batch-script.Rmd

---
title: "Batch processing script"
date: "Last updated: `r format(Sys.time(), '%B %d, %Y')`"
output: html_document
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r, child = "js/back-to-top.js"}
```

```{css, echo = FALSE}
body .main-container {
  max-width: 900px;
}
```

<br>

```{octave, eval = FALSE}
% Example batch script for Philips MEGA-PRESS data with accompanying water references and structural images
% Remember to check GannetPreInitialise.m has the appropriate settings for your data

data_dir = '/Users/username/Documents/my_project/data';

metab = {'S01_GABA_68_act.sdat'
         'S02_GABA_68_act.sdat'
         'S03_GABA_68_act.sdat'};
metab = fullfile(data_dir, metab); % It is good practice to include the full path of files
         
water = {'S01_GABA_68_ref.sdat'
         'S02_GABA_68_ref.sdat'
         'S03_GABA_68_ref.sdat'};
water = fullfile(data_dir, water);

anat = {'S01_T1_anat.nii'
        'S02_T1_anat.nii'
        'S03_T1_anat.nii'};
anat = fullfile(data_dir, anat);

MRS = GannetLoad(metab, water);
MRS = GannetFit(MRS);
MRS = GannetCoRegister(MRS, anat);
MRS = GannetSegment(MRS);
MRS = GannetQuantify(MRS);
```