-
Notifications
You must be signed in to change notification settings - Fork 0
/
gannetpreinitialise-settings.Rmd
executable file
·167 lines (146 loc) · 11.5 KB
/
gannetpreinitialise-settings.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
---
title: "GannetPreInitialise settings"
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: 1200px;
}
```
<br>
::: warning
<i class="fa fa-exclamation-circle" style="color: white"></i> These examples were created in release 3.3.0. Take care copy-pasting these examples into your version of `GannetPreInitialise.m`. You may be using a different release that has older/newer variables that could result in an error during the analysis pipeline.
:::
## {.tabset .tabset-fade .tabset-pills}
### GABA-edited MEGA-PRESS data
```{octave, eval = FALSE}
% Acquisition parameters
MRS_struct.p.target = {'GABAGlx'}; % Edited metabolite(s) of interest; permitted options are:
% If MEGA-PRESS:
% {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
% If HERMES:
% {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
% If HERCULES:
% {'GABAGlx','GSH'}
% If phantom data:
% and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
% and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
% options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
% Analysis parameters
MRS_struct.p.LB = 3; % Exponential line-broadening (in Hz)
MRS_struct.p.water_ECC = 1; % 1 = YES, perform eddy current correction on water data
MRS_struct.p.metab_ECC = 0; % 1 = YES, perform eddy current correction on metabolite data (requires a water reference)
MRS_struct.p.water_removal = 1; % 1 = YES, remove residual water signal in DIFF spectrum using HSVD
MRS_struct.p.alignment = 'RobustSpecReg'; % Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',
% 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)
MRS_struct.p.use_prealign_ref = 0; % 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in
% worse alignment compared to the pre-aligned data; setting this parameter to 1 will
% make RobustSpecReg use the averaged pre-aligned subspectra as references to align the
% averaged post-aligned subspectra, which may improve the final alignment
MRS_struct.p.vox = {'vox1'}; % For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.
MRS_struct.p.fit_resid_water = 0; % 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor
MRS_struct.p.weighted_averaging = 1; % 1 = YES, average subspectra using weighted averaging
% Flags(0 = NO; 1 = YES)
MRS_struct.p.HERMES = 0; % Data acquired using HERMES
MRS_struct.p.HERCULES = 0; % Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well
MRS_struct.p.PRIAM = 0; % Data acquired using PRIAM
MRS_struct.p.phantom = 0; % Data are from a phantom (assumes phantom was scanned at room temperature)
MRS_struct.p.join = 0; % Join multiple files (this can be batched across subjects)
MRS_struct.p.mat = 0; % Save MRS_struct as a .mat file
MRS_struct.p.csv = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
% GannetSegment and GannetQuantify)
MRS_struct.p.append = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
% folder to be added to the search path and Ghostscript to be installed)
MRS_struct.p.hide = 0; % Do not display output figures
```
### GABA-/GSH-edited HERMES data
```{octave, eval = FALSE}
% Acquisition parameters
MRS_struct.p.target = {'GABAGlx','GSH'}; % Edited metabolite(s) of interest; permitted options are:
% If MEGA-PRESS:
% {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
% If HERMES:
% {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
% If HERCULES:
% {'GABAGlx','GSH'}
% If phantom data:
% and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
% and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
% options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
% Analysis parameters
MRS_struct.p.LB = 3; % Exponential line-broadening (in Hz)
MRS_struct.p.water_ECC = 1; % 1 = YES, perform eddy current correction on water data
MRS_struct.p.metab_ECC = 0; % 1 = YES, perform eddy current correction on metabolite data (requires a water reference)
MRS_struct.p.water_removal = 1; % 1 = YES, remove residual water signal in DIFF spectrum using HSVD
MRS_struct.p.alignment = 'RobustSpecReg'; % Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',
% 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)
MRS_struct.p.use_prealign_ref = 0; % 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in
% worse alignment compared to the pre-aligned data; setting this parameter to 1 will
% make RobustSpecReg use the averaged pre-aligned subspectra as references to align the
% averaged post-aligned subspectra, which may improve the final alignment
MRS_struct.p.vox = {'vox1'}; % For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.
MRS_struct.p.fit_resid_water = 0; % 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor
MRS_struct.p.weighted_averaging = 1; % 1 = YES, average subspectra using weighted averaging
% Flags(0 = NO; 1 = YES)
MRS_struct.p.HERMES = 1; % Data acquired using HERMES
MRS_struct.p.HERCULES = 0; % Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well
MRS_struct.p.PRIAM = 0; % Data acquired using PRIAM
MRS_struct.p.phantom = 0; % Data are from a phantom (assumes phantom was scanned at room temperature)
MRS_struct.p.join = 0; % Join multiple files (this can be batched across subjects)
MRS_struct.p.mat = 0; % Save MRS_struct as a .mat file
MRS_struct.p.csv = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
% GannetSegment and GannetQuantify)
MRS_struct.p.append = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
% folder to be added to the search path and Ghostscript to be installed)
MRS_struct.p.hide = 0; % Do not display output figures
```
### Phantom GABA-edited MEGA-PRESS data
```{octave, eval = FALSE}
% Acquisition parameters
MRS_struct.p.target = {'GABA'}; % Edited metabolite(s) of interest; permitted options are:
% If MEGA-PRESS:
% {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
% If HERMES:
% {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
% If HERCULES:
% {'GABAGlx','GSH'}
% If phantom data:
% and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
% and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
% options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
% Analysis parameters
MRS_struct.p.LB = 3; % Exponential line-broadening (in Hz)
MRS_struct.p.water_ECC = 1; % 1 = YES, perform eddy current correction on water data
MRS_struct.p.metab_ECC = 0; % 1 = YES, perform eddy current correction on metabolite data (requires a water reference)
MRS_struct.p.water_removal = 1; % 1 = YES, remove residual water signal in DIFF spectrum using HSVD
MRS_struct.p.alignment = 'none'; % Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',
% 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)
MRS_struct.p.use_prealign_ref = 0; % 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in
% worse alignment compared to the pre-aligned data; setting this parameter to 1 will
% make RobustSpecReg use the averaged pre-aligned subspectra as references to align the
% averaged post-aligned subspectra, which may improve the final alignment
MRS_struct.p.vox = {'vox1'}; % For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.
MRS_struct.p.fit_resid_water = 0; % 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor
MRS_struct.p.weighted_averaging = 1; % 1 = YES, average subspectra using weighted averaging
% Flags(0 = NO; 1 = YES)
MRS_struct.p.HERMES = 0; % Data acquired using HERMES
MRS_struct.p.HERCULES = 0; % Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well
MRS_struct.p.PRIAM = 0; % Data acquired using PRIAM
MRS_struct.p.phantom = 1; % Data are from a phantom (assumes phantom was scanned at room temperature)
MRS_struct.p.join = 0; % Join multiple files (this can be batched across subjects)
MRS_struct.p.mat = 0; % Save MRS_struct as a .mat file
MRS_struct.p.csv = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
% GannetSegment and GannetQuantify)
MRS_struct.p.append = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
% directory to be added to the search path and Ghostscript to be installed)
MRS_struct.p.hide = 0; % Do not display output figures
```