I will show that the Hagedorn phase of string gas cosmology may provide a causal mechanism for generating a nearly scale-invariant spectrum of scalar metric fluctuations, without the need for an intervening period of de Sitter expansion. A distinctive signature of this structure formation scenario would be a slight blue tilt of the spectrum of gravitational waves. At the end, the generation of cosmological perturbations in the Hagedorn phase seeded by a gas of long closed strings in thermal equilibrium is reconsidered, both from the point of view of the string frame (in which it is easier to understand the generation of fluctuations) and the Einstein frame (in which the evolution equations are well known). It is shown that fixing the dilaton at some early stage is important in order to obtain a scale-invariant spectrum of cosmological fluctuations in string gas cosmology. I will try to answer all the concerned that were raised by Linde et al. about the working of this model.