Mary K. Askren

The contribution of this paper is to describe how we can program neuroimaging workflow using Make, a software development tool designed for describing how to build executables from source files. We show that we can achieve many of the features of more sophisticated neuroimaging pipeline systems, including reproducibility, parallelization, fault tolerance, and quality assurance reports. We suggest that Make represents a large step towards these features with only a modest increase in programming demands over shell scripts. This approach reduces the technical skill and time required to write, debug, and maintain neuroimaging workflows in a dynamic environment, where pipelines are often modified to accommodate new best practices or to study the effect of alternative preprocessing steps, and where the underlying packages change frequently. This paper has a comprehensive accompanying manual with lab practicals and examples (see Supplemental Materials) and all data, scripts and makefiles necessary to run the practicals and examples are available in the “makepipelines” project at NITRC.

Cortical dysfunction in Parkinson's disease (PD) may be caused by disruption to ascending systems or by intrinsic cortical neuropathology. We introduce and conduct a joint analysis of metabolism and atrophy capable of identifying whether metabolic disruption occurs in mild PD without cortical atrophy, to determine the extent and spatial pattern of cortical involvement in mild PD. The design was observational, studying 23 cognitively normal participants with mild PD (mean Hoehn & Yahr stage 2) and 21 healthy controls. Cortical thickness (obtained from analysis of structural magnetic resonance imaging [MRI] with FreeSurfer) and cerebral perfusion measures (obtained from arterial spin labeling [ASL]) analyzed independently and then together in a joint multiple factorial analysis to identify spatial patterns of perfusion and cortical thickness. We identify a pattern of changes in perfusion and cortical thickness characterized by symmetric parietal cortical thinning and reduced precuneus perfusion, with relative preservation of thickness and perfusion in the anterior cingulate cortex (ACC), right prefrontal gyrus, and medial frontal gyrus. The expression of this pattern is correlated with motor system symptoms and speed of processing. A spatial pattern of joint parietal cortical thinning and disproportionate reduction in perfusion occurs in our nondemented PD sample. We found no PD‐related components of reduced perfusion without cortical thinning. This suggests that PD affects the cortex itself, even when symptoms are relatively mild. © 2015 International Parkinson and Movement Disorder Society

The aim of this study is to use functional magnetic resonance imaging (fMRI) to prospectively examine pre-treatment predictors of post-treatment fatigue and cognitive dysfunction in women treated with adjuvant chemotherapy for breast cancer. Fatigue and cognitive dysfunction often co-occur in women treated for breast cancer. We hypothesized that pre-treatment factors, unrelated to chemotherapy per se, might increase vulnerability to post-treatment fatigue and cognitive dysfunction. Patients treated with (n = 28) or without chemotherapy (n = 37) and healthy controls (n = 32) were scanned coincident with pre- and one-month post-chemotherapy during a verbal working memory task (VWMT) and assessed for fatigue, worry, and cognitive dysfunction. fMRI activity measures in the frontoparietal executive network were used in multiple linear regression to predict post-treatment fatigue and cognitive function. The chemotherapy group reported greater pre-treatment fatigue than controls and showed compromised neural response, characterized by higher spatial variance in executive network activity, than the non-chemotherapy group. Also, the chemotherapy group reported greater post-treatment fatigue than the other groups. Linear regression indicated that pre-treatment spatial variance in executive network activation predicted post-treatment fatigue severity and cognitive complaints, while treatment group, age, hemoglobin, worry, and mean executive network activity levels did not predict these outcomes. Pre-treatment neural inefficiency (indexed by high spatial variance) in the executive network, which supports attention and working memory, was a better predictor of post-treatment cognitive and fatigue complaints than exposure to chemotherapy per se. This executive network compromise could be a pre-treatment neuromarker of risk, indicating patients most likely to benefit from early intervention for fatigue and cognitive dysfunction.

We have developed a pen and writing tablet for use by subjects during fMRI scanning. The pen consists of two jacketed, multi-mode optical fibers routed to the tip of a hollowed-out ball-point pen. The pen has been further modified by addition of a plastic plate to maintain a perpendicular pen-tablet orientation. The tablet is simply a non-metallic frame holding a paper print of continuously varying color gradients. The optical fibers are routed out of the MRI bore to a light-tight box in an adjacent control room. Within the box, light from a high intensity LED is coupled into one of the fibers, while the other fiber abuts a color sensor. Light from the LED exits the pen tip, illuminating a small spot on the tablet, and the resulting reflected light is routed to the color sensor. Given a lookup table of position for each color on the tablet, the coordinates of the pen on the tablet may be displayed and digitized in real-time. While simple and inexpensive, the system achieves sufficient resolution to grade writing tasks testing dysgraphic and dyslexic phenomena.