10 research outputs found
Can parametric statistical methods be trusted for fMRI based group studies?
The most widely used task fMRI analyses use parametric methods that depend on
a variety of assumptions. While individual aspects of these fMRI models have
been evaluated, they have not been evaluated in a comprehensive manner with
empirical data. In this work, a total of 2 million random task fMRI group
analyses have been performed using resting state fMRI data, to compute
empirical familywise error rates for the software packages SPM, FSL and AFNI,
as well as a standard non-parametric permutation method. While there is some
variation, for a nominal familywise error rate of 5% the parametric statistical
methods are shown to be conservative for voxel-wise inference and invalid for
cluster-wise inference; in particular, cluster size inference with a cluster
defining threshold of p = 0.01 generates familywise error rates up to 60%. We
conduct a number of follow up analyses and investigations that suggest the
cause of the invalid cluster inferences is spatial auto correlation functions
that do not follow the assumed Gaussian shape. By comparison, the
non-parametric permutation test, which is based on a small number of
assumptions, is found to produce valid results for voxel as well as cluster
wise inference. Using real task data, we compare the results between one
parametric method and the permutation test, and find stark differences in the
conclusions drawn between the two using cluster inference. These findings speak
to the need of validating the statistical methods being used in the
neuroimaging field
Accelerating Permutation Testing in Voxel-wise Analysis through Subspace Tracking: A new plugin for SnPM
Permutation testing is a non-parametric method for obtaining the max null
distribution used to compute corrected -values that provide strong control
of false positives. In neuroimaging, however, the computational burden of
running such an algorithm can be significant. We find that by viewing the
permutation testing procedure as the construction of a very large permutation
testing matrix, , one can exploit structural properties derived from the
data and the test statistics to reduce the runtime under certain conditions. In
particular, we see that is low-rank plus a low-variance residual. This
makes a good candidate for low-rank matrix completion, where only a very
small number of entries of ( of all entries in our experiments)
have to be computed to obtain a good estimate. Based on this observation, we
present RapidPT, an algorithm that efficiently recovers the max null
distribution commonly obtained through regular permutation testing in
voxel-wise analysis. We present an extensive validation on a synthetic dataset
and four varying sized datasets against two baselines: Statistical
NonParametric Mapping (SnPM13) and a standard permutation testing
implementation (referred as NaivePT). We find that RapidPT achieves its best
runtime performance on medium sized datasets (), with
speedups of 1.5x - 38x (vs. SnPM13) and 20x-1000x (vs. NaivePT). For larger
datasets () RapidPT outperforms NaivePT (6x - 200x) on all
datasets, and provides large speedups over SnPM13 when more than 10000
permutations (2x - 15x) are needed. The implementation is a standalone toolbox
and also integrated within SnPM13, able to leverage multi-core architectures
when available.Comment: 36 pages, 16 figure
True 4D Image Denoising on the GPU
The use of image denoising techniques is an important part of many medical imaging applications. One common application is to improve the image quality of low-dose (noisy) computed tomography (CT) data. While 3D image denoising previously has been applied to several volumes independently, there has not been much work done on true 4D image denoising, where the algorithm considers several volumes at the same time. The problem with 4D image denoising, compared to 2D and 3D denoising, is that the computational complexity increases exponentially. In this paper we describe a novel algorithm for true 4D image denoising, based on local adaptive filtering, and how to implement it on the graphics processing unit (GPU). The algorithm was applied to a 4D CT heart dataset of the resolution 512 × 512 × 445 × 20. The result is that the GPU can complete the denoising in about 25 minutes if spatial filtering is used and in about 8 minutes if FFT-based filtering is used. The CPU implementation requires several days of processing time for spatial filtering and about 50 minutes for FFT-based filtering. The short processing time increases the clinical value of true 4D image denoising significantly
Fast Random Permutation Tests Enable Objective Evaluation of Methods for Single Subject fMRI Analysis
Parametric statistical methods, such as Z-, t-, and F-values are traditionally employed in functional magnetic resonance imaging (fMRI) for identifying areas in the brain that are active with a certain degree of statistical significance. These parametric methods, however, have two major drawbacks. First, it is assumed that the observed data are Gaussian distributed and independent; assumptions that generally are not valid for fMRI data. Second, the statistical test distribution can be derived theoretically only for very simple linear detection statistics. With non-parametric statistical methods, the two limitations described above can be overcome. The major drawback of non-parametric methods is the computational burden with processing times ranging from hours to days, which so far have made them impractical for routine use in single subject fMRI analysis. In this work, it is shown how the computational power of cost-efficient Graphics Processing Units (GPUs) can be used to speed up random permutation tests. A test with 10 000 permutations takes less than a minute, making statistical analysis of advanced detection methods in fMRI practically feasible. To exemplify the permutation based approach, brain activity maps generated by the General Linear Model (GLM) and Canonical Correlation Analysis (CCA) are compared at the same significance level. During the development of the routines and writing of the paper, 3-4 years of processing time has been saved by using the GPU
Permutation Inference for Canonical Correlation Analysis
Canonical correlation analysis (CCA) has become a key tool for population
neuroimaging, allowing investigation of associations between many imaging and
non-imaging measurements. As other variables are often a source of variability
not of direct interest, previous work has used CCA on residuals from a model
that removes these effects, then proceeded directly to permutation inference.
We show that such a simple permutation test leads to inflated error rates. The
reason is that residualisation introduces dependencies among the observations
that violate the exchangeability assumption. Even in the absence of nuisance
variables, however, a simple permutation test for CCA also leads to excess
error rates for all canonical correlations other than the first. The reason is
that a simple permutation scheme does not ignore the variability already
explained by previous canonical variables. Here we propose solutions for both
problems: in the case of nuisance variables, we show that transforming the
residuals to a lower dimensional basis where exchangeability holds results in a
valid permutation test; for more general cases, with or without nuisance
variables, we propose estimating the canonical correlations in a stepwise
manner, removing at each iteration the variance already explained, while
dealing with different number of variables in both sides. We also discuss how
to address the multiplicity of tests, proposing an admissible test that is not
conservative, and provide a complete algorithm for permutation inference for
CCA.Comment: 49 pages, 2 figures, 10 tables, 3 algorithms, 119 reference
Generation of a whole-brain hemodynamic response function and sex-specific differences in cerebral processing of mechano-sensation in mice detected by BOLD fMRI
BOLD fMRI has become a prevalent method to study cerebral sensory processing in rodent disease models, including pain and mechanical hypersensitivity. fMRI data analysis is frequently combined with a general-linear-model (GLM) -based analysis, which uses the convolution of a hemodynamic response function (HRF) with the stimulus paradigm. However, several studies indicated that the HRF differs across species, sexes, brain structures, and experimental factors, including stimulation modalities or anesthesia, and hence might strongly affect the outcome of BOLD analyzes. While considerable work has been done in humans and rats to understand the HRF, much less is known in mice. As a prerequisite to investigate mechano-sensory processing and BOLD fMRI data in male and female mice, we (1) designed a rotating stimulator that allows application of two different mechanical modalities, including innocuous von Frey and noxious pinprick stimuli and (2) determined and statistically compared HRFs across 30 brain structures and experimental conditions, including sex and, stimulus modalities. We found that mechanical stimulation lead to brain-wide BOLD signal changes thereby allowing extraction of HRFs from multiple brain structures. However, we did not find differences in HRFs across all brain structures and experimental conditions. Hence, we computed a whole-brain mouse HRF, which is based on 88 functional scans from 30 mice. A comparison of this mouse-specific HRF with our previously reported rat-derived HRF showed significantly slower kinetics in mice. Finally, we detected pronounced differences in cerebral BOLD activation between male and female mice with mechanical stimulation, thereby exposing divergent processing of noxious and innocuous stimuli in both sexes
The speed of visual processing of complex objects in the human brain. Sensitivity to image properties, the influence of aging, optical factors and individual differences.
Visual processing of complex objects is a feat that the brain accomplishes with remarkable speed – generally in the order of a few hundred milliseconds. Our knowledge with regards to what visual information the brain uses to categorise objects, and how early the first object-sensitive responses occur in the brain, remains fragmented. It seems that neuronal processing speed slows down with age due to a variety of physiological changes occurring in the aging brain, including myelin degeneration, a decrease in the selectivity of neuronal responses and a reduced efficiency of cortical networks. There are also considerable individual differences in age-related alterations of processing speed, the origins of which remain unclear. Neural processing speed in humans can be studied using electroencephalogram (EEG), which records the activity of neurons contained in Event-Related-Potentials (ERPs) with millisecond precision. Research presented in this thesis had several goals. First, it aimed to measure the sensitivity of object-related ERPs to visual information contained in the Fourier phase and amplitude spectra of images. The second goal was to measure age-related changes in ERP visual processing speed and to find out if their individual variability is due to individual differences in optical factors, such as senile miosis (reduction in pupil size with age), which affects retinal illuminance. The final aim was to quantify the onsets of ERP sensitivity to objects (in particular faces) in the human brain. To answer these questions, parametric experimental designs, novel approaches to EEG data pre-processing and analyses on a single-subject and group basis, robust statistics and large samples of subjects were employed. The results show that object-related ERPs are highly sensitive to phase spectrum and minimally to amplitude spectrum. Furthermore, when age-related changes in the whole shape of ERP waveform between 0-500 ms were considered, a 1 ms/year delay in visual processing speed has been revealed. This delay could not be explained by individual variability in pupil size or retinal illuminance. In addition, a new benchmark for the onset of ERP sensitivity to faces has been found at ~90 ms post-stimulus in a sample of 120 subjects age 18-81. The onsets did not change with age and aging started to affect object-related ERP activity ~125-130 ms after stimulus presentation. Taken together, this thesis presents novel findings with regards to the speed of visual processing in the human brain and outlines a range of robust methods for application in ERP vision research