diff --git a/README.md b/README.md index eace966..0754244 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ Matlab: Python: - see `requirements.txt` file - - ![WinawerLab's MRI_tools](https://github.com/WinawerLab/MRI_tools)) + - [WinawerLab's MRI_tools](https://github.com/WinawerLab/MRI_tools) (which requires [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)) Other: @@ -81,17 +81,17 @@ need it. # Snakemake A Snakefile is included with this project to enable the use -of ![snakemake](http://snakemake.readthedocs.io/en/latest/). This is +of [snakemake](http://snakemake.readthedocs.io/en/latest/). This is highly recommended, since it will allow you to easily to rerun the analyses exactly as I have performed them and it enables easy use on a cluster. To use, -![install snakemake](http://snakemake.readthedocs.io/en/latest/getting_started/installation.html) and, +[install snakemake](http://snakemake.readthedocs.io/en/latest/getting_started/installation.html) and, if using on a cluster, set up your appropriate -![Snakemake profile](https://github.com/Snakemake-Profiles/doc) (see +[Snakemake profile](https://github.com/Snakemake-Profiles/doc) (see the -![snakemake docs](http://snakemake.readthedocs.io/en/latest/executable.html#profiles)for +[snakemake docs](http://snakemake.readthedocs.io/en/latest/executable.html#profiles)for more info on profiles). Then simply type `snakemake {target}` to re-run the analyses.