Commit 72a269dd authored by William Clarke's avatar William Clarke
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Update README

parent 9c4434fc
...@@ -6,13 +6,18 @@ ...@@ -6,13 +6,18 @@
FSL-MRS is a collection of python modules and wrapper scripts for pre-processing and model fitting of Magnetic Resonance Spectroscopy (MRS) data. FSL-MRS is a collection of python modules and wrapper scripts for pre-processing and model fitting of Magnetic Resonance Spectroscopy (MRS) data.
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### Installation ### Installation
git clone https://git.fmrib.ox.ac.uk/saad/fsl_mrs.git git clone https://git.fmrib.ox.ac.uk/saad/fsl_mrs.git
cd fsl_mrs cd fsl_mrs
pip install . pip install .
#### Dependencies
pip install spec2nii
After installation see the [quick start guide](https://users.fmrib.ox.ac.uk/~wclarke/fsl_mrs/userdoc/quick_start.html).
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### Content ### Content
...@@ -22,35 +27,45 @@ FSL-MRS is a collection of python modules and wrapper scripts for pre-processing ...@@ -22,35 +27,45 @@ FSL-MRS is a collection of python modules and wrapper scripts for pre-processing
- **fsl\_mrs** - **fsl\_mrs**
: fit a single spectrum : fit a single spectrum
- **fsl\_mrsi** - **fsl\_mrsi**
: fit a 4D volume of spectra : fit a 3D volume of 1D spectra
- **fsl\_mrs\_preproc** - **fsl\_mrs\_proc**
: pre-processing (coil combination, averaging, eddy-current correction) : pre-processing (coil combination, averaging, eddy-current correction)
- **fsl\_mrs\_preproc**
: Pre-packaged processing for non-edited SVS.
- **fsl\_mrs\_sim** - **fsl\_mrs\_sim**
: simulate basis : simulate basis spectra
- **mrs_vis** - **mrs_vis**
: quick visualisation of the spectrum : quick visualisation of the spectra or basis spectra
- **svs_segment & mrsi_segment**
: Run tissue segmentation for SVS/MRSI from T1 image.
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#### Usage ### Usage
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.).
Documentation can be found online [here](https://users.fmrib.ox.ac.uk/~wclarke/fsl_mrs/userdoc/index.html).
#### File types ### File types
FSL-MRS accepts FID data in NIFTI format. It can also read .RAW format (like LCModel). FSL-MRS accepts FID data in NIfTI + JSON format. Some scripts can also read .RAW (LCModel) and text (jMRUI).
#### Working in python Conversion to NIfTI is provided by [spec2nii](https://github.com/wexeee/spec2nii).
If you don't want to use the wrapper scripts, you can use the python modules directly in your own python scripts/programs. Here are some examples below: ### Working in python
- Pre-processing If you don't want to use the wrapper scripts, you can use the python modules directly in your own python scripts/programs. Or in an interactive Python environment (see example [notebook](https://git.fmrib.ox.ac.uk/saad/fsl_mrs/-/blob/master/example_usage/Example%20SVS%20processing%20-%20interactive%20notebook.ipynb))
- Model fitting - single voxel
- Model fitting - MRSImaging ---
### Permissions and citations
If you use FSL-MRS in your research please cite:
Please see the LICENSE file for licensing information.
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