In general the FSLDIR variable needs to be set up for freesurfer scripts to find FSL executables. Others on the list will be more qualified than me to address the VM aspects of this.

On Tue, 5 Feb 2013, Varghese Chikku wrote:

Hi Anastasia, First of all,thanks  for your mail and  forgive my ignorance again. I have  now  downloaded FSL on VMplayer I also have FS running on Oracle VM.So my question is if I run dti_recon,will  freesurfer  automatically detect FSL,which is   running on a  different VM.- Many thanks for  your help, Chikku

On 4 February 2013 16:39, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Yes.

  On Mon, 4 Feb 2013, Varghese Chikku wrote:

        Dear Team,
           I tried to run dt_recon and  the  systems
        says  cannot find
        eddy_correct,Make  sure FSL is installed. So ,do I
        need to  install the
        whole FSL package to run this.
        In Thanks
        Chikku

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