The relationship between the folding structure of the brain and cortical visual representation was first described in schematic form by Gordon Holmes in 1918.1) This mapping of structure-to-function was further refined based upon lesion analysis 2), but remained a general scheme and not a system for individual prediction. An important advance in 2008 was provided by Oliver Hinds, Bruce Fischl, and their colleagues 3) when they demonstrated that the location of the stria of Gennari (an anatomical marker of primary visual cortex) may be accurately predicted with reference to cortical surface topology. This provided a means of aligning the edges of primary visual cortex across individuals using a surface based atlas (FreeSurfer). We have now shown that the retinotopic organization of different people is well aligned within primary visual cortex once transformed to the surface atlas space (and following some basic surface transformations). Moreover, we can use a simple algebraic form to fit these functional data on the cortical surface and successfully extend the prediction beyond the mapping data.
Practically, we find that cortical surface anatomy predicts the retinotopic organization of area V1 at least as accurately as a 10-25 minute, retinotopic mapping fMRI scan at 3 Tesla conducted in a young, cooperative subject4). Additionally, as the retinotopic organization of left and right area V1 within the template space is highly similar and statistically independent, the measures from the two hemispheres may be treated as separate subjects.
Please refer any questions to aguirreg@mail.med.upenn.edu.
This page provides the templates described in the following papers:
This page describes a template of the human brain that can be used to predict with known accuracy and precision the retinotopic organization of early visual cortical areas V1, V2, and V3 based upon the sulcal topology of the cortical surface.
The template is comprised of cortical surface representations in MGH/MGZ format suitable for use in FreeSurfer. This page provides links to download these files, access to the raw data used to construct the template, and additional information about the template not reported in the paper.
The template is free to use (with appropriate attribution) for academic or commercial purposes. The atlas may not be distributed for commercial gain.
The template has, at this point, gone through a number of iterations and improvements. The original template, published in Current Biology in 2012, included only the polar angle and eccentricity predictions for area V1. In 2014, we updated the template to include areas V2 and V3; this template was constructed with a much different method, the details of which have been published in PLOS Computational Biology (see above citations). In brief, while the original V1 template was purely algebraic, the updated template uses a model of V1-V3 retinotopy and makes a prediction by registering the aggregate retinotopy of our subjects, as represented on FreeSurfer's fsaverage_sym left-right symmetric pseudo-hemisphere, to the model.
Since we published this V1-V3 template in early 2014, we have continued to improve our registration methods and model parameterization. As of October 2014, the following templates have been produced (details below):
We consider the 2.0 and 2.1 versions to be deprecated but will continue to keep them available for comparison and reference.
The file formats used to distribute the template include:
fsaverage_sym
space.We provide the raw retinotopy data for each of our retinotopy subjects in a tab-delimited data file with six columns. The colums are x, y, z, t, r, f where x, y, z are the 3D coordinates of a point on the FreeSurfer fsaverage_sym hemisphere, t is the polar angle (in absolute degrees), r is the eccentricity in degrees, and f is the F-statistic of the polar angle and eccentricity assignment. If the F-statistic is 0, then the t and r columns should be considered unassigned. In the case of subjects from the 20° dataset, because their retinotopy was measured using rings and wedges, eccentricity and polar angle were assigned in separate model fits and thus have separate F-statistics; accordingly, subjects from the 20° dataset have an additional column, with the last two columns being the polar angle and eccentricity F-statistic values, respectively.
<WRAP LEFT download round box 80%>Link to downloadable raw retinotopy data
https://cfn.upenn.edu/aguirreg/public/V1/data/
Raw retinotopy data - tab delimited tables - link to directory listings.</WRAP>
<WRAP LEFT download round box 33%>Polar Angle
angle-template-2.5.sym.mgh
V1, V2, and V3 Polar Angle template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Eccentricity
eccen-template-2.5.sym.mgh
V1, V2, and V3 Eccentricity template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Visual Areas
areas-template-2.5.sym.mgh
V1, V2, and V3 Area Definitions template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Angle, Eccentricity, and Areas
all-template-2.5.sym.mgh
Angle, Eccentricity, and Visual Area (1st, 2nd, and 3rd frames of the overlay) - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Download
extrastriate-analysis-2.5.nb
Mathematica notebook containing all analysis and visualization code for template version 2.5 - Mathematica notebook (.nb) format.</WRAP>
<WRAP LEFT download round box 33%>Download
extrastriate-analysis-2.5.pdf
PDF rendering of the Mathematica analysis notebook containing all analysis and visualization code for this project. This file includes code and figures..</WRAP>
<WRAP LEFT download round box 80%>GitHub Repository
MmaSurfer Library
MmaSurfer GitHub repository. MmaSurfer is an open source Mathematica library for use with FreeSurfer and for registering data on the cortical surface to 2D map-like models. </WRAP>
<WRAP LEFT download round box 33%>Polar Angle
angle-template-2.1.sym.mgh
V1, V2, and V3 Polar Angle template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Eccentricity
eccen-template-2.1.sym.mgh
V1, V2, and V3 Eccentricity template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Visual Areas
areas-template-2.1.sym.mgh
V1, V2, and V3 Area Definitions template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Polar Angle
angle-template.sym.mgh
V1, V2, and V3 Polar Angle template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Eccentricity
eccen-template.sym.mgh
V1, V2, and V3 Eccentricity template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 80%>Visual Areas
areas-template.sym.mgh
V1, V2, and V3 Area Definitions template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Download
extrastriate-analysis.nb
Mathematica notebook containing all analysis and visualization code for this project - Mathematica notebook (.nb) format.</WRAP>
<WRAP LEFT download round box 33%>Download
extrastriate-analysis.pdf
PDF rendering of the Mathematica analysis notebook containing all analysis and visualization code for this project. This file includes code and figures..</WRAP>
<WRAP LEFT download round box 80%>GitHub Repository
SpringRegister
C++ source code for the mass-spring-damper simulation engine used to register the functional data to the Schira model is freely available at the gitHub repository noahbenson/SpringRegister. </WRAP>
<WRAP LEFT download round box 80%>Download
simulationData10.mov
Spring simulation movie (QuickTime). This movie shows the positions of the vertices, colored by aggregate measured polar angle, during the spring simulation used in this paper. The aggregate was produced using the 10° dataset. Note that the level of confidence in each vertex is also shown by blending the polar angle color with the cortical surface color in the case of low-confidence measurements.
The movie shows every 50th frame of the simulation.</WRAP>
<WRAP LEFT download round box 33%>Polar Angle
mh.V1.poltmp.sym.mgh
V1 Polar Angle template - fsaverage_sym MGH overlay.</WRAP>
<WRAP download round box 33%>Eccentricity
mh.V1.ecctmp.sym.mgh
V1 Eccentricity template - fsaverage_sym MGH overlay.</WRAP>
<WRAP LEFT download round box 33%>Normalized Polar Angle
mh.V1.polnorm.sym.mgh
V1 Polar Angle template (Axis Normalized distance)- fsaverage_sym MGH overlay.</WRAP>
<WRAP download round box 33%>Normalized Eccentricity
mh.V1.eccnorm.sym.mgh
V1 Eccentricity template (Axis Normalized distance)- fsaverage_sym MGH overlay.</WRAP>
The polar angle and eccentricity templates are stored as a FreeSurfer overlay (MGH) file sampled for the hemisphere-symmetric fsaverage_sym
surface space. The hemisphere-symmetric atlas was created by Douglas Greve and colleagues and is described in this conference abstract:
Below we describe the steps required to convert data from the standard FreeSurfer atlas to the hemisphere-symmetric template.
To run the data through the combining hemispheres pipeline,
recon-all -s subjid -autorecon-all
)surfreg
) and an atlas (fsaverage_sym
), is not part of the standard FreeSurfer 5.1 distribution and should be installedsurfreg
should be installed in <FREESURFER_HOME>/bin/
fsaverage_sym
should be copied to the FreeSufer subject data directoryThese two steps first mirror reverses the right hemisphere of the subject, and then registers the surface to the left hemisphere. The data are therefore cast within a pseudo-left hemisphere space.
surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi
Steps for resampling a subject overlay data to the symmetric hemisphere:
mri_surf2surf --srcsubject <subject> --srcsurfreg fsaverage_sym.sphere.reg --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval <lh.data.mgh> --tval <lh.data.sym.mgh>
mri_surf2surf --srcsubject <subject>/xhemi --srcsurfreg fsaverage_sym.sphere.reg --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval <rh.data.mgh> --tval <rh.data.sym.mgh>
Note that the above code accomplishes the transformation of a subject's specific surface topology to the fsaverage_sym topology. If you wish to, for example, compare the polar angle predictions in V1 with the BOLD activation pattern from an fMRI experiment, you will need to either inverse this transform, such that the polar angle data is resampled to the subject's specific space, or transform your subject's BOLD activation data to the fsaverage_sym sphere as well.
To transform the fsaverage_sym template files to match your subject's specific topology, the following code should be used:
mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject <subject> --trgsurfreg fsaverage_sym.sphere.reg --hemi lh --sval <lh.data.sym.mgh> --tval <lh.data.mgh>
mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject <subject>/xhemi --trgsurfreg fsaverage_sym.sphere.reg --hemi lh --sval <rh.data.sym.mgh> --tval <rh.data.mgh>