faq.Rmd

---
title: "FAQ"
date: "Last updated: `r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    toc: TRUE
    toc_depth: 2
    toc_float:
      collapsed: FALSE
---

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

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

<br>

::: info
<i class="fa fa-info-circle" style="color: white"></i>&nbsp; When encountering an error or bug in Gannet, please first check you are using the latest <a href="https://github.com/markmikkelsen/Gannet" target="_blank"><u>version</u></a>. It may be that your issue has already been addressed.

If your issue has not been addressed or is not found in this FAQ, please report the issue to us on <a href="https://github.com/markmikkelsen/Gannet/issues" target="_blank"><u>GitHub</u></a> or the <a href="https://forum.mrshub.org/c/mrs-software/gannet/9" target="_blank"><u>MRSHub Forum</u></a>.
:::

## General

#### **1. Can Gannet process non-edited data?**

No, Gannet is designed to process edited single-voxel data only. However, the standalone tool [CoRegStandAlone](https://markmikkelsen.github.io/Gannet-docs/additional-tools.html#coregstandalone) can be used with non-edited single-voxel data to co-register voxels to structural images and segment the images to obtain voxel tissue fractions.

#### **2. Can Gannet process MRSI data?**

No.

#### **3. Can Gannet process GSH-edited data?**

Yes, Gannet can process GABA-, GSH-, Lac-, and EtOH-edited MEGA-PRESS data, as well as GABA-/GSH-, Lac-/GSH-, and EtOH-/GABA-/GSH-edited HERMES and HERCULES data. (Fitting of HERCULES phantom data is not supported, however.) Simply set the appropriate `target` option(s) in `GannetPreInitialise.m`.

#### **4. Can Gannet process HERMES/HERCULES data?**

`GannetLoad.m` can load and preprocess HERMES and HERCULES data, but only HERMES data can be modeled in `GannetFit.m`. HERCULES data can be fully processed and fitted using the <a href="https://github.com/schorschinho/osprey" target="_blank">Osprey</a> software package.

#### **5. Can Gannet process phantom data?**

Yes, Gannet can process and fit phantom edited data as described above. Make sure to set `phantom` to `1` under `Flags` in `GannetPreInitialise.m`. If you want to fit your data, run `GannetFitPhantom(MRS_struct);` instead of `GannetFit(MRS_struct);`. (Fitting of HERCULES phantom data is not supported.)

## Output

#### **1. Why is my spectrum upside down?**

<img id="img_50" src="images/faq/upside-down-spectrum.png" alt="A screenshot example of upside-down MRS spectra">

Gannet has a routine that automatically phases spectra so that they are not upside-down or otherwise out of phase. However, this routine can fail. It is best to contact the developers for assistance to resolve the problem. A possible, but not infallible, solution is to add the following line of code to `GannetLoad.m` after the function `PhaseCorrection.m` is run for global zero-order phase correction (around line 400):

```{octave, eval = FALSE}
MRS_struct.fids.data = -MRS_struct.fids.data;
```

## Errors

#### **1. You have issues with SPM MEX files on macOS Catalina, Big Sur, Monterey, Ventura**

Specifically:

```{verbatim}
"*.mexmaci64" cannot be opened because the developer cannot be verified. macOS cannot verify that this app is free from malware.
```

or

```{verbatim}
Code signature not valid for use in process using Library Validation: library load disallowed by system policy.
```

Please visit the <a href="https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)#macOS_Catalina,_Big_Sur,_Monterey,_Ventura" target="_blank">SPM Wikibooks page</a> for troubleshooting.

#### **2. MATLAB says my structural image does not exist**

For example:

```{octave, eval = FALSE}
Error using spm_vol>spm_vol_hdr (line 80)
File “image1.nii” does not exist.

Error in spm_vol (line 61)
** v = spm_vol_hdr(deblank(P(i,:)));**

Error in GannetMask_SiemensTWIX (line 110)
V = spm_vol(nii_file);

Error in GannetCoRegister (line 74)
** MRS_struct = GannetMask_SiemensTWIX(fname, nii_name{ii}, MRS_struct, ii, vox, kk);**

Error in gannetcode (line 19)
** MRS_struct = GannetCoRegister(MRS_struct,{‘image1.nii’});**
```

A possible fix for this is to input filenames using their full path. So, instead of `{'image1.nii'}`, input `{'/Users/username/Documents/my_project/data/image1.nii'}`.