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THE BLENDS METHOD FOR DATA
AUGMENTATION OF 4-DIMENSIONAL
BRAIN IMAGES
Kevin P. Nguyen a
Vyom Raval a, b
Abu Minhajuddin c
Thomas Carmody c, d
Madhukar H. Trivedi d
Richard B. Dewey, Jr. e
Albert A. Montillo a, f, g
a Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas,
Texas, USA
b University of Texas at Dallas, Dallas, Texas, USA
c Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical
Center, Dallas, Texas, USA
d Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
e Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
f Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
f Advanced imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
Address correspondence to:
Albert Montillo, PhD
Director, Deep Learning for Precision Health Laboratory
albert.montillo@utsouthwestern.edu
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ABSTRACT
Purpose: Data augmentation improves the accuracy of deep learning models when training data is
scarce by synthesizing additional samples. This work addresses the lack of validated augmentation
methods specific for synthesizing anatomically realistic 4D (3D+time) images for neuroimaging, such as
fMRI, by proposing a new augmentation method.
Materials and Methods: The proposed method, BLENDS, generates new nonlinear warp fields by
combining intersubject coregistration maps, computed using symmetric normalization, through spatial
blending. These new warp fields can be applied to existing 4D fMRI to create new augmented images.
BLENDS is tested on two neuroimaging problems using de-identified datasets: 1) the prediction of
antidepressant response from task-based fMRI in the EMBARC dataset (n = 163), and 2) the prediction of
Parkinson’s Disease symptom trajectory from baseline resting-state fMRI regional homogeneity in the
PPMI dataset (n = 43).
Results: BLENDS readily generates hundreds of new fMRI from existing images, with unique anatomical
variations from the source images, that significantly improve prediction performance. For
antidepressant response prediction, augmenting each original image once (2x the original training data)
significantly increased prediction from 0.055 to 0.098 (), while at 10x augmentation
increased to 0.103. For the prediction of Parkinson’s Disease trajectory, 10x augmentation increased
from 0.294 to 0.548 ().
Conclusion: Augmentation of fMRI through nonlinear transformations with BLENDS significantly
improves the performance of deep learning models on clinically relevant predictive tasks. This method
will help neuroimaging researchers overcome dataset size limitations and achieve more accurate
predictive models.
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1. INTRODUCTION
Data augmentation is an important tool for improving the performance of machine learning
models, especially when limited data is available for training. Augmentation aims to simulate new data
samples by introducing randomly generated variations to existing samples. Many applications of
machine learning and deep learning to neuroimaging are limited by small dataset sizes, which could be
readily addressed by augmentation. However, there are currently no augmentation methods to
synthesize new, anatomically realistic functional magnetic resonance images (fMRI), complete with four-
dimensional (3D + time) data.
The proposed method, Brain Library Enrichment through Nonlinear Deformation Synthesis
(BLENDS), is the first that be applied to 4D MRI data including fMRI to generate new image timeseries. It
is computationally efficient, requiring only 2 minutes on most hardware to generate each new image. It
is also easily scalable and can generate up to hundreds of augmented images per original image by
introducing brain morphological variations derived from large public repositories of MRI. Minimal user
parameterization is required, making BLENDS straightforward to apply. BLENDS is shown to improve
deep learning predictor accuracy in two use cases: prediction of antidepressant treatment outcome
from task-based fMRI and Parkinson’s Disease total symptom trajectory prediction from resting-state
fMRI. Beyond fMRI, the same method could also be applied to other neuroimaging modalities, including
structural or diffusion MRI. Source code is available on a public repository and is ready for community
use and extension.
Prior work in MRI augmentation has primarily focused on augmentation of T1-weighted
structural MRI. Previously algorithms were developed that used ICA decomposition and random latent
vectors to generate new T1-weighted images and improve a deep learning classifier of schizophrenic vs.
healthy individuals (1, 2). Minimal work exists on methods for other brain MRI contrasts. Zhuang et al.
proposed the synthesis of 3D task fMRI brain activation maps using a generative adversarial network
(GAN) (3). However, we are the first to present a method to generate augmented 4D fMRI timeseries
and demonstrate applications to multiple regression problems. This approach is compared to a
previously reported algorithm in which augmented images by performing coregistrations with other,
randomly selected images (4). A substantial improvement to the prediction of antidepressant outcomes
was shown, however the method was limited by high computational cost and reliance on a two-step T1-
based registration. This registration approach was limited to introducing only anatomical variations
present in the sample at hand. The current algorithm, proposed herein, overcomes these limitations and
demonstrates marked improvement in deep learning performance for two clinical problems while
simultaneously reducing computation time by 15x and also generating out-of-sample augmentations.
2. METHODS
2.1. AUGMENTATION
A given brain’s morphology can be nearly completely characterized by a warp field and a brain
template. The brain template, such as the popular Montreal Neurological Institute 152-brain (MNI152)
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template, serves as an initial condition . A warp field is a three-dimensional vector field which
describes the nonlinear transformation of each point in the brain template to the given brain. For a
specific point in space, the transformation between and is modeled as:
(1)
where are the x, y, and z components of the three-dimensional vector field. This warp field
can be accurately computed at the voxel level through modern nonlinear coregistration tools such as
ANTs and FNIRT (5, 6).
In the proposed method, a set of hundreds of warp fields are produced by coregistering T1-
weighted images to the MNI152 template. ANTs Symmetric Normalization is used to perform an initial
rough affine registration, followed by a multi-scale nonlinear registration (6). The resultant affine matrix
for each image is decomposed into translation, rotation, shearing, and scaling components. The shearing
and anisotropic scaling components are then composed with the nonlinear registration to obtain the
warp field which includes the non-rigid body and nonlinear transformation components. The rigid
body translation and rotation components are excluded as they characterize the head position within
the scanner bore, rather than characteristics of brain morphology. The generated warps are stored in set
containing for generated warps.
2.1.1. BLENDED WARP GENERATION
Previous work showed that warping a given brain to a different, randomly selected brain
through coregistration was effective for augmentation (4). However, this previous method could not
introduce morphological variations beyond what exists in the dataset. Also, performing these
coregistrations on-the-fly required ~30 minutes for every augmentation, which quickly becomes
computationally costly when 100-1000 or more augmented images are desired. BLENDS eliminates this
most costly step by generating new warps directly from the set of precomputed warps. Thus, an
inordinate number of new warps can be rapidly created for the one-time fixed cost of creating the
warpset. In many cases, a neuroimaging researcher may already have such a warp set on hand which
may be repurposed for BLENDS. To generate new warps from the set, fully learning the distribution of
warp fields, particularly at the voxel level, is computationally costly and unnecessary. Instead, a new
warp can be created by spatially blending combinations of existing warps. With the assumption that a
weighted combination of real anatomical warps yields an anatomically realistic warp, this approach
allows the combinatorial generation of far more warps than are present in the set (Figure 1).
For each augmentation operation, real warps, for , are drawn from the set and
blended through a weighted sum. First, isotropic Gaussian point clusters are generated in 3D space
for each warp, with random centroids within the image dimensions and standard deviation . Next,
these discrete point clusters are converted into smooth, continuous 3D matrices through a distance
transform:
(2)
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which computes, for each voxel in , the Euclidean distance to the nearest point in . The
sagittal dimension is omitted from the calculation to ensure left-right symmetry in the blended warp.
Finally, the new, blended warp is computed as the sum of the real warps weighted by the blending
matrices:
(3)
In the following applications, BLENDS was performed with the number of sampled real warps
and Gaussian point cluster (unitless). Point cluster coordinates were then min-max scaled
to span the image dimensions (i.e. such that the range of coordinate values was
for each dimension).
2.1.2. IMAGE PREPARATION
The image to be augmented is the source image. In order to apply the newly generated warp
to the source image, the image must first be spatially normalized to the brain template, i.e. the
initial condition. This is performed through a direct coregistration to an MNI152 EPI template.
Registration to an EPI (i.e. fMRI template) has been shown to be more robust to EPI magnetic
susceptibility artifacts and distortions than the conventional two-step T1-based normalization (EPI to T1
image, T1 image to template) (7, 8). This coregistration step is the most computationally expensive step
of the augmentation procedure but can be completed in around 30 minutes with ANTs Symmetric
Figure 1. fMRI augmentation using BLENDS to combine 4 existing warp fields for .
Steps shown include: 1) Isotropic Gaussian point clusters in 3D space are generated for each of the 4
warp fields. 2) The distance transform is applied to each point cluster to smooth blending matrices
. 3) The blending matrices are used to compute a weighted sum of the warp fields, resulting in a
new blended warp . 4) The blended warp is used to transform a pair of sMRI and fMRI images
and produce a new, augmented sample. Colors in the warp fields indicate principal direction of local
vector (red: sagittal, green: coronal, blue: axial).
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Normalization (6). Importantly, this step need only be performed once per source image, irrespective of
the number of desired augmented images.
Since the warps can be applied agnostically to any 3D or 4D image, the same generated warp
can be used to transform multiple contrasts from the same individual such as fMRI, structural MRI,
diffusion MRI, etc. In the case of a 4D fMRI timeseries, the warp is applied to each volume in the
timeseries, assuming that the volumes have been realigned with a tool such as FSL MCFLIRT to correct
for inter-volume motion (9).
2.2. APPLICATIONS
BLENDS is demonstrated on two distinct neuroimaging use cases involving common brain
disorders. Both use de-identified, publicly available data containing fMRI and structural MRI (sMRI). Brief
details are provided here with full dataset characteristics and MRI parameters available in the
Supplemental Tables S1-4.
2.2.1. MAJOR DEPRESSIVE DISORDER
The objective in the first application is to predict future antidepressant response from brain
activation measures of pre-treatment fMRI. Imaging data for 163 participants with major depressive
disorder (MDD) are obtained from the Establishing Moderators and Biosignatures of Antidepressant
Response in Clinical care (EMBARC) study (10). Demographics are shown in Supplemental Table S1.
Functional imaging during a reward processing task and structural imaging were acquired at pre-
treatment baseline, before the participants underwent an 8-week course of the antidepressant
sertraline (task paradigm and acquisition parameters are detailed in Supplemental Methods Section 1
and Supplemental Table S2). Depression severity was measured by trained clinical raters using the
Hamilton Rating Scale for Depression 17-item score (HAMD) before and after treatment. Antidepressant
response is defined as the difference in HAMD score.
The precomputed set of warps is generated by computing coregistrations between the MNI152
template and each of 290 structural (T1-weighted) images from EMBARC. BLENDS is applied to augment
each fMRI twice (2x), five times (5x), and ten times (10x). Augmented fMRI are then preprocessed with a
standard fMRI pipeline including head motion correction, spatial normalization, and nuisance regression
(further details are provided in Supplemental Methods Sections 2 and 3). Brain activation maps are
computed using a generalized linear model. A custom 200-region brain atlas was created from using the
pyClusterROI tool, which performs spectral clustering normalized cuts on fMRI data (11). Mean regional
values are computed using this atlas and passed as input features into a neural network to predict post-
treatment change in HAMD score. The augmentation is performed on the “raw” 4D fMRI timeseries
rather than the 3D brain activation maps. This both demonstrates the general applicability of BLENDS to
4D images and affords flexibility. In further applications, augmenting the original 4D images allows the
user the ability to re-process and extract other measurements (e.g. functional connectivity, ReHo, fALFF,
etc.) as needed for a targeted application.
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2.2.2. PARKINSON’S DISEASE
For the second application, the goal is to predict Parkinson’s Disease (PD) total symptom
trajectory from baseline resting-state fMRI. In this case, disease severity 12 months after baseline is to
be predicted from the baseline regional homogeneity (ReHo) measures extracted from resting-state
fMRI. From the Parkinson’s Progression Marker Initiative (PPMI) dataset, 43 PD participants are selected
who had functional and structural imaging and who also had disease severity measured at 12 months
after their baseline imaging time. Severity is measured by clinical raters using the total score from the
Movement Disorder Society’s Unified Parkinson’s Disease Rating Scale (MDS-UPDRS), which was
assessed with participants in the medicated state. See Supplemental Table S3 for demographics and
Table S4 for acquisition parameters. The warp set contains 399 warps, computed from all available
structural images from PPMI. As with the MDD application, BLENDS is applied at 2x, 5x, and 10x.
Augmented fMRI are preprocessed with the same fMRI pipeline (Supplemental Methods
Sections 2 and 4). Regional homogeneity (ReHo), which measures the similarity in activity of each brain
voxel with its 26-voxel neighborhood, is computed using the C-PAC software (v1.0.3) (12). ReHo reflects
the synchronicity of a voxel with its immediate surrounding brain tissue, and abnormalities in ReHo have
been observed in PD (13). The Schaefer 200-region atlas was used to compute the mean ReHo in each
brain region. These values were used as inputs into the neural network, described in the next section,
along with clinical covariates including age, sex, race, ethnicity, disease duration, and baseline MDS-
UPDRS. The clinical covariates were not altered during the creation of each augmented sample.
2.3. NEURAL NETWORKS
Deep feed-forward, fully connected neural networks were constructed for both applications.
Hyperparameter optimization was conducted using Bayesian Optimization with Hyperband (BOHB), a
fully automated hyperparameter search algorithm unbiased to user expertise or hand-tuning (14). Full
details of the hyperparameter optimization, model architectures, and hyperparameter ranges can be
found in the Supplemental Methods Section 5, Figure S1, and Table S5.
Model performance was validated using nested K-fold cross-validation with 3 outer and 5 inner
folds. For each outer fold, testing data was held aside and the remaining data was used to perform a
random search over 100 hyperparameter configurations with 5-fold inner cross-validation. The best
performing model from the random search was retrained on all inner data and evaluated on the testing
data. This retraining and evaluation was repeated 100 times per outer fold, with different random
weight initializations, for significance testing. No augmented data was included in validation or testing
and data splits were grouped such that each augmented sample remained in the same fold as the
original sample.
Neural networks were implemented in Tensorflow v1.12 and BOHB searches were performed
with Ray Tune v1.2 with parallelization across 4 Nvidia Tesla P100 GPUs.
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3. RESULTS
3.1. AUGMENTED IMAGES
Examples of augmented images generated with BLENDS are shown in Figure 2. A pair of
structural and functional images from the same individual are augmented 5 times (same blended warp
applied to both images) to introduce morphological variations throughout the brain. Comparing the
augmented fMRI to the original image (Figure 2, 3rd row) highlights areas where variations have been
introduced: for example, the cerebellum size and the convexity of the frontal lobe have been altered to
varying degrees. Due to the process of blending together multiple existing warps, these resultant
augmented images are distinct from those in the original sample. Figure S2 illustrates examples of brain
activation maps computed from original and augmented fMRI from the MDD dataset, showing that the
Figure 2. BLENDS applied to structural T1-weighted (sMRI, 1st row) and functional MRI (fMRI, 2nd
row) from a Parkinson’s Disease patient to synthesize 5 new samples. Morphological variations are
introduced in global brain shape as well as in neuroanatomical structures throughout the cerebellum
and cerebrum. In the third row, an edge map of each augmented fMRI is overlaid over the original
fMRI to illustrate the morphological differences.
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variability is carried into subsequent measurements derived from fMRI. Additionally, each augmentation
operation, including the generation of the blended warp and the transformation of the original image,
required 2 minutes on a conventional workstation CPU (Xeon E5-2680) compared to 30 minutes
required by our previous coregistration-based method, on the same hardware.
3.2. MAJOR DEPRESSIVE DISORDER
Performance in predicting antidepressant response from task-based brain activation measures
substantially increased with augmentation (Figure 3). At baseline before augmentation, (mean over
all outer cross-validation folds) was 0.055. This indicates that the model was able to explain about 5.5%
of the variance in the change in depression symptoms 8 weeks after antidepressant treatment from the
pre-treatment neuroimaging. Performance significantly increased with 2x augmentation to 0.098 (
), and it continued to increase with 5x ( 0.099) and 10x ( 0.103) augmentation. Thus with
BLENDS augmentation the percent variance explained nearly doubled from 5.5% to 9.9%, a substantial
and statistically significant improvement.
Figure 3. Performance (coefficient of determination, ) in predicting antidepressant outcomes from
pre-treatment task-based fMRI. Error bars indicate the 95% confidence interval, computed by
retraining each model 100 times per cross-validation fold with different random weight initializations.
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3.3. PARKINSON’S DISEASE
BLENDS also markedly improved the accuracy of predicting Parkinson’s Disease total MDS-
UPDRS severity at 12 months after the baseline imaging scan using regional homogeneity measures
(Figure 4). Before augmentation, was 0.294, indicating that 29% of the variance in the total symptom
level in the 12 months after baseline imaging was explained by the model. A significant increase to an
of 0.535 was seen with 5x augmentation (). The trend continued with 10x augmentation
( 0.548). Thus again, with BLENDS augmentation increased from 29% to 55%, which is also a
substantial and statistically significant improvement.
4. DISCUSSION
4.1. IMPACT ON PREDICTOR PERFORMANCE
For both clinical applications, the prediction of antidepressant response from task-based fMRI
and the prediction of future Parkinson’s Disease severity from resting-state fMRI, BLENDS augmentation
substantially improved neural network performance. In the antidepressant application, treatment
outcome prediction performance improved by a relative 87% with 10x augmentation compared to
baseline. For the prognosis of individuals with Parkinson’s Disease, BLENDS also demonstrated a large
and significant performance increase from baseline. At 10x augmentation, performance was 86%
greater relative to baseline. Of note, the relationship between augmentation amount and performance
is not linear. Consequently, for a new problem, it may not be known a priori what amount of
augmentation is required to achieve a desired performance level. However, a straightforward search
over augmentation amount can be employed to identify the optimal condition.
Figure 4. Performance (coefficient of determination, ) in predicting future Parkinson’s Disease
severity 1 year in the future from regional homogeneity derived from baseline resting-state fMRI. Error
bars indicate the 95% confidence interval, computed by retraining each model 100 times per cross-
validation fold with different random weight initializations.
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Besides (4), there are few published fMRI augmentation methods for comparison. Zhuang et al.
recently reported an approach using a generative adversarial network (GAN) to augment 3D brain
activation maps derived from fMRI (3). They achieve up to a 4.6% accuracy increase (7.6% relative
increase from baseline) in classifying cognitive states with a neural network. A main limitation of this
approach is that it is constrained to 3D images; 4D GANs are computationally prohibitive to train on
current hardware due to the sheer memory and compute required. Thisprevents usage on “raw” fMRI
timeseries (3D + time) or other 4D data such as dynamic contrast-enhanced MRI or diffusion MRI (where
the fourth dimension is direction). Similarly, Eslami et al. propose an extension to the Synthetic Minority
Over-sampling Technique (SMOTE) using a similarity measure optimized for fMRI data (15). However,
this method is also limited to generating fMRI derivatives (e.g. functional connectivity matrices) instead
of full 4D images. Augmentation of the full fMRI timeseries is essential if subsequent analysis requires
deriving scalar measures, such as functional connectivity or causal connectivity, or multiple
complementary measures such as regional homogeneity (ReHo) and amplitude of low frequency
fluctuations (ALFF). Instead of directly synthesizing images, BLENDS generates new warps that can be
applied to any image type, allowing more flexibility than a GAN-based approach. An additional limitation
to these existing methods is that they are restricted to classification tasks (i.e. with a discrete prediction
target), which prevents application to the regression tasks investigated in this work. The GAN approach
generates samples conditioned on the desired target label, and GANs conditioned on continuous labels
do not yet exist. SMOTE is inherently limited to classification and while an extension to regression exists
(SMOTER), it depends on a linearity assumption to interpolate new target values (16).
To demonstrate applicability to classification problems, BLENDS was also applied to the
diagnosis of Parkinson’s Disease from resting-state functional connectivity (see Supplemental Methods
Section 6). On this problem, BLENDS achieved a similar increase to classification accuracy as SMOTE, up
to 10% compared to the baseline without augmentation (Figure S3). This highlights how BLENDS can
achieve competitive performance boosting augmentation results for both regression and classification
applications.
4.2. LIMITATIONS
There are two limitations of BLENDS that warrant discussion. The first is that BLENDS requires a
precomputed set of warps, which can entail a large upfront computational cost. However, the
combinatorial nature of sampling and blending warps means that a large range of morphological
diversity can be generated from a relatively small warp set. For example, sampling 4 warps at a time
from a set of 100 warps yields 4 million unique combinations, with further variations introduced through
the random blending process. To mitigate this limitation, we will provide a large set of warps computed
from over 1000 healthy brains to the community for ready download, facilitating immediate testing and
application of BLENDS. For applications where the cohort may have aberrant morphology compared to
healthy brains (e.g. Parkinson’s Disease), we recommend that researchers compute their own warp set.
In many cases, researchers already have such a set of study specific warps computed, as coregistration
of brains to an atlas is a common step in many preprocessing pipelines. The second limitation is that
BLENDS may not be applicable to situations where random warping may perturb biological information
of interest in images, including cases where morphology is directly associated with the prediction target.
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However, this limitation is inherent to any data augmentation method that relies on random
transformations. In the case of BLENDS, this could be partially mitigated by using stratified or separate
sets for each class, as was done with the Parkinson’s Disease diagnosis application.
4.3. CONCLUSION
These results establish clear evidence to augment neuroimaging data for deep learning when
the data is limited. BLENDS demonstrated a substantial performance benefit when applied to two
distinct neuroimaging problems encompassing psychiatric and neurological disease. Main advantages to
the method include its 1) flexibility in synthesizing full 4D images, 2) computational speed, and 3) ability
to produce out-of-sample variations through warp blending. These results support the use of BLENDS for
task-based and resting-state fMRI, though future work could investigate applications to other MRI
contrasts, including diffusion or dynamic contrast enhanced MRI, where the four-dimensional data is
costly and could benefit from augmentation. Consequently, BLENDS is anticipated to be of general
interest to the neuroimaging community and especially to researchers looking to improve performance
of deep learning on their existing data.
ACKNOWLEDGEMENTS
We thank Drs. Andrew Jamieson, Jeon Lee, and Jian Zhou for their feedback during the writing of this
manuscript.
Data used in the preparation of this article were obtained from the Parkinson’s Progression
Markers Initiative (PPMI) database (www.ppmi-info.org/data). For up-to-date information on the study,
visit www.ppmi-info.org. PPMI – a public-private partnership – is funded by the Michael J. Fox
Foundation for Parkinson’s Research and funding partners, including Abbvie, Allergan, Amathus
Therapeutics, Avid Radiopharmaceuticals, Biogen, BioLegend, Bristol-Myers Squibb, Celgene, Denali, GE
Healthcare, Genentech, GlaxoSmithKline, Golub Capital, Handl Therapeutics, Insitro, Janssen
Neuroscience, Lilly, Lundbeck, Merck, Meso Scale Discovery, Pfizer, Piramal, Prevail Therapeutics, Roche,
Sanofi Genzyme, Servier, Takeda, Teva, UCB, Verily, and Voyager Therapeutics.
CODE AVAILABILITY
To facilitate reuse and extension, the source code for our method can be found at
https://github.com/DeepLearningForPrecisionHealthLab/BLENDS.
FUNDING AND FINANCIAL DISCLOSURES
Dr. Montillo was supported by NIH NIA R01AG059288, the King Foundation, the Lyda Hill Foundation,
and the UT Southwestern Lyda Hill Department of Bioinformatics. Dr. Dewey was supported by the Jean
Walter Center for Research in Movement Disorders. Unrelated to this work, Dr. Dewey is a consultant
for Supernus, Acorda and Amneal Pharmaceuticals. Dr. Trivedi has served as an adviser or consultant for
Abbott Laboratories, Abdi Ibrahim, Akzo (Organon Pharmaceuticals), Alkermes, AstraZeneca, Axon
Advisors, Bristol- Myers Squibb, Cephalon, Cerecor, CME Institute of Physicians, Concert
Pharmaceuticals, Eli Lilly, Evotec, Fabre Kramer Pharmaceuticals, Forest Pharmaceuticals,
GlaxoSmithKline, Janssen Global Services, Janssen Pharmaceutica Products, Johnson & Johnson PRD,
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Libby, Lundbeck, Meade Johnson, MedAvante, Medtronic, Merck, Mitsubishi Tanabe Pharma
Development America, Naurex, Neuronetics, Otsuka Pharmaceuticals, Pamlab, Parke-Davis
Pharmaceuticals, Pfizer, PgxHealth, Phoenix Marketing Solutions, Rexahn Pharmaceuticals, Ridge
Diagnostics, Roche Products, Sepracor, Shire Development, Sierra, SK Life and Science, Sunovion,
Takeda, Tal Medical/Puretech Venture, Targacept, Transcept, VantagePoint, Vivus, and Wyeth-Ayerst
Laboratories; he has received grants or research support from the Agency for Healthcare Research and
Quality, Cyberonics, NARSAD, NIDA, and NIMH.
REFERENCES
1. Castro E, Ulloa A, Plis SM, Turner JA, Calhoun VD. Generation of synthetic structural magnetic
resonance images for deep learning pre-training. In: 2015 IEEE 12th International Symposium on
Biomedical Imaging (ISBI). IEEE, 2015; 1057–1060.
2. Ulloa A, Plis S, Erhardt E, Calhoun V. Synthetic structural magnetic resonance image generator
improves deep learning prediction of schizophrenia. In: 2015 IEEE 25th International Workshop on
Machine Learning for Signal Processing (MLSP). [S.l.]: IEEE, 2015; 1–6.
3. Zhuang P, Schwing AG, Koyejo O. FMRI Data Augmentation Via Synthesis. In: IEEE International
Symposium on Biomedical Imaging (ISBI). [Piscataway, New Jersey]: IEEE, 2019; 1783–1787.
4. Nguyen KP, Chin Fatt C, Treacher A, Mellema C, Trivedi MH, Montillo A. Anatomically-informed data
augmentation for functional MRI with applications to deep learning. In: Landman BA, Išgum I, eds.
Medical Imaging: Image Processing. SPIE, 2020; 28–33.
5. Andersson J, Jenkinson M, Smith S, 2007. Non-linear registration, aka Spatial normalisation: FMRIB
Technical Report TR07JA2. Oxford.
6. Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC. A Reproducible Evaluation of ANTs
Similarity Metric Performance in Brain Image Registration. Neuroimage 2010;54(3):2033–2044.
doi:10.1016/j.neuroimage.2010.09.025.
7. Calhoun VD, Wager TD, Krishnan A, et al. The impact of T1 versus EPI spatial normalization templates
for fMRI data analyses. Hum Brain Mapp 2017;38(11):5331–5342. doi:10.1002/hbm.23737.
8. Dohmatob E, Varoquaux G, Thirion B. Inter-subject Registration of Functional Images: Do We Need
Anatomical Images? Front Neurosci 2018;12:64. doi:10.3389/fnins.2018.00064.
9. Jenkinson M, Bannister P, Brady M, Smith S. Improved Optimization for the Robust and Accurate
Linear Registration and Motion Correction of Brain Images. Neuroimage 2002;17(2):825–841.
doi:10.1016/S1053-8119(02)91132-8.
10. Trivedi MH, McGrath PJ, Fava M, et al. Establishing moderators and biosignatures of antidepressant
response in clinical care (EMBARC): Rationale and design. J Psychiatr Res 2016;78:11–23.
doi:10.1016/j.jpsychires.2016.03.001.
11. Craddock RC, James GA, Holtzheimer PE, Hu XP, Mayberg HS. A whole brain fMRI atlas generated via
spatially constrained spectral clustering. Hum Brain Mapp 2012;33(8):1914–1928.
doi:10.1002/hbm.21333.
12. Craddock C, Sikka S, Cheung B, et al. Towards Automated Analysis of Connectomes: The Configurable
Pipeline for the Analysis of Connectomes (C-PAC). Front Neuroinform 2013;7.
doi:10.3389/conf.fninf.2013.09.00042.
.CC-BY-NC-ND 4.0 International licenseavailable under a
was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.06.02.446748doi: bioRxiv preprint
Nguyen et al. BLENDS
14
13. Hu J, Xiao C, Gong D, Qiu C, Liu W, Zhang W. Regional homogeneity analysis of major Parkinson's
disease subtypes based on functional magnetic resonance imaging. Neuroscience Letters
2019;706:81–87. doi:10.1016/j.neulet.2019.05.013.
14. Falkner S, Klein A, Hutter F. BOHB: Robust and Efficient Hyperparameter Optimization at Scale. In:
Jennifer Dy, Andreas Krause, eds. Proceedings of the 35th International Conference on Machine
Learning. Stockholmsmässan, Stockholm Sweden: PMLR, 2018; 1437–1446.
15. Eslami T, Mirjalili V, Fong A, Laird AR, Saeed F. ASD-DiagNet: A Hybrid Learning Approach for
Detection of Autism Spectrum Disorder Using fMRI Data. Front Neuroinform 2019;13:70.
doi:10.3389/fninf.2019.00070.
16. Torgo L, Ribeiro RP, Pfahringer B, Branco P. SMOTE for Regression. In: Correia LM, Reis LP, Cascalho
J, eds. Progress in artificial intelligence: 16th Portuguese Conference on Artificial Intelligence, EPIA
2013, Angra do Heroísmo, Azores, Portugal, September 9-12, 2013, proceedings / Luís Correia, Luís
Paulo Reis, José Cascalho (eds.). Heidelberg: Springer, 2013; 378–389.
.CC-BY-NC-ND 4.0 International licenseavailable under a
was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.06.02.446748doi: bioRxiv preprint