Computational protocol: Imaging learned fear circuitry in awake mice using fMRI

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Protocol publication

[…] First‐level analysis (intra‐subject) was performed on each mouse using a general linear model in SPM8. The three CS presentations were modelled as a single regressor, and the 5‐min baseline period and rest periods were modelled as an implicit baseline in the model. It was predicted that the amygdala may show extinction of activation across the three CS presentations, and so parametric modulation was used to model a linear decrease from first CS to the third CS to investigate any extinction of neuronal response to the CS. All data were modelled by a boxcar convolved with the SPM8 canonical haemodynamic response function (HRF). Movement parameters generated in the realignment step were added to the model as multiple regressors. Event‐dependent high‐pass filtering was used whereby the cutoff period was 580 s. One contrast image per mouse was entered into a second‐level random effects model (inter‐subject), within‐group effects were examined using one‐sample t‐test and between‐group effects were examined using a two‐sample t‐test.Group‐level SPMs were considered significant at P < 0.05 corrected for multiple comparisons using cluster‐level correction based on random field theory (P FWE; FWE, family‐wise error). SPMs are presented overlaid onto an average structural image (created using the average of all normalised structural images) with voxel‐wise threshold P uncorrected  < 0.001 (unless otherwise stated), and the number of voxels within the cluster; peak T‐value and coordinates in x, y and z dimensions of the peak voxel within the cluster are reported.Our previous fMRI studies in rats and other human fMRI studies demonstrate that the left amygdala is activated more often than the right in response to fear (Baas et al., ); therefore, a small volume correction (SVC) was applied (with P uncorrected  < 0.001 voxel‐wise threshold) using an anatomically defined left amygdala mask (see below) to test the a priori determined hypothesis that the left amygdala would show greater activation in the PG than in the UG in response to the CS (clusters with cluster‐level P FWE  < 0.05 were considered significant).To explicitly investigate laterality of amygdala activation across the three CS presentations, a second general linear model was used to model the three CSs as separate regressors and the rest periods as an implicit baseline. This enabled parameter estimates to be extracted from the left and right amygdala during the first, second and third CS presentations for the PG and UG. Anatomically defined masks covering anterior to posterior basolateral, central and basomedial nuclei were created using MRIcro (Rorden & Brett, ) using the Franklin and Paxinos atlas as a guide. MarsBaR Region of Interest toolbox for SPM (Brett et al., ) was then used to extract and export the parameter estimates for statistical analysis with JMP software using RM anova, group (PG or UG) was a main effect, and CS presentation (CS1, CS2, CS3) and hemisphere (left or right) were repeated measures. To formally test for lateralisation of amygdala activation, left and right parameter estimates from the PG were analysed by paired t‐test, P < 0.05 was deemed significant. […]

Pipeline specifications

Software tools SPM, MRIcro
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Mus musculus, Rattus norvegicus
Chemicals Oxygen