.mri_nu_correct.mni.2621 /media/sf_Desktop/Patients/A.o/000003_1_4/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2621/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2621/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -3.72529e-09) j_ras = (-1.86265e-09, -1.16415e-10, -1) k_ras = (-7.45233e-09, 1, -5.82338e-11) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2621/nu0.mnc...

-------------------------------------------------------- Iteration 1 Tue Dec 22 17:52:03 EST 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.2621/nu0.mnc ./tmp.mri_nu_correct.mni.2621/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2621/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37.

ERROR: file ./tmp.mri_nu_correct.mni.2621/nu1.mnc does not exist!

It seems that it fails finding some pearl scripts. I tried installing pearl on the VM, also with any success.

Any pointers here would be really appreciated? What you think is happening in this installation?

Best,

Luis ​