Diverse Time Encoding Strategies Within the Medial Premotor Areas of the Primate.

The measurement of time in the subsecond scale is critical for many sophisticated behaviors, yet its neural underpinnings are largely unknown. Recent neurophysiological experiments from our laboratory have shown that the neural activity in the medial premotor areas (MPC) of macaques can represent different aspects of temporal processing. During single interval categorization, we found that preSMA encodes a subjective category limit by reaching a peak of activity at a time that divides the set of test intervals into short and long. We also observed neural signals associated with the category selected by the subjects and the reward outcomes of the perceptual decision. On the other hand, we have studied the behavioral and neurophysiological basis of rhythmic timing. First, we have shown in different tapping tasks that macaques are able to produce predictively and accurately intervals that are cued by auditory or visual metronomes or when intervals are produced internally without sensory guidance. In addition, we found that the rhythmic timing mechanism in MPC is governed by different layers of neural clocks. Next, the instantaneous activity of single cells shows ramping activity that encodes the elapsed or remaining time for a tapping movement. In addition, we found MPC neurons that build neural sequences, forming dynamic patterns of activation that flexibly cover all the produced interval depending on the tapping tempo. This rhythmic neural clock resets on every interval providing an internal representation of pulse. Furthermore, the MPC cells show mixed selectivity, encoding not only elapsed time, but also the tempo of the tapping and the serial order element in the rhythmic sequence. Hence, MPC can map different task parameters, including the passage of time, using different cell populations. Finally, the projection of the time varying activity of MPC hundreds of cells into a low dimensional state space showed circular neural trajectories whose geometry represented the internal pulse and the tapping tempo. Overall, these findings support the notion that MPC is part of the core timing mechanism for both single interval and rhythmic timing, using neural clocks with different encoding principles, probably to flexibly encode and mix the timing representation with other task parameters.

Strengths and challenges of longitudinal non-human primate neuroimaging.

Longitudinal non-human primate neuroimaging has the potential to greatly enhance our understanding of primate brain structure and function. Here we describe its specific strengths, compared to both cross-sectional non-human primate neuroimaging and longitudinal human neuroimaging, but also its associated challenges. We elaborate on factors guiding the use of different analytical tools, subject-specific versus age-specific templates for analyses, and issues related to statistical power.

U-net model for brain extraction: Trained on humans for transfer to non-human primates.

Brain extraction (a.k.a. skull stripping) is a fundamental step in the neuroimaging pipeline as it can affect the accuracy of downstream preprocess such as image registration, tissue classification, etc. Most brain extraction tools have been designed for and applied to human data and are often challenged by non-human primates (NHP) data. Amongst recent attempts to improve performance on NHP data, deep learning models appear to outperform the traditional tools. However, given the minimal sample size of most NHP studies and notable variations in data quality, the deep learning models are very rarely applied to multi-site samples in NHP imaging. To overcome this challenge, we used a transfer-learning framework that leverages a large human imaging dataset to pretrain a convolutional neural network (i.e. U-Net Model), and then transferred this to NHP data using a small NHP training sample. The resulting transfer-learning model converged faster and achieved more accurate performance than a similar U-Net Model trained exclusively on NHP samples. We improved the generalizability of the model by upgrading the transfer-learned model using additional training datasets from multiple research sites in the Primate Data-Exchange (PRIME-DE) consortium. Our final model outperformed brain extraction routines from popular MRI packages (AFNI, FSL, and FreeSurfer) across a heterogeneous sample from multiple sites in the PRIME-DE with less computational cost (20 s~10 min). We also demonstrated the transfer-learning process enables the macaque model to be updated for use with scans from chimpanzees, marmosets, and other mammals (e.g. pig). Our model, code, and the skull-stripped mask repository of 136 macaque monkeys are publicly available for unrestricted use by the neuroimaging community at https://github.com/HumanBrainED/NHP-BrainExtraction.

Beyond MRI: on the scientific value of combining non-human primate neuroimaging with metadata.

Sharing and pooling large amounts of non-human primate neuroimaging data offer new exciting opportunities to understand the primate brain. The potential of big data in non-human primate neuroimaging could however be tremendously enhanced by combining such neuroimaging data with other types of information. Here we describe metadata that have been identified as particularly valuable by the non-human primate neuroimaging community, including behavioural, genetic, physiological and phylogenetic data.

PREEMACS: Pipeline for preprocessing and extraction of the macaque brain surface.

Accurate extraction of the cortical brain surface is critical for cortical thickness estimation and a key element to perform multimodal imaging analysis, where different metrics are integrated and compared in a common space. While brain surface extraction has become widespread practice in human studies, several challenges unique to neuroimaging of non-human primates (NHP) have hindered its adoption for the study of macaques. Although, some of these difficulties can be addressed at the acquisition stage, several common artifacts can be minimized through image preprocessing. Likewise, there are several image analysis pipelines for human MRIs, but very few automated methods for extraction of cortical surfaces have been reported for NHPs and none have been tested on data from diverse sources. We present PREEMACS, a pipeline that standardizes the preprocessing of structural MRI images (T1- and T2-weighted) and carries out an automatic surface extraction of the macaque brain. Building upon and extending pre-existing tools, the first module performs volume orientation, image cropping, intensity non-uniformity correction, and volume averaging, before skull-stripping through a convolutional neural network. The second module performs quality control using an adaptation of MRIqc method to extract objective quality metrics that are then used to determine the likelihood of accurate brain surface estimation. The third and final module estimates the white matter (wm) and pial surfaces from the T1-weighted volume (T1w) using an NHP customized version of FreeSurfer aided by the T2-weighted volumes (T2w). To evaluate the generalizability of PREEMACS, we tested the pipeline using 57 T1w/T2w NHP volumes acquired at 11 different sites from the PRIME-DE public dataset. Results showed an accurate and robust automatic brain surface extraction from images that passed the quality control segment of our pipeline. This work offers a robust, efficient and generalizable pipeline for the automatic standardization of MRI surface analysis on NHP.

A collaborative resource platform for non-human primate neuroimaging.

Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field .

Cambios en el perfil funcional de pacientes con patología psiquiátrica resistente sometidos a neurocirugía funcional estereotáctica / Changes in the functional profile of patients with resistant psychiatric disorders subjected to stereotactic functional neurosurgery / Mudanças no perfil funcional de pacientes con patologia psiquiátrica resistente submetidos a neurocirurgia funcional estereotáxica

Con el objetivo de evaluar los resultados de la Neurocirugía Funcional Estereotáctica (NFE) sobre el perfil funcional de los pacientes diagnosticados con Patología Psiquiátrica Resistente (PPR), se realizó un diseño pre/post tratamiento. 13 pacientes fueron evaluados ( = 31 ± 8 años): siete mujeres diagnosticadas con algún Trastorno de la Conducta Alimentaria Resistente (TCAR); tres mujeres diagnosticadas con Trastornos Resistentes Obsesivo Compulsivo y Depresivo (TOC y DR) y tres pacientes (dos mujeres y un hombre) diagnosticados con Depresión Resistente (DR). A estos pacientes se les aplicó la Escala de funcionamiento del paciente Eje K, la cual consta de siete subescalas, y una Escala de Evaluación de la Actividad Global (EAG) antes del tratamiento y después de éste (seis meses posteriores a la NFE). Todos los grupos diagnósticos y el total de los pacientes evaluados presentaron cambios clínicos positivos; sin embargo, sólo el grupo de TCAR mostró importantes cambios clínicos de mejoría en el perfil de funcionamiento, siendo esta diferencia estadísticamente significativa (pre Md = 56; post Md = 84; z= - 2.36, p <0.05). Con la evidencia obtenida se observó que la NFE representa una opción terapéutica emergente efectiva orientada a disminuir el sufrimiento de los pacientes con PPR, así como a mejorar el nivel de funcionamiento global y por ende su calidad de vida. Todos los pacientes del estudio presentaban una condición de resistencia a tratamientos convencionales indicados, la cual había sido documentada por un equipo interdisciplinario experto.

In order to evaluate the results of the Stereotactic Functional Neurosurgery (SFN) on the functional profile of patients diagnosed with Resistant Psychiatric Pathology (RPP), a pre / post treatment design was performed. Thirteen patients were assessed ( = 31 ± 8 years): seven women diagnosed with some type of Resistant Eating Disorder (RED); three women diagnosed with Resistant Obsessive Compulsive Disorder and Resistant Depression (TOC and RD), and three patients (two women and one man) diagnosed with Resistant Depression (RD). The Patient's Functioning Scale, axis K, consisting of seven subscales, and the Assessment of Global Activity Scale (AGAS) were applied before and after treatment (6 months after FSN). All diagnostic groups and all the patients assessed showed positive clinical changes. However, only the RED group showed important clinical improvement in the performance profile with a statistically significant difference (pre Md = 56, Md = 84 post , z = - 2.36, p <0.05). With the evidence obtained it was noted that SFN represents an effective therapeutic option aimed at reducing the suffering of patients with RPP and improve their overall level of functioning and therefore their quality of life. All patients in the study had a condition indicating resistance to conventional treatments which had been documented by an expert multidisciplinary team.

Con o objetivo de avaliar os resultados da Neurocirurgía Funcional Estereotáxica (NFE) sobre o perfil funcional dos pacientes diagnosticados com Patologia Psiquiátrica Resistente (PPR), realizou-se um desenho pré/pós tratamento. 13 pacientes foram avaliados ( = 31 ± 8 anos): sete mulheres diagnosticadas com algum Transtorno da Conduta Alimentar Resistente (TCAR); três mulheres diagnosticadas com Transtornos Resistentes Obsessivo Compulsivo e Depressivo (TOC e DR) e três pacientes (duas mulheres e um homem) diagnosticados com Depressão Resistente (DR). A estes pacientes foi aplicada a Escala de funcionamento do paciente Eixo K, a qual consta de sete sub-escalas, e uma Escala de Avaliação da Atividade Global (EAG) antes do tratamento e depois dele (seis meses posteriores à NFE). Todos os grupos diagnósticos e o total dos pacientes avaliados apresentaram mudanças clínicas positivas; porém, só o grupo de TCAR mostrou importantes mudanças clínicas de melhoria no perfil de funcionamento, sendo esta diferença estatisticamente significativa (pré Md= 56; pós Md= 84; z= - 2.36, p <0.05). Com a evidência obtida observou-se que a NFE representa uma opção terapêutica emergente efetiva orientada a diminuir o sofrimento dos pacientes com PPR, bem como a melhorar o nível de funcionamento global e portanto sua qualidade de vida. Todos os pacientes do estudo apresentavam uma condição de resistência a tratamentos convencionais indicados, a qual havia sido documentada por uma equipe interdisciplinar de especialistas.