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

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