| rt.indices.from.roi {espadon} | R Documentation |
The rt.indices.from.roi function calculates, from a "volume"
class object of modality "rtdose", standard indicators of radiotherapy
in relation to the target and healthy RoI, as long as their options are transmitted.
rt.indices.from.roi(
vol,
struct = NULL,
T.MAT = NULL,
target.roi.name = NULL,
target.roi.sname = NULL,
target.roi.idx = NULL,
healthy.roi.name = NULL,
healthy.roi.sname = NULL,
healthy.roi.idx = NULL,
presc.dose = NA,
healthy.tol.dose = NA,
healthy.weight = 1,
dosimetry = c("D.min", "D.max", "D.mean", "STD"),
volume.indices = c("V.tot", "area", "V.prescdose"),
conformity.indices = c("PITV", "PDS", "CI.lomax2003", "CN", "NCI", "DSC",
"CI.distance", "CI.abs_distance", "CDI", "CS3", "ULF", "OHTF", "gCI", "COIN",
"G_COSI", "COSI"),
homogeneity.indices = c("HI.RTOG.max_ref", "HI.RTOG.5_95", "HI.ICRU.max_min",
"HI.ICRU.2.98_ref", "HI.ICRU.2.98_50", "HI.ICRU.5.95_ref", "HI.mayo2010",
"HI.heufelder"),
gradient.indices = c("GI.ratio.50", "mGI"),
D.xpc = NULL,
D.xcc = NULL,
V.xpc = NULL,
V.xGy = NULL,
verbose = TRUE
)
vol |
"volume" class object, of "rtdose" modality. |
struct |
"struct" class object. |
T.MAT |
"t.mat" class object, created by load.patient.from.Rdcm
or load.T.MAT. If |
target.roi.name |
Exact name of target RoI in |
target.roi.sname |
Name or part of name of target RoI in |
target.roi.idx |
Value of the index of target RoI that belong to the
|
healthy.roi.name |
Exact name of healthy RoI in |
healthy.roi.sname |
Name or part of name of healthy RoI in |
healthy.roi.idx |
Value of the index of healthy RoI that belong to the
|
presc.dose |
Vector of prescription doses that serve as reference doses for the target RoI. |
healthy.tol.dose |
Vector of tolerance doses of each healthy RoI. |
healthy.weight |
Vector of weights, indicating the importance of the healthy RoI. |
dosimetry |
Vector indicating the requested dose indicators from among
'D.min', 'D.max', 'D.mean' and 'STD.' If |
volume.indices |
Vector indicating the requested volume indices from among
'V.tot', 'V.prescdose' (i.e. volume over |
conformity.indices |
Vector. Requested conformity indices from among 'PITV', 'PDS', 'CI.lomax2003', 'CN', 'NCI', 'DSC', 'CI.distance', 'CI.abs_distance', 'CDI', 'CS3', 'ULF', 'OHTF', 'gCI', 'COIN', 'COSI' and 'G_COSI'. |
homogeneity.indices |
Vector. Requested homogeneity indices from among 'HI.RTOG.max_ref', 'HI.RTOG.5_95', 'HI.ICRU.max_min', 'HI.ICRU.2.98_ref', 'HI.ICRU.2.98_50', 'HI.ICRU.5.95_ref', 'HI.mayo2010' and 'HI.heufelder.' |
gradient.indices |
Vector. Requested gradient indices from among 'GI.ratio.50', 'mGI'. |
D.xpc |
Vector of the percentage of the volume, for which the dose coverage is requested. |
D.xcc |
Vector of the volume in \(cm^3\), for which the dose coverage is requested. |
V.xpc |
Vector of the percentage of the reference dose, received by the volume to be calculated. |
V.xGy |
Vector of the minimum dose in Gy, received by the volume to be calculated. |
verbose |
Boolean. if |
If target.roi.name, target.roi.sname, and
target.roi.idx are all set to NULL, all RoI containing 'ptv'
(if they exist) are selected.
If target.roi.name, target.roi.sname, and target.roi.idx
are all set to NULL,no target RoI are selected.
If healthy.roi.name, healthy.roi.sname, and
healthy.roi.idx are all set to NULL, no healthy RoI are selected.
Return a list containing (if requested)
\(-~dosimetry\) : dataframe containing, for all target and healthy structures:
the requested dosimetry : D.min (Gy), D.max (Gy),
D.mean (Gy) and STD (Gy), respectively the minimum, maximum,
mean and standard deviation of the dose in the regions of interest.
the requested $D.x% : (Gy) Dose covering x percent of structure volume.
the requested $D.xcc : (Gy) Dose covering x (\(cm^3\))
of structure volume.
\(-~volume\) : dataframe containing, for all target and healthy structures, and isodoses:
the requested volume.indices : V_tot (\(cm^3\))
(except for isodose) the total volume of the regions of interest, area
(\(cm^2\)) (except for isodose) their surface areas,
V.prescdose (\(cm^3\)) the volumes receiving at least
presc.dose Gy,
the requested V.xGy (\(cm^3\)):
volumes receiving at least x Gy.
the requested V.xpc (\(cm^3\))
Volume receiving at least x% of the reference dose.
\(-~conformity\) : dataframe containing, if requested,
PITV : (1) Prescription Isodose Target Volume, or conformity index
defined by E.Shaw [1]
\[PITV = \frac{V_{presc.dose}}{V_{target}}\]
PDS : (1) Prescription Dose Spillage
defined by SABR UK Consortium 2019 [2]
\[PDS = \frac{V_{presc.dose}}{V_{target ~\ge~ presc.dose}} =
\frac{V_{presc.dose}}{V_{target} ~\cap~ V_{presc.dose}}\]
CI.lomax2003 : (1) Conformity Index defined by Lomax and al
[3]
\[CI_{lomax2003} = \frac{V_{target ~\ge~ presc.dose}}{V_{presc.dose}} =
\frac{V_{target} ~\cap~ V_{presc.dose}}{V_{presc.dose}}\]
CN : (1) Conformation Number defined by Van't Riet and al
[4]. It corresponds to conformity index defined by Paddick
[5]
\[CN = CI_{paddick2000} =\frac{V_{target ~\ge~ presc.dose}^2}{V_{target}~\cdot~V_{presc.dose}} =
\frac{(V_{target} ~\cap~ V_{presc.dose})^2}{V_{target}~\cdot~V_{presc.dose}}\]
NCI : (1) New conformity index, inverse of CN, defined by
Nakamura and al [6]
\[NCI =\frac{1}{CN}\]
DSC : (1) Dice Similarity Coefficient [7]
\[DSC = 2 ~\cdot~\frac{V_{target ~\ge~ presc.dose}}{V_{target} + V_{presc.dose}} =
2 ~\cdot~\frac{V_{target} ~\cap~ V_{presc.dose}}{V_{target} + V_{presc.dose}}\]
CI.distance : (1) Conformity Index based on distance defined by
Park and al [8]
\[CI.distance = \frac{100}{N} \sum^N \frac{dist_{S_{presc.dose}~\to~G_{target}} -
dist_{S_{target}~\to~G_{target}}}{dist_{S_{target}~\to~G_{target}}}\]
where \(dist_{S_{presc.dose}~\to~G_{target}}\) is the distance between
the surface of the prescription dose volume and the centroid of the target,
and \(dist_{S_{target}~\to~G_{target}}\) the surface of the target
volume and the centroid of the target.
\(N\) is the number of directions where the distances are calculated.
These directions are computed every 1°. If the centroid is not within the target
volume, then CI.distance = NA.
CI.abs_distance : (1) Conformity Index based on distance defined
by Park and al [8]
\[CI.abs_distance = \frac{100}{N} \sum^N \frac{|dist_{S_{presc.dose}~\to~G_{target}} -
dist_{S_{target}~\to~G_{target}}|}{dist_{S_{target}~\to~G_{target}}}\]
CDI : (1) Conformity Distance Index defined by Wu and al
[9]
\[CDI = 2 \frac{V_{presc.dose} + V_{target} - 2~V_{target ~\ge~ presc.dose}}
{S_{target} + S_{presc.dose}} = \frac{V_{presc.dose} + V_{target} - 2~\cdot~V_{target} ~\cap~ V_{presc.dose}}
{S_{target} + S_{presc.dose}}\]
where \(S_{target}\) is the surface of the target volume and
\(S_{presc.dose}\) is the surface of the prescription dose volume.
CS3 : (1) Triple Point Conformity Scale defined by Ansari
and al [10]
\[CS3 = \frac{V_{0.95~\cdot~presc.dose} + V_{presc.dose} +
V_{1.05~\cdot~presc.dose}}{3~\cdot~V_{target}}\]
ULF : (1) Underdosed lesion factor defined by Lefkopoulos
and al [11]
\[ULF = \frac{V_{target ~<~ presc.dose}}{V_{target}}=
\frac{V_{target} ~\cap~ \overline{V_{presc.dose}}}{V_{target}}\]
OHTF :(1) Overdosed healthy tissues factor defined by Lefkopoulos
and al [11]
\[OHTF = \frac{\sum V_{healthy ~\ge~ presc.dose}}{V_{target}} =
\frac{\sum V_{healthy} ~\cap~ V_{presc.dose}}{V_{target}} \]
gCI : (1) Geometric Conformity Index defined by
Lefkopoulos and al [11]
\[gCI = ULF + OHTF\]
COIN : Conformity Index defined by Baltas and al [12]
\[COIN =\frac{V_{target ~\ge~ presc.dose}^2}{V_{target}~\cdot~V_{presc.dose}}~\cdot~
\prod^{N_{healthy}} \left( 1 -\frac{V_{healthy ~\ge~ presc.dose}}{V_{healthy}}\right)\]
gCOSI : generalized COSI, defined by Menhel and al [13].
\[gCOSI = 1- \sum^{N_{healthy}} healthy.weight~\cdot~
\frac{\frac{V_{healthy ~\ge~ healthy.tol.dose}}{V_{healthy}}}{\frac{V_{target ~\ge~ presc.dose}}{V_{target}}}\]
\(-~COSI\) : if "COSI" is requested in conformity.indices,
it returns a dataframe of Critical Organ Scoring Index for each healthy organ,
at each presc.dose, and for each target. COSI is defined by
Menhel and al [13]
\[COSI = 1-
\frac{\frac{V_{healthy ~\ge~ healthy.tol.dose}}{V_{healthy}}}{\frac{V_{target ~\ge~ presc.dose}}{V_{target}}}\]
\(-~homogeneity\) : dataframe containing
HI.RTOG.max_ref : (1) Homogeneity Index from RTOG defined by
E.Shaw [1]
\[HI.RTOG.max_-ref = \frac{D_{~max}}{presc.dose}\]
where \(D_{max}\) is the maximum dose in the target volume.
HI.RTOG.5_95 : (1) Homogeneity Index from RTOG [1]
\[HI.RTOG.5_-95 = \frac{D.5pc}{D.95pc}\]
where \(D.5pc\) and \(D.95pc\) are respectively the doses
at 5% and 95% of the target volume in cumulative dose-volume histogram.
HI.ICRU.max_min : (1) Homogeneity Index from ICRU report 62
[14]
\[HI.ICRU.max_-min = \frac{D_{~max}}{D_{~min}}\]
where \(D_{max}\) and \(D_{min}\) are respectively the
maximum and the minimum dose in the target volume.
HI.ICRU.2.98_ref : (1) Homogeneity Index from ICRU report 83
[15]
\[HI.ICRU.2.98_-ref = 100 \frac{D.2pc - D.98pc}{presc.dose}\]
where \(D.2pc\) and \(D.98pc\) are respectively the doses
at 2% and 98% of the target volume in cumulative dose-volume histogram.
HI.ICRU.2.98_50 : (1) Homogeneity Index from ICRU report 83
[15]
\[HI.ICRU.2.98_-50 = 100 \frac{D.2pc - D.98pc}{D.50pc}\]
where \(D.2pc\), \(D.98pc\) and \(D.50pc\) are
respectively the doses
at 2%, 98% and 50% of the target volume in cumulative dose-volume histogram.
HI.ICRU.5.95_ref : (1) Homogeneity Index from ICRU report 83
[15]
\[HI.ICRU.5.95_-ref = 100 \frac{D.5pc - D.95pc}{presc.dose}\]
where \(D.5pc\) and \(D.95pc\) are respectively the doses
at 5% and 95% of the target volume in cumulative dose-volume histogram.
HI.mayo2010 : (1) Homogeneity Index defined by Mayo and al
[16]
\[HI.mayo2010 =\sqrt{\frac{D_{~max}}{presc.dose}~\cdot~(1 +
\frac{\sigma_D}{presc.dose})}\]
where \(D_{max}\) is the maximum dose in the target volume, and
\(\sigma_D\) the standard deviation of the dose in the target volume.
HI.heufelder : (1) Homogeneity Index defined by Heufelder and al
[17]
\[HI.heufelder = e^{-0.01~\cdot~ (1-\frac{\mu_D}{presc.dose})^2}~\cdot~
e^{-0.01~\cdot~ (\frac{\sigma_D}{presc.dose})^2}\]
where \(\mu_D\) and \(\sigma_D\) are
respectively the mean and the standard deviation of the dose in the target volume.
\(-~gradient\) : dataframe containing
GI.ratio.50: Gradient Index based on volumes ratio defined by
Paddick and Lippitz [18]
\[GI.ratio.50 = \frac {V_{0.5~\cdot~presc.dose}}{V_{presc.dose}}\]
mGI: Modified Gradient Index defined by SABR UK Consortium 2019
[2]
\[mGI = \frac{V_{0.5~\cdot~presc.dose}}{V_{target ~\ge~ presc.dose}} =
\frac{V_{0.5~\cdot~presc.dose}}{V_{target} ~\cap~ V_{presc.dose}}\]
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# loading of toy-patient objects (decrease dxyz and increase beam.nb
# for better result)
step <- 5
patient <- toy.load.patient (modality = c("rtdose", "rtstruct"), roi.name = "eye",
dxyz = rep (step, 3), beam.nb = 3)
indices <- rt.indices.from.roi (patient$rtdose[[1]], patient$rtstruct[[1]],
target.roi.sname = "ptv",
healthy.roi.sname = "eye", presc.dose = 50,
conformity.indices = c("PITV", "PDS", "CI.lomax2003",
"CN", "NCI", "DSC","COIN"),
verbose = FALSE)
indices