Dataset of 'Treating amblyopia using altered reality enhances the finescale functional correlations in early visual areas'

Amblyopia is a developmental visual disorder that causes substantial visual deficits. Studies using resting-state functional magnetic resonance imaging (rs-fMRI) have disclosed abnormal brain functional connectivity (FC) both across long-range cortical sites and within the visual cortex in amblyopes, which is considered to be related to impaired visual functions. However, little work has examined whether restoring the vision of amblyopes accompanies with an improvement of FC. Here in adult amblyopes and healthy subjects, we compared their brain FC before and after an altered-reality adaptation training.16 amblyopia patients and 14 healthy subjects participated in this study. Due to a scanner malfunction, the data of one patient were excluded. All participants finished 6 daily sessions of complementary patchwork adaptation using altered-reality (Bao, Dong, Liu, Engel, & Jiang, 2018). Their visual acuity (measured with ETDRS charts) and rs-fMRI data were acquired before (pre-test), one day after (post-test), and one month after (post 1 month, patients only) the training. We assessed how the training would affect the voxel-wise FC in early visual areas (V1-V3) and searched for any altered FC between visual areas and other brain networks.The participants were scanned with a Siemens 3T Magnetom Trio scanner, using a 20-channel phased array head coil. High resolution T1 weighted anatomical images were acquired at the beginning of each session (176 interleaved sagittal slices, repetition time (TR) = 2600 ms, echo time (TE) = 3.02 ms, flip angle = 8°, field of view (FOV) = 256 mm, voxel resolution = 1.0 mm × 1.0 mm × 1.0 mm). Resting state data were obtained after the anatomical scan with T2* weighted Echo-planar imaging (EPI) (TR = 2000 ms, TE = 30 ms, flip angle = 90°, 32 axial slices, FOV = 200 mm, voxel resolution = 3.1 mm × 3.1 mm × 3.5 mm). The rs-fMRI run consisted of 300 whole-brain volumes. Participants fixed on a central white cross on the gray background during the scanning.The rs-fMRI data were analyzed using AFNI software package (https://afni.nimh.nih.gov). Visual areas, including V1, V2 and V3, were identified for each participant based on anatomical templates provided by Benson (https://hub.docker.com/r/nben/occipital_atlas/) (Benson et al., 2018) on the surface of each quadrant. The analysis of FC was performed using customized MATLAB and Python codes.‘amblyopia_IMAdata.zip’ and ‘normal_IMAdata.zip’ contain the raw MRI data with the format of .IMA.‘Amblyopia_fMRIdata.zip’, ‘Normal_fMRIdata.zip’ and ‘analysis scripts.zip’ are the .gz data and scripts we used to acquire the results in the paper (Dong, X., Liu, L., Du, X., Wang, Y., Zhang, P., Li, Z., & Bao, M. (2023). Treating amblyopia using altered reality enhances the fine-scale functional correlations in early visual areas. Human Brain Mapping, 1–12. https://doi.org/10.1002/hbm.26526).