Dear all,
I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit).
The mri_convert doesn't work with no error message. which mri_convert gives /usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which exits with errors with no error message in the log).
I made sure all the paths are 777. I did the recommended "sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in x86_64-linux-gnu.
The same problem with freeview, nothing happens.
The output is:

"Mon Feb 22 18:27:05 CET 2016
/usr/local/freesurfer/subjects/myscan
/usr/local/freesurfer/bin/recon-all
-s myscan -i myscan.nii.gz
subjid myscan
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc      15308
maxlocks     unlimited
maxsignal    15308
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:       3940392    3452568     487824     223760     262988    2343920
-/+ buffers/cache:     845660    3094732
Swap:      2023420      77288    1946132

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/usr/local/freesurfer/subjects/myscan

mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz /usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz

Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"
It creates the directory myscan but the folders myscan/mri/orig and myscan/mri/transforms are empty. Before running I changed the rights -R a+w for /usr/local/freesurfer/subjects.

I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do anything, no error message it just skips to a new line.
mri_convert -h or mri_convert --help also don't have any output.
And recon-all -s bert -autorecon1 gives:

"Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 root root 472994 Feb 8 16:54 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /space/freesurfer/centos4.0/stable
#--------------------------------------------
#@# MotionCor Mon Feb 22 18:24:35 CET 2016
Found 3 runs
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016"

If I try to run:

"freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red"
as indicated on the website nothing happens, no error message.

Thank you in advance!
Veronica