mrtransform currently performs FOD reorientation by default if the number of volumes indicates that the series can be interpreted as a series of SH coefficients. This is quite a dangerous practice as it could silently mess up pipelines, e.g. if input data happens to have a number of gradient orientations that corresponds to a number that can be interpreted as a series of SH coefficients. So I feel it would be a safer option to disable FOD reorientation by default.