Is it possible to convert MRI image to MNI standard space with FSL?How?

Hi Farhana,

I assume by convert you mean spatially align to the MNI template. If so, then the following general comments should help you to understand the flirt help and documentation that I pointed to in my previous reply:
http://www.nitrc.org/forum/forum.php?thr...

If we wish to move an input image (the "source") to match a fixed image (the "target" or "reference"), we can find an affine transformation that maps between the two coordinate systems. To actually create the output image, we can consider each voxel in the reference, seeing where the affine mapping says this voxel should come from in the source. We can then interpolate between voxels in the source near to this position in order to find the output intensity. I assume you want to move one of your images to the MNI space, in which case your image will be the source and one of the MNI templates will be the reference.

With FSL's flirt, this would look something like:
flirt -in your_img -ref avg152 -out output -omat src2mni.mat
(all on one line).

For further examples of usage, see:
http://www.fmrib.ox.ac.uk/fsl/flirt/exam...

Best,
Ged