Ernie Tutorials

An end-to-end sequence of tutorials on an example data set

These tutorials download (a) a freesurfer directory, and (b) a sample data set. The freesurfer directory will be copied to your local freesurfer subjects directory. The sample data set will be placed in your vistasoft/local directory. The sameple data set contains a fully processed mrVista session, including the mrSESSION file, pre-processed data, meshes and class files, pRF model solutions, and so on. The tutorials below show, step-by-step, how this fully processed session is created.

Volume anatomy, classification file, and meshes

These tutorials require that you have freesurfer paths available in Matlab. They generate the volume anatomy, class file, meshes, and ROIs, starting from a sample freesurfer directory, which is downloaded in the first tutorial. To run one of the tutorials just type the name at the Matlab command prompt. This assumes you have vistasoft on your path.

• t_initAnatomyFromFreesurfer
• t_meshFromFreesurfer

MRVISTA Initialization and preprocessing

These tutorials initialize a vistasession from raw MRI files, and then preprocess the data.

• t_initVistaSession
• t_alignInplaneToVolume
• t_installSegmentation
• t_sliceTiming
• t_motionCorrection
• t_averageTSeries

Atlases, ROIs, and Population Receptive field modeling

These tutorials set up and solve pRF models.

• t_atlasAndTemplates
• t_pRF
• t_pRFInplane (In development; Currently produces an error)
• t_ROIAnalysis

TODOs

• Tutorial to predict responses from pRF model for a different stimulus
• Publish tutorials by code
• Error in t_pRFInplane
• Visualization tutorials based on results of pRF models