Ok, try running the code below in matlab, replacing '/usr/local/fsl' with wherever FSL is installed. Also, you can change 'NIFTI_GZ' to something else if you want a different output format....

setenv('FSLDIR','/usr/local/fsl')
path_default=getenv('PATH');
path =[path_default,':',getenv('FSLDIR'),'/bin'];
setenv('PATH',path)
setenv('FSLOUTPUTTYPE','NIFTI_GZ')