R: Dosimetry, volume, conformity, homogeneity indices from RoI

rt.indices.from.roi {espadon}

R Documentation

Dosimetry, volume, conformity, homogeneity indices from RoI

Description

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.

Usage

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
)

Arguments

`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 `T.MAT = NULL`, `struct$ref.pseudo` must be equal to `vol$ref.pseudo`.
`target.roi.name`	Exact name of target RoI in `struct` object. By default `target.roi.name = NULL`. See Details.
`target.roi.sname`	Name or part of name of target RoI in `struct` object. By default `target.roi.sname = NULL`. See Details.
`target.roi.idx`	Value of the index of target RoI that belong to the `struct` object. By default `target.roi.idx = NULL`. See Details.
`healthy.roi.name`	Exact name of healthy RoI in `struct` object. By default `healthy.roi.name = NULL`.
`healthy.roi.sname`	Name or part of name of healthy RoI in `struct` object. By default `healthy.roi.sname = NULL`.
`healthy.roi.idx`	Value of the index of healthy RoI that belong to the `struct` object. By default `healthy.roi.idx = NULL`.
`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 `D.xpc` is different from `NULL`, it will be added.
`volume.indices`	Vector indicating the requested volume indices from among 'V.tot', 'V.prescdose' (i.e. volume over `presc.dose`) and 'area'. If `V.xGy` is different from `NULL`, it will be added.
`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 `TRUE` (default) a progress bar is displayed.

Details

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.

Value

Returns 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] \[mGI = \frac{V_{0.5~\cdot~presc.dose}}{V_{target ~\ge~ presc.dose}} = \frac{V_{0.5~\cdot~presc.dose}}{V_{target} ~\cap~ V_{presc.dose}}\]

References

[1] Shaw E, Kline R, Gillin M, Souhami L, Hirschfeld A, Dinapoli R, Martin L (1993). “Radiation therapy oncology group: Radiosurgery quality assurance guidelines.” International journal of radiation oncology, biology, physics, 27(5), 1231-1239. ISSN 0360-3016, doi:10.1016/0360-3016(93)90548-A.

[2] UK SABR Consortium (Online; accessed 2022-04-01). “Stereotactic Ablative Radiation Therapy (SABR): a resource. v6.1, January 2019.” https://www.sabr.org.uk/wp-content/uploads/2019/04/SABRconsortium-guidelines-2019-v6.1.0.pdf.

[3] Lomax NJ, Scheib SG (2003). “Quantifying the degree of conformity in radiosurgery treatment planning.” International journal of radiation oncology, biology, physics, 55(5), 1409-1419. ISSN 0360-3016, doi:10.1016/S0360-3016(02)04599-6.

[4] Riet AV, Mak AC, Moerland MA, Elders LH, Van der Zee W (1997). “A conformation number to quantify the degree of conformality in brachytherapy and external beam irradiation: Application to the prostate.” International journal of radiation oncology, biology, physics, 37(3), 731-736. ISSN 0360-3016, doi:10.1016/S0360-3016(96)00601-3.

[5] Paddick I (2000). “A simple scoring ratio to index the conformity of radiosurgical treatment plans. Technical note.” Journal of neurosurgery, 93 Suppl 3, 219-222.

[6] Nakamura J, Verhey L, Smith V, Petti P, Lamborn K, Larson D, Wara W, Mcdermott M, Sneed P (2002). “Dose conformity of Gamma Knife radiosurgery and risk factors for complications.” International journal of radiation oncology, biology, physics, 51, 1313-9. doi:10.1016/S0360-3016(01)01757-6.

[7] Dice LR (1945). “Measures of the Amount of Ecologic Association Between Species.” Ecology, 26(3), 297–302. ISSN 00129658, 19399170.

[8] Park JM, Park S, Ye S, Kim J, Carlson J, Wu H (2014). “New conformity indices based on the calculation of distances between the target volume and the volume of reference isodose.” The British journal of radiology, 87, 20140342. doi:10.1259/bjr.20140342.

[9] Wu Q, Wessels BW, Einstein DB, Maciunas RJ, Kim EY, Kinsella TJ (2003). “Quality of coverage: Conformity measures for stereotactic radiosurgery.” Journal of Applied Clinical Medical Physics, 4, 374-381.

[10] Ansari S, Satpathy S, Singh P, Lad S, Thappa N, Singh B (2018). “A new index: Triple Point Conformity Scale (CS3) and its implication in qualitative evaluation of radiotherapy plan.” Journal of Radiotherapy in Practice, 17, 1-4. doi:10.1017/S1460396917000772.

[11] Lefkopoulos D, Dejean C, balaa ZE, Platoni K, Grandjean P, Foulquier J, Schlienger M (2000). “Determination of dose-volumes parameters to characterise the conformity of stereotactic treatment plans.” In chapter XIII, 356-358. Springer Berlin Heidelberg. ISBN 978-3-540-67176-3, doi:10.1007/978-3-642-59758-9_135.

[12] Baltas D, Kolotas C, Geramani KN, Mould RF, Ioannidis G, Kekchidi M, Zamboglou N (1998). “A conformal index (COIN) to evaluate implant quality and dose specification in brachytherapy.” International journal of radiation oncology, biology, physics, 40 2, 515-24. doi:10.1016/s0360-3016(97)00732-3.

[13] Menhel J, Levin D, Alezra D, Symon Z, Pfeffer R (2006). “Assessing the quality of conformal treatment planning: a new tool for quantitative comparison.” Physics in Medicine and Biology, 51(20), 5363–5375.

[14] Landberg T, Chavaudra J, Dobbs J, Gerard J, Hanks G, Horiot J, Johansson K, Möller T, Purdy J, Suntharalingam N, Svensson H (1999). “ICRU Report 62: Prescribing, Recording and Reporting Photon Beam Therapy (Supplement to ICRU Report 50),3. Absorbed Doses.” Reports of the International Commission on Radiation Units and Measurements, os-32(1), 21-25.

[15] ICRU (2010). “Report 83 : Prescribing, Recording, and Reporting Photon-Beam Intensity-Modulated Radiation Therapy (IMRT).” Reports of the International Commission on Radiation Units and Measurements, 10(1), 1-3.

[16] Mayo CS, Ding L, Addesa A, Kadish S, Fitzgerald TJ, Moser R (2010). “Initial Experience With Volumetric IMRT (RapidArc) for Intracranial Stereotactic Radiosurgery.” International Journal of Radiation Oncology*Biology*Physics, 78(5), 1457-1466. ISSN 0360-3016, doi:10.1016/j.ijrobp.2009.10.005.

[17] Heufelder J, Zink K, Scholz M, Kramer K, Welker K (2003). “Eine Methode zur automatisierten Bewertung von CT-basierten Bestrahlungsplanen in der perkutanen Strahlentherapie.” Zeitschrift fur Medizinische Physik, 13(4), 231-239. ISSN 0939-3889, doi:10.1078/0939-3889-00175.

[18] Paddick I, Lippitz BE (2006). “A simple dose gradient measurement tool to complement the conformity index.” Journal of neurosurgery, 105 Suppl, 194-201.

All this references are compiled by

Kaplan LP, Korreman SS (2021). “A systematically compiled set of quantitative metrics to describe spatial characteristics of radiotherapy dose distributions and aid in treatment planning.” Physica Medica, 90, 164-175. ISSN 1120-1797, doi:10.1016/j.ejmp.2021.09.014. and
Patel G, Mandal A, Choudhary S, Mishra R, Shende R (2020). “Plan evaluation indices: A journey of evolution.” Reports of Practical Oncology & Radiotherapy, 25. doi:10.1016/j.rpor.2020.03.002..

Examples

# 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

[Package espadon version 1.6.0 Index]