Commit f81bce0a authored by William Clarke's avatar William Clarke
Browse files

Update installation instructions.

parent 8e0b6bb6
...@@ -8,13 +8,27 @@ FSL-MRS is a collection of python modules and wrapper scripts for pre-processing ...@@ -8,13 +8,27 @@ FSL-MRS is a collection of python modules and wrapper scripts for pre-processing
--- ---
### Installation ### Installation
To get the packaged example data, make sure [git-lfs](https://git-lfs.github.com/) is installed. #### Conda package
The primary installation method is via _conda_. After installing conda and creating or activating a suitable [enviroment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) you can install FSL-MRS from the FSL conda channel.
conda install -c conda-forge \
-c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel/ \
fsl_mrs
#### Source code
To get the source code with the packaged example data, make sure [git-lfs](https://git-lfs.github.com/) is installed.
git clone --recurse-submodules https://git.fmrib.ox.ac.uk/saad/fsl_mrs.git git clone --recurse-submodules https://git.fmrib.ox.ac.uk/saad/fsl_mrs.git
cd fsl_mrs cd fsl_mrs
pip install . pip install .
#### Dependencies #### Dependencies
The spec2nii package can be installed to convert data to NIfTI format.
conda install -c conda-forge spec2nii
or
pip install spec2nii pip install spec2nii
...@@ -43,14 +57,14 @@ After installation see the [quick start guide](https://users.fmrib.ox.ac.uk/~saa ...@@ -43,14 +57,14 @@ After installation see the [quick start guide](https://users.fmrib.ox.ac.uk/~saa
--- ---
### Usage ### Documentation
Documentation can be found online [here](https://users.fmrib.ox.ac.uk/~saad/fsl_mrs/html/index.html).
For each of the wrapper scripts above, simply type `<name_of_script> --help` to get the usage. For each of the wrapper scripts above, simply type `<name_of_script> --help` to get the usage.
Example command-line usage is demonstrated in the packaged [Jupyter Notebook](https://git.fmrib.ox.ac.uk/saad/fsl_mrs/-/blob/master/example_usage/Example%20SVS%20processing%20-%20command-line.ipynb.). Example command-line usage is demonstrated in the packaged [Jupyter Notebook](https://git.fmrib.ox.ac.uk/saad/fsl_mrs/-/blob/master/example_usage/Example%20SVS%20processing%20-%20command-line.ipynb.).
Documentation can be found online [here](https://users.fmrib.ox.ac.uk/~saad/fsl_mrs/html/index.html).
### File types ### File types
FSL-MRS accepts FID data in NIfTI + JSON format. Some scripts can also read .RAW (LCModel) and text (jMRUI). FSL-MRS accepts FID data in NIfTI + JSON format. Some scripts can also read .RAW (LCModel) and text (jMRUI).
......
...@@ -36,7 +36,7 @@ rst_epilog = """ ...@@ -36,7 +36,7 @@ rst_epilog = """
.. |fsl_version| replace:: 6.0.4 .. |fsl_version| replace:: 6.0.4
.. |fslmrs_gitlab| replace:: FSL-MRS GitLab .. |fslmrs_gitlab| replace:: FSL-MRS GitLab
.. _fslmrs_gitlab: https://git.fmrib.ox.ac.uk/saad/fsl_mrs .. _fslmrs_gitlab: https://git.fmrib.ox.ac.uk/fsl/fsl_mrs
""" """
......
...@@ -16,7 +16,18 @@ Download or clone from |fslmrs_gitlab|_. `Git LFS <https://git-lfs.github.com/>` ...@@ -16,7 +16,18 @@ Download or clone from |fslmrs_gitlab|_. `Git LFS <https://git-lfs.github.com/>`
2. From Conda 2. From Conda
~~~~~~~~~~~~~ ~~~~~~~~~~~~~
TBC The primary installation method is via *conda*. After installing conda and creating or activating a suitable `enviroment <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_ you can install FSL-MRS from the FSL conda channel.
::
conda install -c conda-forge \
-c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel/ \
fsl_mrs
spec2nii
~~~~~~~~
To convert data to NIfTI install the spec2nii program from conda.
::
conda install -c conda-forge spec2nii
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