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Hi Siamak, You could try to call the FSL commands directly from within Matlab using the unix() command (or the ! function). I hope this helps, wolf On 07/23/2009 10:16 PM, siamak wrote: > Hi, > > I am using a matlab program and I need to register two MRI images using flirt > and fnirt. Implementing them in matlab is very time consuming. For the time > being, I am switch between matlab program and FSL tool and exchnage the > results. Do you know that these two tools have been implemented in matlab > environment yet? Any toolbox? I apprecite any help. > > Regards, > Siamak Yousefi >