The fields
listed on this page are applicable to releases 3.3.0+ and are not
necessarily correct for other versions of Gannet.
All output from Gannet analyses are saved in a structure (e.g.,
MRS_struct, or whatever name the user has chosen) that
contains many fields and subfields. Listed below are lists of these
fields and their descriptions. Note that not possible field that Gannet
can generate during an analysis pipeline is shown for the sake of
brevity.
MRS_struct
Field
Description
version
Structure containing release numbers of Gannet and the
Gannet modules
ii
During analysis, the current file being loaded; after
analysis, the number of files that were loaded
metabfile
Cell array containing the inputted metabolite data
filenames
waterfile
Cell array containing the inputted water reference data
filenames
MRS_struct.p
Field
Description
target
The metabolite(s) targeted by the editing pulses
ON_OFF_order
Order of the editing subexperiments
seqorig
Origin of the Philips MEGA-PRESS or GE HERMES
sequences
LB
Exponential line-broadening applied (Hz)
water_ECC
Whether eddy-current correction was applied to the
water data
metab_ECC
Whether eddy-current correction was applied to the
metabolite data
water_removal
Whether the residual water signal in DIFF spectrum was
removed using HSVD
alignment
Choice of shot-to-shot frequency-and-phase
correction
use_prealign_ref
Whether RobustSpecReg used the averaged
pre-aligned subspectra as references to align the averaged post-aligned
subspectra
fit_resid_water
Whether the residual water signal in the OFF spectrum
was fitted to calculate a water suppression factor
weighted_averaging
Whether weighted signal averaging was implemented
HERMES
Whether the data are HERMES data
HERCULES
Whether the data are HERCULES data
PRIAM
Whether the data are PRIAM data
phantom
Whether the data are phantom data
join
Whether the input files were joined
mat
Whether the output structure was saved as MAT-file
csv
Whether a CSV file of useful data was created
append
Whether the PDF outputs were appended into single
files
hide
Whether the output figures were hidden
vendor
Scanner vendor
reference
Concentrations will be calculated relative to this; if
a water reference is provided, concentrations will be calculated
relative to both water and Cr, otherwise they will be calculated
relative to Cr
numScans
Total number of scans in the batch
numFilesPerScan
When input files are joined, the number of files joined
per scan
npoints
Number of data points of each input file
nrows
Number of data frames stored in each input file
nrows_water
Number of data frames stored in each input water
reference file
Navg
Total number of averages collected at acquisition
Nwateravg
Total number of averages collected at acquisition
TR
Repetition time (ms)
TE
Echo time (ms)
TR_water
Repetition time (ms)
TE_water
Echo time (ms)
LarmorFreq
Larmor frequency (MHz)
sw
Spectral width (Hz)
voxdim
Array of voxel dimensions (mm)
voxoff
Array of voxel position offset (mm)
voxang
Array of voxel angulation (deg)
ZeroFillTo
Processed spectra are zero-filled to this many data
points
zf
Zero-fill factor
dt
Dwell time (s)
SpecRes
Spectral resolution of the raw data (Hz/point)
SpecResNominal
Nominal spectral resolution of the processed data
(Hz/point)
Tacq
Acquisition time (s)
weighted_averaging_method
The algorithm used for weighted signal averaging
MRS_struct.fids
Field
Description
data
Raw time-domain metabolite data (dimensions:
npoints\(\times\)nrows) of the last loaded dataset
data_water
Raw time-domain water reference data (dimensions:
npoints\(\times\)nrows_water) of the last loaded dataset
ON_OFF
Array of the editing order of the last loaded dataset
(1 = ON; 0 = OFF)
data_align
Raw time-domain metabolite data of the last loaded
dataset with frequency-and-phase correction applied
MRS_struct.spec
Field
Description
vox1 (or whatever was set in
MRS_struct.p.vox in
GannetPreInitialise.m)
This structure contains the complex frequency-domain
spectral data for all input datasets
freq
Frequency axis (ppm), calculated from the last loaded
dataset
F0freq
Cell array of the observed frequency of either residual
water signal or the 3 ppm Cr signal for each average
F0freq2
Cell array of the observed frequency of the 3 ppm Cr
signal for each average; this is used in
RobustSpectralRegistration.m as the starting values for
frequency during optimization
AllFramesFT
Spectra of the last loaded dataset without
frequency-and-phase correction applied
AllFramesFTrealign
Spectra of the last loaded dataset with
frequency-and-phase correction applied
MRS_struct.out
Field
Description
AvgDeltaF0
Vector containing a metric of the amount of frequency
offset observed during the acquisition, calculated as the mean
difference between the observed frequency of the residual water signal
(or the 3 ppm Cr signal) in the pre-frequency-corrected subspectra and
the nominal water frequency at 4.68 ppm (or the nominal 3 ppm Cr signal
if HERMES or GSH editing)
SpecReg
Structure containing output from spectral
registration
reject
Cell array of binary integers indicating whether an
individual transient should be rejected during signal averaging
signal_averaging
Structure containing a cell array of the weighting
factors applied if weighted signal averaging is used
vox1 (or whatever was set in
MRS_struct.p.vox in
GannetPreInitialise.m)
This structure contains the output from the signal
modeling, quality analysis, and quantification of all the signals of
interest
QA
Structure containing metrics calculated to quantify the
performance of the tissue segmentation
MRS_struct.mask.(vox1)
Field
Description
outfile
Cell array of the output filenames of the voxel
masks
img
Cell array containing three-dimensional arrays
representing the three orthogonal slices of the
T1-weighted structural images that are displayed in
the figure outputs
T1image
Cell array of the input T1-weighted
structural image filenames
img_montage
Cell array containing three-dimensional arrays
representing a montage of axial slices of the
T1-weighted structural images overlaid by the
tissue-segmented voxel masks that are displayed in the
GannetQuantify.m figure output
