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=====An anatomical template of human striate and extrastriate retinotopy=====

====General Introduction====

{{ :public:papers:benson_2012_holmes_homage.png?225|}}
The relationship between the folding structure of the brain and cortical visual representation was first described in schematic form by Gordon Holmes in 1918.((Independent work by Tatsui Inouye in 1909 described a similar relationship, although not in the map-like format that made Holmes' result so influential. For a review of this history, see: Ronald S. Fishman (1997). [[http://www.scribd.com/doc/8701098/Gordon-Holmes-the-cortical-retina-and-the-wounds-of-war|Gordon Holmes, the cortical retina, and the wounds of war]]. The seventh Charles B. Snyder Lecture Documenta Ophthalmologica 93: 9-28, 1997.)) This mapping of structure-to-function was further refined based upon lesion analysis ((Horton, JC. and W.E Hoyt: [[http://www.ncbi.nlm.nih.gov/pubmed/2043069|The representation of the visual field in human striate cortex. A revision of the classic Holmes map]]. Arch Ophthalmol 1991; 109: 816--824.)), but remained a general scheme and not a system for individual prediction. An important advance in 2008 was provided by [[http://www.cns.bu.edu/~oph/|Oliver Hinds]], Bruce Fischl, and their colleagues ((Hinds, O.P., Rajendran, N., Polimeni, J.R., Augustinack, J.C., Wiggins, G., Wald, L.L., Diana Rosas, H., Potthast, A., Schwartz, E.L., and Fischl, B. (2008). [[http://www.ncbi.nlm.nih.gov/pubmed/18055222|Accurate prediction of V1 location from cortical folds in a surface coordinate system]]. Neuroimage 39, 1585–1599.)) when they demonstrated that the location of the [[http://en.wikipedia.org/wiki/Line_of_Gennari|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 ([[http://surfer.nmr.mgh.harvard.edu|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 subject((The actual performance of the anatomical template relative to functional mapping is likely still better, as we demonstrate that most of the error in prediction from anatomy may be attributed to error in measurement of retinotopy from the individual.)). 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>.

====Description====

This page provides the templates described in the following papers:

  *  NC Benson, OH Butt, R Datta, PD Radoeva, DH Brainard, GK Aguirre (2012) [[http://www.sciencedirect.com/science/article/pii/S0960982212010779|The retinotopic organization of striate cortex is well predicted by surface topology]]. //Curr. Biol.// **22**(21):2081-5. doi:10.1016/j.cub.2012.09.014
  *  NC Benson, OH Butt, DH Brainard, GK Aguirre (2014) Correction of distortion in flattened representations of the cortical surface allows prediction of V1-V3 functional organization from anatomy. //PLoS Comput. Biol//. **10**(3):e1003538. doi:10.1371/journal.pcbi.1003538

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 [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat|MGH/MGZ format]] suitable for use in [[http://surfer.nmr.mgh.harvard.edu|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):

  * Version 1.0: V1 only. This template was produced by fitting an algebraic model to the aggregate retinotopy measurements from our subject pool. The original wiki page for this version may be found [[data_currbio_2012_benson|here]].
  * Version 2.0: V1-V3. This template was produced by registering the aggregate retinotopy from our subjects to a model of the retinotopic organization of V1-V3 using custom simulation code written in C++. This template was highly accurate but includes some issues, such as attenuation of polar angle near the V1/V2 and V2/V3 reversals. The original wiki page for this template version can be found [[data_ploscomputbiol_2014_benson|here]].
  * Version 2.1: V1-V3. This template was not released outside the Aguirre lab prior to the release of version 2.5, but it has been used in a few publications.
  * Version 2.5: V1-V3. The most recent version of the template includes several improvements over version 2.0. This template was produced by registration of subject data to a model of V1-V3 retinotopy, similarly to version 2.0, but instead of using a C++ simulation program, the entire registration was performed in Mathematica using the open source [[https://github.com/noahbenson/MmaSurfer|MmaSurfer]] library.

We consider the 2.0 and 2.1 versions to be deprecated but will continue to keep them available for comparison and reference.

===File Formats===
The file formats used to distribute the template include:
  * **DAT Files**.  These files contain rows and columns separated by newlines and whitespace.
  * **MGH Files**.  The native file format used by FreeSurfer. All MGH files provided on this page are mapped to the [[data_currbio_2012_benson#symmetric_hemisphere_template|hemisphere-symmetric]] ''fsaverage_sym'' space.

====Downloads====

===Raw Retinotopy Data===

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>

===Version 2.5 (V1, V2, and V3)===

<WRAP LEFT download round box 33%>**Polar Angle**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/angle-template-2.5.sym.mgh|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/eccen-template-2.5.sym.mgh|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/areas-template-2.5.sym.mgh|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/all-template-2.5.sym.mgh|all-template-2.5.sym.mgh]]\\ \\ Angle, Eccentricity, and Visual Area (1st, 2nd, and 3rd frames of the overlay) - fsaverage_sym **MGH** overlay.</WRAP>

==Analysis and Simulation Code (for Template Version 2.5)==

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/extrastriate-analysis-2.5.nb|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/extrastriate-analysis-2.5.pdf|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**\\ \\ [[https://github.com/noahbenson/MmaSurfer|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>

===Version 2.1 (V1, V2, and V3)===

<WRAP LEFT download round box 33%>**Polar Angle**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/angle-template-2.1.sym.mgh|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/eccen-template-2.1.sym.mgh|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/areas-template-2.1.sym.mgh|areas-template-2.1.sym.mgh]]\\ \\ V1, V2, and V3 Area Definitions template - fsaverage_sym **MGH** overlay.</WRAP>

===Version 2.0 (V1, V2, and V3)===

<WRAP LEFT download round box 33%>**Polar Angle**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/angle-template.sym.mgh|angle-template.sym.mgh]]\\ \\ V1, V2, and V3 Polar Angle template - fsaverage_sym **MGH** overlay.</WRAP>

<WRAP LEFT download round box 33%>**Eccentricity**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/eccen-template.sym.mgh|eccen-template.sym.mgh]]\\ \\ V1, V2, and V3 Eccentricity template - fsaverage_sym **MGH** overlay.</WRAP>

<WRAP LEFT download round box 80%>**Visual Areas**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/areas-template.sym.mgh|areas-template.sym.mgh]]\\ \\ V1, V2, and V3 Area Definitions template - fsaverage_sym **MGH** overlay.</WRAP>

==Analysis and Simulation Code (for Template Version 2.0)==

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/extrastriate-analysis.nb|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/extrastriate-analysis.pdf|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**\\ \\ [[https://github.com/noahbenson/SpringRegister|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**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/simulationData10.mov|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>

===Version 1.0 (V1 Only)===

<WRAP LEFT download round box 33%>**Polar Angle**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/V1/mgh_files/mh.V1.poltmp.sym.mgh|mh.V1.poltmp.sym.mgh]]\\ \\ V1 Polar Angle template - fsaverage_sym **MGH** overlay.</WRAP>

<WRAP download round box 33%>**Eccentricity**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/V1/mgh_files/mh.V1.ecctmp.sym.mgh|mh.V1.ecctmp.sym.mgh]]\\ \\ V1 Eccentricity template - fsaverage_sym **MGH** overlay.</WRAP>

<WRAP LEFT download round box 33%>**Normalized Polar Angle**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/V1/mgh_files/mh.V1.polnorm.sym.mgh|mh.V1.polnorm.sym.mgh]]\\ \\ V1 Polar Angle template (Axis Normalized distance)- fsaverage_sym **MGH** overlay.</WRAP>

<WRAP download round box 33%>**Normalized Eccentricity**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/V1/mgh_files/mh.V1.eccnorm.sym.mgh|mh.V1.eccnorm.sym.mgh]]\\ \\ V1 Eccentricity template (Axis Normalized distance)- fsaverage_sym **MGH** overlay.</WRAP>


====Symmetric hemisphere template====

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:

    * Greve, D.N., Sabuncu, M.R., Shafee, R., Schmansky, N., Buckner, R.L., and Fischl, B. (2011). [[http://www.nmr.mgh.harvard.edu/martinos/publications/posters/HBM-2011/HBM11-Greve.pdf|Automatic surface-based interhemispheric registration with FreeSurfer]] (Quebec City, Canada: 17th Annual Meeting of the Organization on Human Brain Mapping, June 26–30, 2011).\\ [ [[http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi|FreeSurfer page describing the hemisphere-symmetric atlas]] ]

Below we describe the steps required to convert data from the standard FreeSurfer atlas to the hemisphere-symmetric template.

==Prerequisities==

To run the data through the combining hemispheres pipeline, 

  - The data should be processed using the cross-sectional stream in FreeSurfer (i.e. ''recon-all -s subjid -autorecon-all'')
  - Use FreeSurfer [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/|version 5.1]] or [[http://surfer.nmr.mgh.harvard.edu/fswiki/Download|version 5.3]] (note that these templates were developed using version 5.1)
  - The xhemi package, which includes scripts (''surfreg'') and an atlas (''fsaverage_sym''), is not part of the standard FreeSurfer 5.1 distribution and should be installed
    - Note that there is a separate installation of the xhemi package for FreeSurfer version 5.1 ([[https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi|xhemi 5.1 instructions]]) and version 5.3, so be sure that you have the correct version of the surfreg scripts
    - For FreeSurfer version 5.3, the xhemi and surfreg packages should be included in the installation
  - ''surfreg'' should be installed in ''<FREESURFER_HOME>/bin/''
  - ''fsaverage_sym'' should be copied to the FreeSufer subject data directory

==Registering to fsaverage_sym==

These 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.

<code>surfreg --s $subject --t fsaverage_sym --lh
surfreg --s $subject --t fsaverage_sym --lh --xhemi </code>

Steps for resampling a subject overlay data to the symmetric hemisphere:

<code=bash - LH resample subject to fsaverage_sym> 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> </code>

<code=bash - RH resample subject to fsaverage_sym> 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> </code>

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:

<code=bash - LH resample fsaverage_sym to subject> 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></code>

<code=bash - RH resample fsaverage_sym to subject> 
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> </code>
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