Hi Jason

you need to talk to a local sysadmin, but basically you need to add the path to matlab to your path environment variable. The syntax for this depends on the shell you are using, but for example in csh/tcsh it would be something like (in your .cshrc file in your home directory)

set path = ($path /usr/local/matlab/bin) rehash

or wherever matlab is

cheers Bruce

On Wed, 28 Oct 2015, Jason Haberman wrote:

Hi Bruce, Thanks so much for your response. I can only start Matlab from the terminal when I use the following command within the Matlab applications folder:

./matlab

Am I to understand that the matlab command must be globally accessible? If so, how might I achieve that?

Thanks so much, Jason

On Wed, Oct 28, 2015 at 8:39 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jason

  do you have matlab installed? If so, you need to setup your
  environment so that it is in your path. This doesn't really have
  anything to do with FreeSurfer - you need to be able to type
  "matlab" from the command line and have it find the binary

  cheers
  Bruce
  On Wed, 28 Oct 2015, Jason Haberman wrote:

        Dear Freesurfer Community,
        I am very new to Freesurfer and am trying to work my
        way through the
        tutorial. I am currently stuck at the 
        mkcontrast-sess -analysis my-workmem.sm05.lh
        -contrast encode-v-base -a 1
        section, having received the error:
        ERROR: cannot find matlab. Is it in your path?

        I have searched the forums and found one instance of
        this being reported,
        but the suggested solutions did not resolve the
        problem. Is there anyway
        further recommendations you might make?

        I have attached a screenshot of my .bash_profile and
        of my attempts to run
        mkcontrast. I would be most grateful for any
        assistance you might offer.

        Warm Regards,
        Jason

        Inline image 1

        --

        Jason Haberman
        Assistant Professor of Psychology
        Rhodes College
        Clough Hall 119
        901-843-3231
        http://jasonmarchaberman.wordpress.com/



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