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Last pushed: 2 years ago
Short Description
Applies V1, V2, and V3 retinotopy template from Benson et al. (2014) to a given FreeSurfer subject
Full Description

Deprication Notice

This Docker has been replaced with the nben/occipital_atlas Docker; the new Docker does is smaller (only ~500 MB), faster, independent (although it applies data to a FreeSurfer subject, it does not rely directly on FreeSurfer) and more complete, in that it applies both the Benson et al. (2014) retinotopy atlas as well as the Wang et al. (2015) probabilistic atlas. This Docker will eventually be removed.


This docker applies the V1, V2, and V3 anatomical template of retinotopy from Benson et al. (2014). Currently this does not use the original paper's version of the template but rather an updated version.


Noah C. Benson <>


docker run -ti --rm -v /path/to/your/freesurfer/subject:/input \

The script writes the following surface data files to /path/to/your/freesurfer/subject/surf:

  • lh.template_angle.mgz, rh.template_angle.mgz
  • lh.template_eccen.mgz, rh.template_eccen.mgz
  • lh.template_areas.mgz, rh.template_areas.mgz

It additionally writes out the following volume files to /path/to/your/freesurfer/subject/mri:

  • native.template_angle.mgz
  • native.template_eccen.mgz
  • native.template_areas.mgz
  • scanner.template_angle.mgz
  • scanner.template_eccen.mgz
  • scanner.template_areas.mgz

The latter volume files are oriented as in the subject's rawavg.mgz file while the native volume files are oriented as in orig.mgz (FreeSurfer orientation). Both the angle and eccentricity are measured in degrees (polar angle between 0 and 180 and eccentricity between 0 and 90 for both hemispheres). The areas template specifies visual area (V1, V2, V3) as 1/-1 2/-2, and 3/-3 (to express dorsal and ventral).

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