FSL-MRS

https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/
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FSL-MRS is an end-to-end software suite for the processing, quantification, and analysis of magnetic...
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### Convert GE pfile with spec2nii GE

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert GE pfiles (.7) using the GE subcommand.

```bash
spec2nii GE <file>

```

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### Convert LCModel RAW with spec2nii raw

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert LCModel .RAW text files containing one FID as two columns (real and imaginary). Optionally specify location with a 4x4 affine matrix passed as a plain text file (-a, --affine).

```bash
spec2nii raw [-a <affine>] <file>

```

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### Convert Philips SDAT/SPAR with spec2nii philips

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert Philips SDAT/SPAR files. Requires both the SDAT and SPAR file paths as arguments.

```bash
spec2nii philips <SDAT> <SPAR>

```

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### Convert plain text FID with spec2nii text

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert plain text files containing one FID as two columns (real and imaginary). Required inputs are central frequency (-i, --imagingfreq; MHz) and bandwidth (-b, --bandwidth; Hz). Optionally specify location with a 4x4 affine matrix passed as a plain text file (-a, --affine).

```bash
spec2nii text -i <imaging_freq> -b <bandwidth> [-a <affine>]  <file>

```

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### Inspect Twix file with spec2nii twix -v

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Inspect the contents of a Twix file before conversion. Produces a list of data with associated 'evalinfo' flags and data dimensions.

```bash
spec2nii twix -v <file>

```

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### Convert Twix data with spec2nii twix -e

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert all data from a single 'evalinfo' flag in a Twix file. The 'Image' flag is typically used for the main dataset; other flags may be used for noise, water reference, or other sequence-specific data.

```bash
spec2nii twix -e <flag> <file>

```

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### Convert jMRUI text with spec2nii jmrui

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert jMRUI text format files containing one FID as two columns (real and imaginary). Optionally specify location with a 4x4 affine matrix passed as a plain text file (-a, --affine).

```bash
spec2nii jmrui [-a <affine>] <file>

```

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### Convert DICOM with spec2nii dicom

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert a single DICOM file or a directory of DICOM files. NIfTI-MRS dimension tags (e.g. DIM_COIL) can be specified using the -t command line argument.

```bash
spec2nii dicom <file_or_dir>

```

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### Convert UIH DICOM with spec2nii uih

Source: https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/data_conversion.html

Convert UIH DICOM format SVS and CSI spectroscopy data. NIfTI-MRS dimension tags (e.g. DIM_COIL) can be specified using the -t command line argument.

```bash
spec2nii uih DCM_FILE_or_DIR

```
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