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
#### Conda package
### Conda package
The primary installation method is via _conda_. After installing conda and creating or activating a suitable [environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) you can install FSL-MRS from the FSL conda channel.
The primary installation method is via _conda_. First you should install conda and creating a suitable [environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). For example, in the base conda environment execute:
The spec2nii package can be installed to convert data to NIfTI format.
conda install -c conda-forge spec2nii
or
pip install spec2nii
After installation see the [quick start guide](https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/quick_start.html).
After installation see the [quick start guide](https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/quick_start.html).
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### Content
## Content
#### Scripts:
### Scripts:
-**fsl\_mrs**
-**fsl\_mrs**
: fit a single voxel spectroscopy (SVS) spectrum
: fit a single voxel spectroscopy (SVS) spectrum
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### Documentation
## Documentation
Documentation can be found online on the [WIN open science website](https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/).
Documentation can be found online on the [WIN open science website](https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/).
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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.).
### File types
## Getting help
Please seek help via the [FSL JISC email list](mailto:FSL@JISCMAIL.AC.UK) or by submitting an issue on the [FSL-MRS Github mirror](https://github.com/wexeee/fsl_mrs/issues).
## File types
FSL-MRS accepts FID data in NIfTI-MRS format. Some scripts can also read .RAW (LCModel) and text (jMRUI).
FSL-MRS accepts FID data in NIfTI-MRS format. Some scripts can also read .RAW (LCModel) and text (jMRUI).
Conversion to NIfTI-MRS is provided by [spec2nii](https://github.com/wexeee/spec2nii).
Conversion to NIfTI-MRS is provided by [spec2nii](https://github.com/wexeee/spec2nii).
### Working in python
## Working in python
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))
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))
Installation with conda is easy, but you won't get the packaged example data and notebooks. This can be downloaded separately here: |fslmrs_pkg_data|_.
Installation with conda is easy, but you won't get the packaged example data and notebooks. This can be downloaded separately here: |fslmrs_pkg_data|_.
spec2nii
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To convert data to NIfTI install the spec2nii program from conda.
::
conda install -c conda-forge spec2nii
Operating systems
Operating systems
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FSL-MRS has been tested thoroughly on Mac and Linux operating systems. FSL-MRS dependencies and FSL-MRS is available on native Windows installations, but has not currently been tested. `Windows Subsytem for Linux <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ (or WSL2) offers a Linux interface on Windows. FSL-MRS has been tested on WSL.
FSL-MRS has been tested thoroughly on Mac and Linux operating systems. FSL-MRS dependencies and FSL-MRS is available on native Windows installations, but has not currently been tested. `Windows Subsystem for Linux <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ (or WSL2) offers a Linux interface on Windows. FSL-MRS has been tested on WSL.
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For a description of the sequence file parameters see the :ref:`sequence file <seq_file_params>` page. Alternatively see the examples in the simulator package (examplePRESS.json & exampleSTEAM.json).
For a description of the sequence file parameters see the :ref:`sequence file <seq_file_params>` page. Alternatively see the examples in the simulator package (examplePRESS.json & exampleSTEAM.json).
Please note that delays in the sequence description file do not include the duration of the pulse. I.e., the time from the centroid to the start/end of the RF pulse must be added to the delay to calculate the time between pulse centroids.
