Christopher G. Thomas

Optimizing Preprocessing and Analysis Pipelines for Single-Subject FMRI. I. Standard Temporal Motion and Physiological Noise Correction Methods

Subject‐specific artifacts caused by head motion and physiological noise are major confounds in BOLD fMRI analyses. However, there is little consensus on the optimal choice of data preprocessing steps to minimize these effects. To evaluate the effects of various preprocessing strategies, we present a framework which comprises a combination of (1) nonparametric testing including reproducibility and prediction metrics of the data‐driven NPAIRS framework (Strother et al. [2002]: NeuroImage 15:747–771), and (2) intersubject comparison of SPM effects, using DISTATIS (a three‐way version of metric multidimensional scaling (Abdi et al. [2009]: NeuroImage 45:89–95). It is shown that the quality of brain activation maps may be significantly limited by sub‐optimal choices of data preprocessing steps (or “pipeline”) in a clinical task‐design, an fMRI adaptation of the widely used Trail‐Making Test. The relative importance of motion correction, physiological noise correction, motion parameter regression, and temporal detrending were examined for fMRI data acquired in young, healthy adults. Analysis performance and the quality of activation maps were evaluated based on Penalized Discriminant Analysis (PDA). The relative importance of different preprocessing steps was assessed by (1) a nonparametric Friedman rank test for fixed sets of preprocessing steps, applied to all subjects; and (2) evaluating pipelines chosen specifically for each subject. Results demonstrate that preprocessing choices have significant, but subject‐dependant effects, and that individually‐optimized pipelines may significantly improve the reproducibility of fMRI results over fixed pipelines. This was demonstrated by the detection of a significant interaction with motion parameter regression and physiological noise correction, even though the range of subject head motion was small across the group (≪ 1 voxel). Optimizing pipelines on an individual‐subject basis also revealed brain activation patterns either weak or absent under fixed pipelines, which has implications for the overall interpretation of fMRI data, and the relative importance of preprocessing methods. Hum Brain Mapp, 2012.

HybridArc: A novel radiation therapy technique combining optimized dynamic arcs and intensity modulation

This investigation focuses on possible dosimetric and efficiency advantages of HybridArc-a novel treatment planning approach combining optimized dynamic arcs with intensity-modulated radiation therapy (IMRT) beams. Application of this technique to two disparate sites, complex cranial tumors, and prostate was examined. HybridArc plans were compared with either dynamic conformal arc (DCA) or IMRT plans to determine whether HybridArc offers a synergy through combination of these 2 techniques. Plans were compared with regard to target volume dose conformity, target volume dose homogeneity, sparing of proximal organs at risk, normal tissue sparing, and monitor unit (MU) efficiency. For cranial cases, HybridArc produced significantly improved dose conformity compared with both DCA and IMRT but did not improve sparing of the brainstem or optic chiasm. For prostate cases, conformity was improved compared with DCA but not IMRT. Compared with IMRT, the dose homogeneity in the planning target volume was improved, and the maximum doses received by the bladder and rectum were reduced. Both arc-based techniques distribute peripheral dose over larger volumes of normal tissue compared with IMRT, whereas HybridArc involved slightly greater volumes of normal tissues compared with DCA. Compared with IMRT, cranial cases required 38% more MUs, whereas for prostate cases, MUs were reduced by 7%. For cranial cases, HybridArc improves dose conformity to the target. For prostate cases, dose conformity and homogeneity are improved compared with DCA and IMRT, respectively. Compared with IMRT, whether required MUs increase or decrease with HybridArc was site-dependent.

Intra-arc binary collimation algorithm for the optimization of stereotactic radiotherapy treatment of multiple metastases with multiple prescriptions

PURPOSE To design and implement a novel treatment planning algorithm based on a modification of dynamic conformal arc (DCA) therapy for the treatment of multiple cranial metastases with variable prescription doses. METHODS A workflow was developed in which separate dose matrices were calculated for each target at each control point (i.e., the multileaf collimator (MLC) was fit conformally to that single target). A cost function was used to quantify the relative contributions of each dose matrix in the plan to the overall plan objectives. Simulated annealing was used to allow for the inclusion or exclusion of individual dose matrices at each control point. The exclusion of individual targets at a given control point is termed intra-arc binary collimation (iABC) in this work and is accomplished by closing the MLCs over the target for a duration specified by simulated annealing optimization. Dynamic collimator motions were employed to minimize the variation between the idealized dose matrices (i.e., perfectly collimated targets) and actual dose matrices (i.e., MLC apertures that include quantities of nontarget tissue due to the relative orientations of targets in the field). An additional simulated annealing optimization was performed to weight the relative contributions of dose at each control point [referred to as the monitor unit distribution (MUD)] to improve compliance with plan objectives. The algorithm was tested on seven previously treated multiple metastases patients and plans were compared to the clinically treated VMAT plans. RESULTS Treatment plans generated with iABC used an average of 2716 (34%) fewer MU in the total plan than VMAT (P = 0.01). All normal tissue metrics for all plans and all patients were clinically acceptable. There were no statistically significant differences in any normal tissue dose metrics. Normalized prescription target coverage accuracy for all targets was 3% better on average for VMAT plans when compared to iABC (P = 0.07), and 14% better on average for iABC when compared to optimized DCA (P = 0.03). CONCLUSION A novel method of aperture and dose distribution design has been developed to significantly increase the MU efficiency of single isocenter treatment of multiple metastases with variable prescription doses when compared to VMAT, and which improves target coverage accuracy significantly when compared to optimized DCA. By applying a DCA approach to subsets of targets across control points, a hybrid method of treatment delivery has been developed that combines the efficiency of dynamic conformal treatments and the dosimetric flexibility of VMAT.

Overlap‐guided fixed‐patient support positioning optimization for cranial SRT

Purpose: To investigate potential dosimetric improvements through the optimization of fixed‐couch rotational position in cranial cancer stereotactic treatments. Methods: Using previously delivered cranial stereotactic radiotherapy plans treated at the Nova Scotia Health Authority (NSHA), we have redesigned the treatment arrangement to find the optimal couch rotation positions based on the reduction of overlap between organs‐at‐risk of exposure (OARs) and target volume (PTV). Maintaining the gantry arrangements from the delivered treatment, the couch positions were determined based on a cost function analysis of accumulation of overlap score from an equation developed by Yang et al.1 and refined by MacDonald et al.2 The algorithm incorporates factors for radiation dose sensitivities of each OAR, depth of both OARs and target (PTV) volumes, and orthogonality of the 3D vector between OAR and PTV in the case of proximal OAR position. Results: The plan evaluation was conducted on 16 acoustic neuroma patients treated with stereotactic radiotherapy plans at the NSHA. Maximum and mean doses to the OARs were reduced by approximately 14.30% ± 2.86% and 19.25% ± 2.10%, respectively, with application of this optimization technique as compared to the delivered treatment plans. In addition, PTV conformity and homogeneity were improved with application of this optimization technique. Conclusion: This variation of the existing delivery techniques with guidance from a PTV‐OAR overlap cost function analysis technique can yield significant dosimetric improvements with no increase to delivery or planning time.