Matlab 2011b

Resting-state data were preprocessed using SPM12 (Wellcome Trust Centre for Neuroimaging, London, UK) in MATLAB 2011b (MathWorks, Sherbon, MA, USA). Standard preprocessing steps included slice-timing correction, motion correction with realignment to each scan’s middle volume, coregistration to T1-weighted structural MRI, normalization to the Montreal Neurological Institute template (MNI), and finally, spatial smoothing using a 6mm³ Gaussian kernel (FWHM). The Artifact Detection Tool (ART; www.nitrc.org/projects/artifact_detect/) was also used to mark potentially confounding outliers in fMRI time series for exclusion (i.e., rotation > .02 radians from prior volume, or translation > .4 mm from the prior volume) (Chai et al. 2014 (link)). Physiological confounds, including respiratory and cardiac activity, were accounted for by using masks for white matter and CSF generated through anatomical segmentation as regressors in FC analysis (Behzadi et al. 2007 (link)).

Cogent 2000 software (www.vislab.ucl.ac.uk/cogent_2000.php) implemented in Matlab 2011b (www.mathworks.com) was used for stimulus presentation. The stimuli were presented on a 30” Dell LCD monitor with a screen resolution of 1024 X 768 pixels at a viewing distance of ~100 cm. The stimuli comprised 256 semantically unrelated word pairs (de Chastelaine et al., 2011 (link)). For each participant, four sets of 48 randomly selected pairs of concrete words served as the stimuli for the study phase and the remaining 64 word pairs served as new items for the test phase. Two sets of 48 word pairs were assigned to the angular gyrus stimulation condition, and the remaining two sets were assigned to the vertex (control) stimulation condition. A single test list was created that comprised 128 intact word pairs (32 from each of the four study lists), 64 rearranged word pairs (16 from each of the four study lists), and 64 new word pairs. Rearranged word pairs were created by re-pairing word pairs presented within the same study phase. A randomized stimulus set was created for each participant.
An additional 16 word pairs with similar characteristics to those just described were used as practice stimuli. The practice study list comprised 12 pairs, and the practice test list comprised 8 intact word pairs from the practice study list, 4 rearranged word pairs, and 4 new word pairs.

Magnetic resonance Chemical shift Imaging (CSI) was used to determine extravascular brain Na⁺ content of rat brains with the NMR chemical shift/relaxation reagent Dysprosium triethylenetetraminehexaacetic acid (DyTTHA) as described previously.^{17 (link), 18 (link)} Following ligation of both sides of the renal artery and vein, 250 mmol/L of DyTTHA (Sigma-Aldrich, Louis, MO) was infused intravenously at 0.3 mL/min to achieve a final dose of 1.5 mmol per liter per kg and allowed to equilibrate across the various body compartments for 20 minutes before MCAO. A 7-T Bruker Biospec MRS/MRI system (Bruker) with a double tuned ^{1 (link)}_H/²³Na probe (Doty Scientific, Columbia, SC) was used for Na⁺ CSI imaging. Two-dimensional Na⁺ CSI images were acquired via the standard Bruker CSI protocol with Paravision 2.1 software (Bruker Biospin GmbH, Rheinstetten, Germany) and each ²³Na CSI data set was acquired in 21 minutes. Na⁺ CSI spectra were further analyzed using MATLAB 2011b (MathWorks, Natick, MA) to integrate over the unshifted extravascular Na⁺ peak and that of an external standard to calculate the extravascular Na⁺ concentration in the core of the infarct up to 170 min after MCAO.