Refinement of RF position across time for VD and HC.

(A) Average phase maps obtained for 4 different slices of VD and HC at the 4 measured time points (t = 0, t = 7d, t = 17d, and t = 27d). (B) Variation of the pRF estimated phase as function of the cortical distance across gradient direction, shown in Fig F in S1 Text, measured for the SC of HC (green) and VD (orange) across multiple time points (t = 0, t = 7d, t = 17d, and t = 27d). The green and orange lines correspond to the linear fit for HC and VD, respectively. (C) Violin plot of the slope of the correlation between the pRF phase variation and cortical distance measured for HC and VD, for each ROI (LGN, SC, and VC) for multiple time points (t = 0, t = 7d, t = 17d, and t = 27d). Each dot corresponds to a different animal. Only the animals that performed the 4 scanning sessions were included in the analysis. The *** represents a p-value p-value p-value 10.18112/openneuro.ds004509.v1.0.0. HC, healthy control; LGN, lateral geniculate nucleus; pRF, population receptive field; RF, receptive field; ROI, region of interest; SC, superior colliculus; VC, visual cortex; VD, visual deprivation.</p

Spatial frequency selectivity across the visual pathway in HC animals at t = 0.

(A) Anatomical images with the ROIs highlighted. (B) Optimal SF estimated per voxel for HC, averaged across animals. (C) Maximum PSC during the activation period as a function of the SF of the stimulus, calculated for HC. The error bar represents the 10% confidence interval across animals. The continuous lines represent the Gaussian model fitted to the data. The goodness of fit is shown in Table D in S1 Text. The orange band denotes the range of optimal SF values reported in the literature measured using electrophysiology. A compilation of 22 studies reporting on the optimal SF of the rat and mouse visual pathway can be found in Table C in S1 Text. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. HC, healthy control; PSC, percentage signal change; ROI, region of interest; SF, spatial frequency.</p

Visual experience following VDM promotes the specialization of spatial frequency tuning curves.

(A) Optimal SF estimated per voxel obtained for 4 different slices of HC and VD, at t = 0, t = 7d, t = 17d, and t = 27d, respectively. (B) Maximum PSC during the activation period as a function of the SF of the stimulus, calculated for each ROI (LGN, SC, and VC) of VD (orange) and HC (green) at the 4 measured time points. The error bar represents the std. The continuous lines represent the Gaussian model fitted to the data. (C, D) Estimated optimal SF (Gaussian center, panel C) and broadness of the SF tuning curve (Gaussian width, panel D) for the LGN, SC, and VC at t = 0, t = 7d, t = 17d, and t = 27d for HC and VD. The error bar corresponds to std. The *** represents a p-value p-value p-value 10.18112/openneuro.ds004509.v1.0.0. HC, healthy control; LGN, lateral geniculate nucleus; PSC, percentage signal change; ROI, region of interest; SC, superior colliculus; SF, spatial frequency; VC, visual cortex; VD, visual deprivation; VDM, visual deprivation model.</p

S1 Text -

Fig A in S1 Text. Photographs of the visual setup mounted to an MRI animal cradle. Animal life-support equipment: temperature and respiration sensors, subcutaneous catheter, and homeothermic water blanket were connected to the cradle. The surface coil was placed on the head of the rats and the preamplifier was placed behind the animal. The visual stimulus was projected to a mirror that reflected the image to the screen placed in front of the animal eyes. Fig B in S1 Text. Retinotopic and SF tuning visual stimuli result in robust BOLD signals confined to the visual pathway in HC at t = 0. A, B, and E: Percentage of BOLD signal change (PSC) of the ROIs defined in D averaged across animals, runs (B), and cycles (A, E), upon retinotopic (A, B) and SF tuning (E) visual stimulation. The colored areas correspond to the 95% confidence interval and the gray area to the stimulation period. C and F: GLM functional maps obtained after retinotopic (C) and SF tuning (F) visual stimulation. The maps are FDR corrected using a p-value of 0.001 and minimum cluster size of 20 voxels. The ROIs defined based on the SIGMA atlas are overlaid on the functional maps. D: Anatomical images with the delineation of the ROIs. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Fig C in S1 Text. Differential responses between VD animals and HC driven by the SF tuning stimulus. A: Raw fMRI images with the ROIs (LGN, SC, and VC) overlaid. B, E, H, K: fMRI activation patterns of t-contrast maps obtained for HC and VD animals at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The GLM maps are FDR corrected using a p-value of 0.001 and minimum cluster size of 20 voxels. C, F, I, L: PSC of the LGN, SC and VC for the HC and VD animals at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The gray area represents the stimulation period. D,G, J, M: Violin plot of the amplitude of the BOLD response of VD and HC during the total duration of the activation period obtained with the SF tuning stimulus (right) at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The white dot represents the mean, and the gray bar represents the 25% and 75% percentiles. The blue, yellow, and red colors represent the VC, LGN, and SC, respectively. The *** represents a p-value p-value p-value 10.18112/openneuro.ds004509.v1.0.0. Fig D in S1 Text. Differential responses between VD animals and HC driven by the retinotopic stimulus. A: Raw fMRI images with the ROIs (LGN, SC, and VC) overlaid. B, E, H, K: fMRI activation patterns of t-contrast maps obtained for HC and VD animals at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The GLM maps are FDR corrected using a p-value of 0.001 and minimum cluster size of 20 voxels. C, F, I, L: PSC of the LGN, SC, and VC for the HC and VD animals at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The gray area represents the stimulation period. D, G, J, M: Violin plot of the amplitude of the BOLD response of VD and HC during the total duration of the activation period obtained with the SF tuning stimulus (right) at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The white dot represents the mean, and the gray bar represents the 25% and 75% percentiles. The blue, yellow, and red colors represent the VC, LGN, and SC, respectively. The *** represents a p-value p-value p-value 10.18112/openneuro.ds004509.v1.0.0. Fig E. Spatial frequency selectivity across the visual pathway in HC animals at t = 0. A: Anatomical images with the ROIs highlighted. B: Optimal spatial frequency estimated per voxel for HC, averaged across animals. C: Maximum PSC during the activation period as a function of the spatial frequency of the stimulus, calculated for HC. The error bar represents the 10% confidence interval across animals. The continuous lines represent the Gaussian model fitted to the data. The goodness of fit is shown in Table D. The orange and red bands denote the range of optimal spatial frequency values reported in the literature measured using electrophysiology for rats and mice, respectively. A compilation of 22 studies reporting on the optimal spatial frequency of the rat and mouse visual pathway can be found in Table C. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Fig F in S1 Text. Gradient direction for VC, LGN, and SC. Fig G in S1 Text. Quantification of the topographical organization of the visual pathway. A: pRF profiles of 2 adjacent pRFs. B: Distance matrix of all the SC voxels. C: PRF similarity analysis of all SC voxels averaged for all the animals. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Fig H in S1 Text. PRF estimates in the AC, MC, and BG. A and B: Violin plots of the variance explained calculated for visual areas (VC, LGN, and SC) and for areas not visually responsive (AC, MC, and BG) for HC and VD, respectively. C: Anatomical image with the ROIs AC, MC, and BG overlapped. D: PRF profiles obtained for HC and VD animals (left and right, respectively) for AC, MC, and BG. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Fig I in S1 Text. Hypercapnia experiment testing the dynamics of vascular responses. A: Hypercapnia paradigm consisted of a manual switch, after 1.5 min of medical air, to a hypercapnic state with 6.5% CO2 for 1.5 min. This was followed by a manual switch again to medical air for 1.5 min. Each run consisted in only 1 repetition of this block. B, C, and D: PSC response profile (mean ± std) obtained for VD (red) and HC (blue) for different ROIs: VC, LGN, and SC, respectively. The shaded gray area indicates the hypercapnic period. E, F and G: Normalized PSC response profile (mean ± std) obtained for VD (red) and HC (blue) for different ROIs: VC, LGN, and SC, respectively. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Table A in S1 Text. Statistical analysis HC vs. VD BOLD changes. P-values associated with the ANOVA Bonferroni corrected for multiple comparisons (brain areas and sessions) statistical analysis of the BOLD amplitude changes between HC and VD in response to the retinotopic stimulus (Fig 4). The data underlying this table can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Table B in S1 Text. P-values obtained for the pRF size changes between HC and VD, calculated using ANOVA Bonferroni corrected for multiple comparisons (brain areas and sessions). The data underlying this table can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Table C in S1 Text. Summary of the optimal spatial frequency measured for rat and mice across multiple studies. The rat studies used to define the reference interval of Fig 3 are highlighted in yellow. Table D in S1 Text. Pearson’s coefficient between the maximum BOLD response to each SF and the Gaussian fit. The data underlying this table can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. Table E in S1 Text. Fraction of voxels excluded by the variance explained threshold. The data underlying this table can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. (DOCX)</p

Differential responses between VD animals and HC driven by the retinotopic stimulus.

(A) Raw fMRI images with the ROIs (LGN, SC, and VC) overlaid. (B, E, H, K) fMRI activation patterns of t-contrast maps obtained for HC and VD animals at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The GLM maps are FDR corrected using a p-value of 0.001 and minimum cluster size of 20 voxels. (C, F, I, L) PSC of the LGN, SC, and VC for the HC (green) and VD (orange) animals at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The gray area represents the stimulation period. (D, G, J, M) Violin plot of the amplitude of the BOLD response of VD and HC during the initial 10 s of the activation period (left) and the total duration of the activation period obtained with the retinotopy stimulus (right) at t = 0, t = 7d, t = 17d, and t = 27d, respectively. The white dot represents the mean, and the gray bar represents the 25% and 75% percentiles. The yellow, red, and blue colors represent the LGN, SC, and VC, respectively. The *** represents a p-value p-value p-value p-values are reported in Table A in S1 Text. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. fMRI, functional magnetic resonance imaging; HC, healthy control; LGN, lateral geniculate nucleus; PSC, percentage signal change; ROI, region of interest; SC, superior colliculus; VC, visual cortex; VD, visual deprivation.</p

PRF estimates of HC animals across ROIs and cortical layers at t = 0.

(A) Phase maps averaged across animals obtained for VC, LGN and SC, respectively. The color bar shows the preferred angle estimated per each voxel. (B) Visual representation of 2 pRF profiles located in the left and right hemispheres, respectively. The color bar shows the VE of each individual probe. (C) Average visual field reconstruction maps across animals for VC (obtained by summing the RF maps across some voxels of VC) and an image of the visual setup depicting the portion of the field of view covered by the animal bed. (D) Profile of the pRF size across cortical depth averaged across subjects, obtained from 2 slices of the VC. The green area corresponds to the 10% confidence interval. (E) Visual representation of 8 pRF profiles located across layers of the VC. (F) pRF size maps averaged across animals in 4 different slices of the VC. The color bar corresponds to the degree of visual angle. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. HC, healthy control; LGN, lateral geniculate nucleus; pRF, population receptive field; RF, receptive field; ROI, region of interest; SC, superior colliculus; VC, visual cortex; VE, variance explained.</p

The complex visual stimuli setup for preclinical MRI scanners, stimulation paradigms, and scheme of the dark rearing timeline.

(A) Visual stimulus display setup. (B) Picture of the visual stimulus displayed inside the scanner. (C) The retinotopy stimulation paradigm: checkerboard bar moving in 8 different directions (2 directions per stimulation block during 36 s followed by a 45 s rest period, repeated 4 times). (D) The SF tuning paradigm: 15 s stimulation period followed by a 45 s baseline. Ten different SFs were randomly presented at each stimulation block ranging between 0.003 and 0.5 cpd. (E) Timeline of the visual deprivation experiment for HCs and visually deprived (VD) animals. HC, healthy control; MRI, magnetic resonance imaging; SF, spatial frequency; VD, visual deprivation.</p

Refinement of RF size across time for VD and HC.

(A) Average pRF size measured for HC and VD at multiple time points for VC, LGN, and SC. The error bar corresponds to std. The ** represents a p-value p-value p-values are detailed in Table B in S1 Text. (B) Variation of the pRF size averaged across animals as a function of the cortical depth for 2 slices of the VC for VD and HC at multiple time points. The data underlying this figure can be found here: doi:10.18112/openneuro.ds004509.v1.0.0. HC, healthy control; LGN, lateral geniculate nucleus; pRF, population receptive field; RF, receptive field; SC, superior colliculus; VC, visual cortex; VD, visual deprivation.</p

Mean ± SD and coefficient of variation for 6MWT Actual and 6MWT Predicted using different validated regression equations.

<p>*P<0.01, significantly different to actual.</p><p>Mean ± SD and coefficient of variation for 6MWT Actual and 6MWT Predicted using different validated regression equations.</p

Pearson’s product moment correlation coefficients between 6MWT Actual and 6MWT Predicted using different validated regression equations.

<p>*P<0.05.</p><p>**P<0.01.</p><p>Pearson’s product moment correlation coefficients between 6MWT Actual and 6MWT Predicted using different validated regression equations.</p