Well, there is a command in FSL that calculates the volume from T1 or T2 anatomical images that gives pretty much the same result for both. Never tried for fMRI but you can apply to see if it can capture the changes for fMRI. The command is:

fslstats [input] - V

Before that, you have to remove skull though (with fsl bet).

Thanks Reza, sounds like a feasible option

There was some works done for doing contour fit the time I was in Erlangen. We used a 1-slice T1 volumetric scan, and stripped it of zero-pixels, resulting in the contours of the skull. I think doing it with sliced MRI data is too prone to give non-significant results even if there are significant ones.

Hello Juan,

    The resolution of fMRI is poor.

    If you wanna measure the brain volume, you'd better a 10-mins T1 images.

    The DICOM files of T1 images could be converted to NIFTI format and analyzed by "MATLAB+VBM toolbox". The gray matter density could be considered as cortical gray matter volume.

    Best regards,

    Hanna Lu