Avoiding Duplicate Installation of Mamba and Miniconda for FSL Installation

Hello NeuroStars community,

I’m currently working on installing FSL, and the current process involves a fresh install of Mamba. However, I already have Miniconda installed on my Ubuntu device. Now, I find myself with both Mamba and Miniconda, and I’m wondering if there’s a way to avoid this duplication. I’ve searched for a Conda package to install FSL directly but haven’t found a suitable solution.

Any guidance on streamlining the installation process or finding a Conda package for FSL would be greatly appreciated.

Thank you!

Hi @roymustang, I don’t think it’s really worth worrying about having multiple conda/mamba installations, unless you are really tight on space, or you are looking to optimise a cloud/container installation. Recent FSL versions are based on conda/mamba ($FSLDIR is itself a base miniforge environment), but FSL should be able to be installed and used alongside an existing miniconda/anaconda installation.

If you do want to manage your own conda/FSL environments, we publish FSL packages to a self-hosted conda channel, and we publish FSL releases as conda environment files, which can be installed using the conda env [create|update] commands.

The FSL environment files are currently published here; files for each FSL release are named as fsl-<version>_<platform>.yml, e.g. fsl-

You can find some more information on using FSL via conda here (although nore that this documentation URL is provisional and will change in the near future).

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