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Hi, You can easily make a manual mask with fslview (or any other way) and then transfer it to the fmri by using flirt. First you need to register your fmri to your structural using flirt (6 dof) and then you need to apply the inverse transform to the ROI. The easiest way to do all these is with the GUIs: Flirt, InvertXFM and ApplyXFM. See the FSL documentation and the FSL course practicals for more details. All the best, Mark On 24 Nov 2008, at 17:54, Lazar Fleysher wrote: > On Mon, Nov 24, 2008 at 12:45 PM, Lazar Fleysher > <[log in to unmask]> wrote: >>> Hello >>> >>> I would like to define an roi manually, based on anatomical >>> structure >>> of the brain. >>> For this purpose I have a high resolution image. In addition to >>> this, >>> I have a low-resolution >>> fmri image. >>> >>> What I would like to do is to draw and ROI on the high resolution >>> anatomy image and have it >>> mapped to the low resolution fmri. >>> >>> It is possible to do it with fsl? If yes, could someone tell how? >>> >>> If not, could someone point me to some software package which >>> could do it? >>> >>> Thanks a lot for your help >>> >>> Lazar >>> >> >