You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Open-source, MATLAB-based software for automated data processing and quantification of edited magnetic resonance spectroscopy (MRS) data.
11
+
Open-source, MATLAB-based software for automated data processing and quantification of edited <sup>1</sup>H magnetic resonance spectroscopy (MRS) data.
11
12
12
-
Full software documentation can be found [here](https://markmikkelsen.github.io/Gannet-docs/index.html). Visit our [blog](http://www.gabamrs.com/) for the latest news on Gannet and our developments in edited MRS methodology.
13
+
Full software documentation can be found [here](https://markmikkelsen.github.io/Gannet-docs/index.html). Visit our [blog](https://gabamrs.com/) for the latest news on Gannet and our developments in edited MRS methodology.
13
14
14
15
## Overview
15
16
@@ -25,49 +26,54 @@ Several existing software packages for MRS data analysis require substantial use
25
26
26
27
Additionally, as open-source software, advanced users have the ability to modify the underlying routines for ad hoc purposes.
27
28
28
-
Gannet is continually being updated and has an active support base. Visit our [blog](http://www.gabamrs.com/) for the latest news on Gannet and our developments in edited MRS methodology.
29
-
30
29
## Installation
31
30
32
31
### Prerequisites
33
32
34
-
Gannet runs in [MATLAB](https://www.mathworks.com/products/matlab.html). For best performance, we recommend using the latest release if possible. Additionally, Gannet requires that the following MATLAB toolboxes are installed:
33
+
Gannet runs in [MATLAB](https://mathworks.com/products/matlab.html). For best performance, we recommend using the latest release if possible. Additionally, Gannet requires that the following MATLAB toolboxes are installed:
35
34
36
35
- Image Processing
37
36
- Optimization
38
37
- Signal Processing
39
38
- Statistics and Machine Learning
40
39
41
-
You can check which toolboxes you have installed by typing `ver` in the MATLAB command window. To install any missing toolboxes, please follow these [instructions](https://www.mathworks.com/matlabcentral/answers/101885-how-do-i-install-additional-toolboxes-into-an-existing-installation-of-matlab).
40
+
You can check which toolboxes you have installed by typing `ver` in the MATLAB command window. To install any missing toolboxes, please follow these [instructions](https://mathworks.com/matlabcentral/answers/101885-how-do-i-install-additional-toolboxes-into-an-existing-installation-of-matlab).
42
41
43
42
To run the voxel co-registration and structural image segmentation modules, [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) must be installed.
44
43
45
44
### Download
46
45
47
-
The simplest way to install Gannet is to download the zipped [main folder](https://github.com/markmikkelsen/Gannet/archive/main.zip)from the [repository](https://github.com/markmikkelsen/Gannet)on GitHub, unzip it, and move the _Gannet-main_ folder into your MATLAB directory.
46
+
The simplest way to install Gannet is to download the code from the [GitHub repository](https://github.com/markmikkelsen/Gannet) and move the `Gannet-main/` directory into your MATLAB directory.
48
47
49
48
Alternatively, git-savvy users can clone the Gannet repository into a directory of their choice:
The development version can downloaded from the [development branch](https://github.com/markmikkelsen/Gannet/tree/dev) on GitHub or by using the following git command if the repository was cloned:
53
+
54
+
`git checkout dev`
55
+
56
+
Stable releases can be found [here](https://github.com/markmikkelsen/Gannet/releases).
57
+
53
58
### Setup
54
59
55
-
Open the _Set Path_ dialog box from the MATLAB menu (or run the command `pathtool` in the Command Window), click _Add with Subfolders_, find the _Gannet-main_ folder and then select it. When done, press _Save_ to permanently save the Gannet folder to MATLAB's default search path.
60
+
Open the *Set Path* dialog box from the MATLAB menu (or run the command `pathtool` in the Command Window), click *Add with Subfolders...*, find the downloaded Gannet directory and then select it. When done, press *Save* to permanently save the Gannet directory to MATLAB's default search path.
56
61
57
62
SPM12 can be installed in the same manner after it has been downloaded from the SPM website.
58
63
59
-
__It is highly recommended that you only add the main SPM12 folder (_spm12_) to your search path instead of including all the subfolders. This prevents potential function conflicts.__
64
+
**It is highly recommended that you only add the main SPM12 directory (`spm12/`) to your search path instead of including all the subdirectories. This prevents function conflicts.**
60
65
61
66
## Compatibility
62
67
63
-
Gannet is currently being developed in MATLAB R2022b in macOS 12.6 Monterey. While reasonable effort is made to ensure legacy and cross-OS compatibility, an error-free user experience is not guaranteed.
68
+
Gannet is currently being developed in MATLAB R2022b in macOS 13.1 Ventura. While reasonable effort is made to ensure legacy and cross-OS compatibility, an error-free user experience is not guaranteed.
64
69
65
70
## Supported file formats
66
71
67
72
At present, the following MRS data file formats are supported:
68
73
69
74
- DICOM (.dcm)
70
75
- GE P-file (.7)
76
+
- NIfTI-MRS (.nii[.gz])
71
77
- Philips .data/.list
72
78
- Philips .raw
73
79
- Philips .sdat/.spar
@@ -77,15 +83,15 @@ At present, the following MRS data file formats are supported:
77
83
78
84
For creating and co-registering voxel masks, structural images need to be in NIfTI format (DICOM files can also be used if processing GE P-files).
79
85
80
-
__Philips users: Do not use structural images exported using the _fsl-nifti_ option as this creates problems with co-registration in Gannet.__
86
+
**Philips users: Do not use structural images exported using the *fsl-nifti* option as this creates problems with co-registration in Gannet.**
81
87
82
88
## Getting help
83
89
84
90
If you encounter any problems, please first check the [documentation website](https://markmikkelsen.github.io/Gannet-docs/index.html) or the [FAQ](https://markmikkelsen.github.io/Gannet-docs/faq.html) page for a solution.
85
91
86
92
Otherwise, you can post your query on the [Gannet forum](https://forum.mrshub.org/c/mrs-software/gannet/9) on the [MRSHub](https://mrshub.org/).
87
93
88
-
The support team can also be directly reached using our blog's [contact form](http://www.gabamrs.com/contact). We will do our best to work with you to solve your issue.
94
+
The support team can also be directly reached using our blog's [contact form](https://gabamrs.com/contact). We will do our best to work with you to solve your issue.
89
95
90
96
## Versioning
91
97
@@ -105,50 +111,48 @@ The support team can also be directly reached using our blog's [contact form](ht
105
111
106
112
This software is licensed under the open-source [BSD-3-Clause License](https://github.com/markmikkelsen/Gannet/blob/main/LICENSE). Should you disseminate material that made use of Gannet, please cite the following publications, as appropriate:
107
113
108
-
**For all work using Gannet:**
109
-
110
-
- Edden RAE, Puts NAJ, Harris AD, Barker PB, Evans CJ. [Gannet: A batch-processing tool for the quantitative analysis of gamma-aminobutyric acid-edited MR spectroscopy spectra.](https://doi.org/10.1002/jmri.24478)_Journal of Magnetic Resonance Imaging_. 2014;40(6):1445–1452
114
+
- Edden RAE, Puts NAJ, Harris AD, Barker PB, Evans CJ. [Gannet: A batch-processing tool for the quantitative analysis of gamma-aminobutyric acid-edited MR spectroscopy spectra.](https://doi.org/10.1002/jmri.24478)*Journal of Magnetic Resonance Imaging*. 2014;40(6):1445–1452
111
115
112
116
**If you perform frequency-and-phase correction (FPC) using:**
113
117
114
118
Robust spectral registration (`RobustSpecReg`):
115
119
116
-
- Mikkelsen M, Tapper S, Near J, Mostofsky SH, Puts NAJ, Edden RAE. [Correcting frequency and phase offsets in MRS data using robust spectral registration.](https://doi.org/10.1002/nbm.4368)_NMR in Biomedicine_. 2020;33(10):e4368
120
+
- Mikkelsen M, Tapper S, Near J, Mostofsky SH, Puts NAJ, Edden RAE. [Correcting frequency and phase offsets in MRS data using robust spectral registration.](https://doi.org/10.1002/nbm.4368)*NMR in Biomedicine*. 2020;33(10):e4368
117
121
118
122
multi-step FPC (`SpecRegHERMES`):
119
123
120
-
- Mikkelsen M, Saleh MG, Near J, et al. [Frequency and phase correction for multiplexed edited MRS of GABA and glutathione.](https://doi.org/10.1002/mrm.27027)_Magnetic Resonance in Medicine_. 2018;80(1):21-28
124
+
- Mikkelsen M, Saleh MG, Near J, et al. [Frequency and phase correction for multiplexed edited MRS of GABA and glutathione.](https://doi.org/10.1002/mrm.27027)*Magnetic Resonance in Medicine*. 2018;80(1):21-28
121
125
122
126
or spectral registration (`SpecReg`):
123
127
124
-
- Near J, Edden R, Evans CJ, Paquin R, Harris A, Jezzard P. [Frequency and phase drift correction of magnetic resonance spectroscopy data by spectral registration in the time domain.](https://doi.org/10.1002/mrm.25094)_Magnetic Resonance in Medicine_. 2015;73(1):44-50
128
+
- Near J, Edden R, Evans CJ, Paquin R, Harris A, Jezzard P. [Frequency and phase drift correction of magnetic resonance spectroscopy data by spectral registration in the time domain.](https://doi.org/10.1002/mrm.25094)*Magnetic Resonance in Medicine*. 2015;73(1):44-50
**If you report water-referenced measurements tissue-corrected using:**
134
+
**If you report water-referenced, tissue-corrected metabolite measurements using:**
131
135
132
136
The Harris et al. method:
133
137
134
-
- Harris AD, Puts NAJ, Edden RAE. [Tissue correction for GABA-edited MRS: Considerations of voxel composition, tissue segmentation, and tissue relaxations.](https://doi.org/10.1002/jmri.24903)_Journal of Magnetic Resonance Imaging_. 2015;42(5):1431–1440
138
+
- Harris AD, Puts NAJ, Edden RAE. [Tissue correction for GABA-edited MRS: Considerations of voxel composition, tissue segmentation, and tissue relaxations.](https://doi.org/10.1002/jmri.24903)*Journal of Magnetic Resonance Imaging*. 2015;42(5):1431–1440
135
139
136
140
or the Gasparovic et al. method:
137
141
138
-
- Gasparovic C, Song T, Devier D, et al. [Use of tissue water as a concentration reference for proton spectroscopic imaging.](https://doi.org/10.1002/mrm.20901)_Magnetic Resonance in Medicine_. 2006;55(6):1219–1226
142
+
- Gasparovic C, Song T, Devier D, et al. [Use of tissue water as a concentration reference for proton spectroscopic imaging.](https://doi.org/10.1002/mrm.20901)*Magnetic Resonance in Medicine*. 2006;55(6):1219–1226
139
143
140
144
## Acknowledgments
141
145
142
146
The development and dissemination of Gannet has been supported by the following NIH grants:
143
147
144
148
- R01 EB016089
145
-
- R01 EB023963
149
+
- R01 EB023963
150
+
- K99 EB028828
146
151
- P41 EB015909
147
-
- R01MH106564
152
+
- R01MH106564
148
153
- R21 NS077300
149
154
- R21 MH098228
150
155
- R01 MH096263
151
-
- K99 EB028828
152
156
153
157
We wish to thank the following individuals for their direct or indirect contributions:
154
158
@@ -157,6 +161,6 @@ We wish to thank the following individuals for their direct or indirect contribu
157
161
- Alex Craven (University of Bergen)
158
162
- Philipp Ehses (Max Planck Institute for Biological Cybernetics)
0 commit comments