Freesurfer command in matlab

I am trying to execute freesurfer commands from MATLAB. I used the command like: command ='mri_info --vox2ras-tkr subjects/ABC/mri/orig.mgz'. The matlab is showing the following message: "/bin/bash:mri_info: command not found" with status = 127. If I use termainal to execute the same command, it will work. I just wonder if it is related to linking the path? Some other simple commands like: 'whoami' or 'who' are working. Any help will be appreciated.

Thanks,

Answer 1

[Walter Roberson]

It sounds like you have a .bashrc or .env file that is responsible for adding some things to your PATH environment variable. Depending on the details of how you are starting up MATLAB, your shell initialization might not be run, so those things might not be on your PATH.

The easiest thing to do is to provide the complete path for the mri_info command when you invoke it.

[HARI GURAGAIN]

Hi Walter,

while running this it starts showing some other error, something like:

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

/Applications/freesurfer/bin/mri_info --vox2ras-tkr /Applications/freesurfer/subjects/ABC/mri/orig.mgz: Trace/breakpoint trap

status =

     133

I am not sure what this means. Any further suggestions/solution is appreciated.

[Kelly Kearney]

Last I checked, Matlab makes some alterations to a few DYLD-related environment variables when it starts up. I found that those changes can cause problems when running system commands that rely on the dyld library. I put the following commands in my startup file:

setenv('DYLD_LIBRARY_PATH', '');
setenv('DYLD_FRAMEWORK_PATH', '');

and that seems to suffice to undo the errors.

[Walter Roberson]

It sounds as if your shell initialization also adds to DYLD_LIBRARY_PATH to bring in a different version of a library.

Really freesurfer should probably be re-linked; see http://stackoverflow.com/questions/13414786/missing-emutls-get-address-with-gcc-4-7-and-openmp

[HARI GURAGAIN]

It actually didn't solve the problem. I used the setenv suggested by Kelly which didn't help me much. I will try to install older version of freesurfer to see if that can help. Great thanks in advance if someone suggests further solutions.

Thanks,

[Malcolm Lidierth]

Note "shell initialisation" in WR's answer. Running setenv from MATLAB won't affect the path during initialization.

[Walter Roberson]

Each "!setenv" or system('setenv') would run in its own shell, but calling MATLAB's setenv() could work.

[Malcolm Lidierth]

@Walter

My MATLAB's a bit rusty as I've been working in other languages for a few years. Maybe the setenv should be called from matlabrc.m. That would maximise the chance of it having been called when required. If that works, try moving it to startup.m - which is a bit more distribution friendly. And if that works, maybe try including it in a file invoked using the -r switch at the command line so it gets called straight after startup.

There is a general problem that TMW often distributes legacy open-source resources as part of the MATLAB distribution e.g. with jar files (which I'm more familiar with). It's understandable that they should be reluctant to update these on every release as any upgrade runs a risk of breaking their own code. Nevertheless, it does lead to situations where the distro is partially broken at outset: e.g. some time ago, individual jars that together make up the Apache Batik distro for SVG support were from different releases and did not work together fully. Particularly when there are many component files, sorting out which release each comes from can be problematic.

Settling on using the same release distributed with MATLAB often makes sense; until end-users start complaining that their m-code using the latest features doesn't work (prime example until a few years ago: JOGL).

Answer 2

[neuromechanist]

It iturns out the Matlab's shell may not respect the system shell env variables. So, to make FreeSurfer work, you can have the following lines in the startup.m file (find your startup.m using this command: edit(fullfile(userpath,'startup.m')))

bash_path=getenv('PATH');
setenv('PATH',[bash_path,':/Applications/freesurfer/7.4.0',':/Applications/freesurfer/7.4.0/bin']);
setenv('FREESURFER_HOME', '/Applications/freesurfer/7.4.0')
setenv('SUBJECTS_DIR', '$FREESURFER_HOME/subjects')
system('source $FREESURFER_HOME/SetUpFreeSurfer.sh')

This snippet assumes that the freesurfer software is installed under Applications. Thanks @Luis Lacerda for the hint.

Answer 3

[Luis Lacerda]

Dear Hari,

I have recently been able to fix this problem by adding the freesurfer path to the shell path from the system.

As someone said previously, you can use the matlab setenv function to do so; the first step is just to get the current PATH (please see below)

bash_path=getenv ('PATH');

setenv( 'PATH',[bash_path,':/Applications/freesurfer',':/Applications/freesurfer/bin']);

I have added these two lines to my startup.m file and can now run freesurfer commands by calling them with the function system or simply !free_surfer command

Cheers

Luis

[Walter Roberson]

Luis, to check: is the directory /Applications/freesurfer or is it /Applications/freesurfer.app ?