Realignment strategies for awake-monkey fMRI data

Stoewer, S; Goense, Jozien; Keliris, Georgios A.; Bartels, Andreas; Logothetis, Nikos K.; Duncan, John; Sigala, Natasha

doi:10.1016/j.mri.2011.05.003

Cited by 6 publications

(12 citation statements)

References 18 publications

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“…The realignment procedure consisted of a within-trial rigid and a between-trial non-rigid coregistration of volumes [18]. We observed a higher number of suprathreshold voxels for both animals.…”

Section: Discussionmentioning

confidence: 68%

“…It allows more efficient use of acquired animal data, thereby reducing the number of scans needed. Elements of this approach have been laid out in earlier work [3], [11], [18].…”

Section: Discussionmentioning

confidence: 99%

“…We extend this approach by introducing specific realignment strategies that focus on in-plane shifts; moreover, we compensate for brain distortions within and between runs and sessions with a non-rigid coregistration algorithm [18]. Our temporal filtering strategy addresses the issue of discontinuous volume time series and global and local intensity changes over single and multiple runs.…”

Section: Discussionmentioning

confidence: 99%

“…A separate paper [18] lays out the details and reports a detailed comparison of this realignment method with a number of other approaches.…”

Section: Methodsmentioning

confidence: 99%

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An Analysis Approach for High-Field fMRI Data from Awake Non-Human Primates

et al. 2012

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fMRI experiments with awake non-human primates (NHP) have seen a surge of applications in recent years. However, the standard fMRI analysis tools designed for human experiments are not optimal for analysis of NHP fMRI data collected at high fields. There are several reasons for this, including the trial-based nature of NHP experiments, with inter-trial periods being of no interest, and segmentation artefacts and distortions that may result from field changes due to movement. We demonstrate an approach that allows us to address some of these issues consisting of the following steps: 1) Trial-based experimental design. 2) Careful control of subject movement. 3) Computer-assisted selection of trials devoid of artefacts and animal motion. 4) Nonrigid between-trial and rigid within-trial realignment of concatenated data from temporally separated trials and sessions. 5) Linear interpolation of inter-trial intervals and high-pass filtering of temporally continuous data 6) Removal of interpolated data and reconcatenation of datasets before statistical analysis with SPM. We have implemented a software toolbox, fMRI Sandbox (http://code.google.com/p/fmri-sandbox/), for semi-automated application of these processing steps that interfaces with SPM software. Here, we demonstrate that our methodology provides significant improvements for the analysis of awake monkey fMRI data acquired at high-field. The method may also be useful for clinical applications with subjects that are unwilling or unable to remain motionless for the whole duration of a functional scan.

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Section: Discussionmentioning

confidence: 68%

“…It allows more efficient use of acquired animal data, thereby reducing the number of scans needed. Elements of this approach have been laid out in earlier work [3], [11], [18].…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…A separate paper [18] lays out the details and reports a detailed comparison of this realignment method with a number of other approaches.…”

Section: Methodsmentioning

confidence: 99%

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An Analysis Approach for High-Field fMRI Data from Awake Non-Human Primates

et al. 2012

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“…To demonstrate that MCS effects on activity of PO neurons persist after electrolytic lesions of the cortico-spinal tract (months: [18][19][20][21][22][23][24].…”

Section: Task 1ementioning

confidence: 99%

Motor Cortex Stimulation Reverses Maladaptive Plasticity Following Spinal Cord Injury

Masri¹

2012

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The majority of patients with spinal cord injury (SCI) develop intractable chronic neuropathic pain that is resistant to conventional pharmacologic treatments. An alternative and potentially effective modality of treatment-motor cortex stimulation (MCS)-offers hope for these patients. The purpose of this application is to elucidate the neurobiological basis of reduced pain following MCS. We propose that MCS reverses hyperalgesia by enhancing the activity in the GABAergic nucleus zona incerta (ZI), and therefore inhibiting pain processing in the posterior thalamus (PO). Using single cell extracellular electrophysiological recordings from the thalamus of rats with SCI-pain we tested the effect of MCS on the activity of neurons in ZI and PO. We demonstrated last year that MCS significantly enhanced spontaneous and evoked responses in the majority of PO-projecting ZI neurons and caused a significant and robust suppression of activity in PO. We now report that inactivation of ZI using muscimol (GABA A agonist) blocks the effects of MCS stimulation on PO neurons while cutting the pyramidal tracts have no effects on suppressed activity in PO after MCS. These findings further support our overarching hypothesis that MCS alleviates pain by activating the incerto-thalamic pathway.

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In vivo high‐resolution localized ¹H MR spectroscopy in the awake rat brain at 7 T

Chen

et al. 2012

Magnetic Resonance in Med

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In vivo localized high-resolution 1H MR spectroscopy was performed in multiple brain regions without the use of anesthetic or paralytic agents in awake head-restrained rats that were previously trained in a simulated MRI environment using a 7 Tesla MR system. Spectra were obtained using a short echo time single-voxel point-resolved spectroscopy technique with voxel size ranging from 27–32.4 mm3 in the regions of anterior cingulate cortex, somatosensory cortex, hippocampus, and thalamus. Quantifiable spectra, without the need for any additional post-processing to correct for possible motion were reliably detected including the metabolites of interest such as γ-aminobutyric acid, glutamine, glutamate, myo-inositol, N-acetylaspartate, taurine, glycerophosphorylcholine/phosphorylcholine, creatine/phosphocreatine, and N-acetylaspartate/N-acetylaspartylglutamate. The spectral quality was comparable to spectra from anesthetized animals with sufficient spectral dispersion to separate metabolites such as glutamine and glutamate. Results from this study suggest that reliable information on major metabolites can be obtained without the confounding effects of anesthesia or paralytic agents in rodents.

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Realignment strategies for awake-monkey fMRI data

Cited by 6 publications

References 18 publications

An Analysis Approach for High-Field fMRI Data from Awake Non-Human Primates

An Analysis Approach for High-Field fMRI Data from Awake Non-Human Primates

Motor Cortex Stimulation Reverses Maladaptive Plasticity Following Spinal Cord Injury

In vivo high‐resolution localized ¹H MR spectroscopy in the awake rat brain at 7 T

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Realignment strategies for awake-monkey fMRI data

Cited by 6 publications

References 18 publications

An Analysis Approach for High-Field fMRI Data from Awake Non-Human Primates

An Analysis Approach for High-Field fMRI Data from Awake Non-Human Primates

Motor Cortex Stimulation Reverses Maladaptive Plasticity Following Spinal Cord Injury

In vivo high‐resolution localized 1H MR spectroscopy in the awake rat brain at 7 T

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Product

Resources

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In vivo high‐resolution localized ¹H MR spectroscopy in the awake rat brain at 7 T