scitran/retinotopy-templates

Runs FreeSurfer's Recon-All and applies the retinotopy templates from Benson et al. (2014) PLOS Comput Biol to the generated FreeSurfer subject output.

Atlas of the Occipital Cortex

This Gear applies the V1, V2, and V3 anatomical template of retinotopy from Benson et al. (2014) as well as the ROI template of Wang et al. (2015). Currently this does not use the original version of the Benson et al. template but rather an updated version that has also been published on the website indicated in the original paper.

Author

Noah C. Benson <nben@nyu.edu>

Usage

This docker can be run with the following command:

docker run -v /<INPUT_DIRECTORY>:/flywheel/v0/input/anatomical -v <OUTPUT_DIRECTORY>:/flywheel/v0/output scitran/retinotopy-templates

In the above example, the "/path/to/your/freesurfer/subject" is the path to an individual FreeSurfer subject's directory, not to the path of the FreeSurfer SUBJECTS_DIR environment variable, which generally contains the individual subject's directory. The "/input" is the directory inside of the Docker to which the subject's directory is mapped (this must always be /input).

Note that the Docker expects that you have run the xhemireg and surfreg scripts on your subject after having run recon-all in order to register the subject's left and inverted-right hemispheres to the fsaverage_sym subject. (The fsaverage_sym subject is a version of the fsaverage subject with a single the left-right symmetric pseudo-hemisphere.) If your FreeSurfer version is 5.1 or lower, you can obtain the scripts here. The scripts are generally run as follows (using example subject 'bert'):

# Invert the right hemisphere
xhemireg --s bert
# Register the left hemisphere to fsaverage_sym
surfreg --s bert --t fsaverage_sym --lh
# Register the inverted right hemisphere to fsaverage_sym
surfreg --s bert --t fsaverage_sym --lh --xhemi

Additionally, the Gear may be run as follows to view the license file (see the "License" section below) or this README file.

# View the License:
docker run -ti --rm scitran/retinotopy-templates license
# View the README:
docker run -ti --rm scitran/retinotopy-templates readme

Outputs

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
lh.wang2015_atlas.mgz, rh.wang2015_atlas.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
native.wang2015_atlas.mgz

The volume files are labeled native because they are oriented in FreeSurfer's native LIA orientation (like the orig.mgz volume). Both the angle and eccentricity are measured in degrees (for both hemispheres polar angle is between 0 and 180 (0 is the upper vertical meridian) and eccentricity is between 0 and 90). The areas template specifies visual areas V1, V2, and V3 as the numbers 1, 2, and 3, respectively, and is 0 everywhere else. The angle and eccentricity templates are also 0 outside of V1, V2, and V3.

If you wish to make volume files oriented identically to the original T1 used with FreeSurfer's recon-all command (scanner orientation), the following commands may be run after this Docker has completed; the command assumes that your subject is named "bert" and your FreeSurfer SUBJECTS_DIR environment variable is correctly set:

mri_convert -rl "$SUBJECTS_DIR/bert/mri/rawavg.mgz"            \
            "$SUBJECTS_DIR/bert/mri/native.template_angle.mgz" \
            "$SUBJECTS_DIR/bert/mri/scanner.template_angle.mgz"

Coding for each area in the Wang Atlas

01 - V1v
02 - V1d
03 - V2v
04 - V2d
05 - V3v
06 - V3d
07 - hV4
08 - VO1
09 - VO2
10 - PHC1
11 - PHC2
12 - TO2
13 - TO1
14 - LO2
15 - LO1
16 - V3b
17 - V3a
18 - IPS0
19 - IPS1
20 - IPS2
21 - IPS3
22 - IPS4
23 - IPS5
24 - SPL1
25 - FEF

Dependencies

The computations performed by this Docker use the Neuropythy neuroscience library for Python by Noah C. Benson.

References

Benson NC, Butt OH, Datta R, Radoeva PD, Brainard DH, Aguirre GK (2012) The retinotopic organization of striate cortex is well predicted by surface topology. Curr Biol22(21):2081-5. doi:10.1016/j.cub.2012.09.014
Benson NC, Butt OH, Brainard DH, Aguirre GK (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
Wang L, Mruczek RE, Arcaro MJ, Kastner S (2015) Probabilistic Maps of Visual Topography in Human Cortex. Cereb Cortex 25(10):3911-31. doi:10.1093/cercor/bhu277

License

This README file is part of the occipital_atlas Docker.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. if not, see (http://www.gnu.org/licenses/).

scitran-apps/retinotopy-templates