Unable to find matlab when running freesurfer mkcontrast-sess

[adam-coates]

Hello,

I have seen that there have been a few others that have mentioned a previous problem with mcr not being included in a recent FreeSurfer container. However, it seems that some FreeSurfer commands depend upon matlab at least being in the $PATH.

Is there a way to add matlab to the path variable from within the FreeSurfer container? Or is there a way that to explicitly use the mcr runtime environment and alias it to matlab?

I have tried to run FreeSurfers getmatlab command. This just uses which matlab to then add it to $PATH but of course this would fail. I have also tried from the matlab website to add mcr to $LD_LIBRARY_PATH but this didn't work either.

I would appreciate any help and thank you to neurodesk,

Best wishes,
Adam

[stebo85]

Dear @adam-coates ,

We have the matlab runtime environment available inside our freesurfer containers and set it up correclty, but not the full matlab. Do you know if mkcontrast can run with the matlab runtime environment?

[stebo85]

this looks promising:

if($FS_MKCON_USE_BIN == 0) then
  if($#mfile == 0) set mfile = /tmp/mkcontrast2.$$.m
  rm -f $mfile
  echo "Matlab file is $mfile"
  echo "mkcontrast2m('$config');" >> $mfile
  if($monly) exit 0;
  echo "quit;" >> $mfile
  if($UseOctave == 0) then
    echo "------- matlab output --------------------" 
    cat $mfile | $MATLAB -nosplash -display iconic -nodesktop 
  else
    echo "------- octave output --------------------" 
    cat $mfile | octave
  endif
  rm $mfile
else
  echo "FS_MCRROOT $FS_MCRROOT " 
  if($?LD_LIBRARY_PATH == 0) setenv LD_LIBRARY_PATH
  setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":"$FS_MCRROOT/runtime/glnxa64"
  setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":"$FS_MCRROOT/bin/glnxa64"
  setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":"$FS_MCRROOT/sys/os/glnxa64"
  echo "LD_LIBRARY_PATH $LD_LIBRARY_PATH" 
  set cmd = (mkcontrast2m.glnxa64 $config)
  echo $cmd 
  $cmd 
  if($status) exit 1;
  if($configdelete) rm $config
endif

[stebo85]

Can you try this in the Freesurfer container 7.4.1?

freesurfer-7.4.1:~$ export FS_MCRROOT=/opt/MCR2019b/v97/

7.2.0 does not have the the MCR setup correctly.

[adam-coates]

Thanks so much for reaching out! I understand the logic behind this now. However, after exporting and setting the global variable FS_MCRROOT I get a similar error. But good news is that mkcontrast-sess has an option to tell it whether to use mcr or not! (I overlooked this and apologies from my side). By default it seems that nearly all FreeSurfer commands with the appended -sess look for matlab to be on path by default using the script getmatlab. However, there should be options (that are not documented in FreeSurfers help) to use mcr. Therefore the solution in this case was the following steps (I'll leave this here):

1. export FS_MCRROOT=/opt/MCR2019b/v97/
2. run mkcontrast-sess with the flag -mcr 1

[stebo85]

Cool - that's a great solution. I will make this a permanent fix in the next freesurfer container

[adam-coates]

Thanks very much for your help, very appreciated!

[stebo85]

The suggested solution wasn't quite working yet - there is now a new freesurfer version 8.0.0 where we added octave which should hopefully work.