Commit 1fcf3765 authored by Paul McCarthy's avatar Paul McCarthy 🚵
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DOC: Small tweaks to official FSL install page

parent c0f26a95
# Official / full FSL installations
An official FSL installation is a self-contained directory installed on an end user's system, typically located at `/usr/local/fsl/`. The FSL installation directory is identified by the `$FSLDIR` environment variable. A [**miniconda**](https://docs.conda.io/en/latest/miniconda.html#) environment is used to create `$FSLDIR`, and install all FSL projects and their dependencies into `$FSLDIR`, which itself a conda environment<sup>*</sup>.
An official FSL installation is a self-contained directory installed on an end user's system, containing the full collection of FSL commands. An official FSL installation is typically located at `/usr/local/fsl/` - the FSL installation directory is identified by the `$FSLDIR` environment variable. A [**miniconda**](https://docs.conda.io/en/latest/miniconda.html#) environment is used to create `$FSLDIR`, and install all FSL projects and their dependencies into `$FSLDIR`, which is itself a conda environment<sup>*</sup>.
> <sup>*</sup> The [conda documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-envs) recommends against installing packages into a base conda environment, therefore `$FSLDIR` is created as a child environment.
......@@ -18,4 +18,4 @@ To work around this problem, and to isolate all of the FSL executables from the
> <sup>*</sup> More details on FSL project conda recipes are outlined in [`fsl_conda_recipes.md`](fsl_conda_recipes.md).
Users can then add the `$FSLDIR/share/fsl/bin/` directory to their `$PATH`, to the effect that only FSL executables will be made available in their environment.
Users can then add the `$FSLDIR/share/fsl/bin/` directory to their `$PATH`, to the effect that only FSL executables will be made available in their environment. This mechanism also has the advantage that all existing FSL and third-party scripts which refer to `$FSLDIR/bin/<command>` will continue to work without modification.
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