It sounds like you might have an old version.
The current melodic version is 3.15, which is part of FSL 5.0.10.
You can set the output type via the environment variable: FSLOUTPUTTYPE
which should be set to NIFTI_GZ if you want the .nii.gz format.
It is quite unusual that this is not set to give you this, so it might be worth checking
to see if this due to it being an old version or whether you have a clashing version being called (e.g. FreeSurfer distribute a version of FSL and you might be picking that one up by mistake). You can see what version is being used by doing:
and seeing if it is from the same place as $FSLDIR.
All the best,
> On 17 Aug 2017, at 21:29, Chintan <[log in to unmask]> wrote:
> I'm having an issue with the melodic_IC.hdr volume output from melodic.
> I'm currently running melodic 3.1 to find group level independent components in a cohort of 700 subjects. It's running on preprocessed resting state data, via command line on an SGE cluster.
> The issue I'm having is that the components in the melodic_IC.hdr volume are all the same, i.e. it just contains repeated volumes of the first component but with slightly different values. This is strange because in the stats folder, each of the zthresh maps for each component do appear to be correct and do show different components. I've run it with batches of fewer subjects with the same issue.
> I'm also not sure why it is giving me analyze .hdr/img output rather than nifti; all my input files are nii.gz and I don't see an option to change output type.
> Has anyone run into a similar issue or does anyone have any advice?