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Considerations for resting state functional MRI and functional connectivity studies in rodents.

Pan WJ, Billings JC, Grooms JK, Shakil S, Keilholz SD - Front Neurosci (2015)

Bottom Line: However, impediments exist to the optimal application of rs-fMRI in small animals, some similar to those encountered in humans and some quite different.In this review we identify the most prominent of these barriers, discuss differences between rs-fMRI in rodents and in humans, highlight best practices for animal studies, and review selected applications of rs-fMRI in rodents.Our goal is to facilitate the integration of human and animal work to the benefit of both fields.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta, GA, USA.

ABSTRACT
Resting state functional MRI (rs-fMRI) and functional connectivity mapping have become widely used tools in the human neuroimaging community and their use is rapidly spreading into the realm of rodent research as well. One of the many attractive features of rs-fMRI is that it is readily translatable from humans to animals and back again. Changes in functional connectivity observed in human studies can be followed by more invasive animal experiments to determine the neurophysiological basis for the alterations, while exploratory work in animal models can identify possible biomarkers for further investigation in human studies. These types of interwoven human and animal experiments have a potentially large impact on neuroscience and clinical practice. However, impediments exist to the optimal application of rs-fMRI in small animals, some similar to those encountered in humans and some quite different. In this review we identify the most prominent of these barriers, discuss differences between rs-fMRI in rodents and in humans, highlight best practices for animal studies, and review selected applications of rs-fMRI in rodents. Our goal is to facilitate the integration of human and animal work to the benefit of both fields.

No MeSH data available.


Related in: MedlinePlus

A summary of processing steps for rodent rs-fMRI. After acquisition, it is critical that both the image time course and the recordings of physiological parameters are closely examined. Slice timing correction can be performed if needed, depending on the frequency range of interest and the TR of the scan. All data should be inspected for motion and either corrected or discarded. For group studies, co-registration and normalization can be used to align images to a common space. Nuisance signals should be handled carefully. The frequency range for filtering can be chosen based on previous work showing coherence between BOLD and LFP for different anesthetics or empirically based on an examination of the power spectrum of the BOLD fluctuations. Standard frequency ranges from human studies are not necessarily applicable to animal work and may result in the loss of a large amount of information.
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Figure 3: A summary of processing steps for rodent rs-fMRI. After acquisition, it is critical that both the image time course and the recordings of physiological parameters are closely examined. Slice timing correction can be performed if needed, depending on the frequency range of interest and the TR of the scan. All data should be inspected for motion and either corrected or discarded. For group studies, co-registration and normalization can be used to align images to a common space. Nuisance signals should be handled carefully. The frequency range for filtering can be chosen based on previous work showing coherence between BOLD and LFP for different anesthetics or empirically based on an examination of the power spectrum of the BOLD fluctuations. Standard frequency ranges from human studies are not necessarily applicable to animal work and may result in the loss of a large amount of information.

Mentions: Human rs-fMRI data typically undergoes extensive preprocessing prior to further analysis. Motion correction, slice timing, corrections for physiological noise, spatial and temporal filtering, and some type of normalization are commonly applied (Murphy et al., 2013). While many of these steps are also appropriate for rodent data, some changes are necessary to obtain optimal results. Many software packages used for fMRI and rs-fMRI preprocessing in human studies, such as Statistical Parametric Mapping (SPM) and Analysis of Functional NeuroImages (AFNI) (Cox, 1996), can also be used for rodent studies, although modification to the data format and parameters such as field of view may be necessary, and many labs use their own code instead. Here we summarize common preprocessing considerations for rodent rs-fMRI studies (Figure 3).


Considerations for resting state functional MRI and functional connectivity studies in rodents.

Pan WJ, Billings JC, Grooms JK, Shakil S, Keilholz SD - Front Neurosci (2015)

A summary of processing steps for rodent rs-fMRI. After acquisition, it is critical that both the image time course and the recordings of physiological parameters are closely examined. Slice timing correction can be performed if needed, depending on the frequency range of interest and the TR of the scan. All data should be inspected for motion and either corrected or discarded. For group studies, co-registration and normalization can be used to align images to a common space. Nuisance signals should be handled carefully. The frequency range for filtering can be chosen based on previous work showing coherence between BOLD and LFP for different anesthetics or empirically based on an examination of the power spectrum of the BOLD fluctuations. Standard frequency ranges from human studies are not necessarily applicable to animal work and may result in the loss of a large amount of information.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525377&req=5

Figure 3: A summary of processing steps for rodent rs-fMRI. After acquisition, it is critical that both the image time course and the recordings of physiological parameters are closely examined. Slice timing correction can be performed if needed, depending on the frequency range of interest and the TR of the scan. All data should be inspected for motion and either corrected or discarded. For group studies, co-registration and normalization can be used to align images to a common space. Nuisance signals should be handled carefully. The frequency range for filtering can be chosen based on previous work showing coherence between BOLD and LFP for different anesthetics or empirically based on an examination of the power spectrum of the BOLD fluctuations. Standard frequency ranges from human studies are not necessarily applicable to animal work and may result in the loss of a large amount of information.
Mentions: Human rs-fMRI data typically undergoes extensive preprocessing prior to further analysis. Motion correction, slice timing, corrections for physiological noise, spatial and temporal filtering, and some type of normalization are commonly applied (Murphy et al., 2013). While many of these steps are also appropriate for rodent data, some changes are necessary to obtain optimal results. Many software packages used for fMRI and rs-fMRI preprocessing in human studies, such as Statistical Parametric Mapping (SPM) and Analysis of Functional NeuroImages (AFNI) (Cox, 1996), can also be used for rodent studies, although modification to the data format and parameters such as field of view may be necessary, and many labs use their own code instead. Here we summarize common preprocessing considerations for rodent rs-fMRI studies (Figure 3).

Bottom Line: However, impediments exist to the optimal application of rs-fMRI in small animals, some similar to those encountered in humans and some quite different.In this review we identify the most prominent of these barriers, discuss differences between rs-fMRI in rodents and in humans, highlight best practices for animal studies, and review selected applications of rs-fMRI in rodents.Our goal is to facilitate the integration of human and animal work to the benefit of both fields.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta, GA, USA.

ABSTRACT
Resting state functional MRI (rs-fMRI) and functional connectivity mapping have become widely used tools in the human neuroimaging community and their use is rapidly spreading into the realm of rodent research as well. One of the many attractive features of rs-fMRI is that it is readily translatable from humans to animals and back again. Changes in functional connectivity observed in human studies can be followed by more invasive animal experiments to determine the neurophysiological basis for the alterations, while exploratory work in animal models can identify possible biomarkers for further investigation in human studies. These types of interwoven human and animal experiments have a potentially large impact on neuroscience and clinical practice. However, impediments exist to the optimal application of rs-fMRI in small animals, some similar to those encountered in humans and some quite different. In this review we identify the most prominent of these barriers, discuss differences between rs-fMRI in rodents and in humans, highlight best practices for animal studies, and review selected applications of rs-fMRI in rodents. Our goal is to facilitate the integration of human and animal work to the benefit of both fields.

No MeSH data available.


Related in: MedlinePlus