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
• t_bensonTemplate (NYI)
• t_wangAtlasROIs (NYI)

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

Population Receptive field modeling

These tutorials set up and solve pRF models.

• t_pRF
• t_pRFInplane

TODOs

• viewSet is in conflict between vistasoft and the vision toolbox in new Matlab (9.1)
• Two NYI tutorials above (benson template and wang atlas) ** To do so, we probably first want to make loadROI compatible with NIFTIs. This will make it easy to read in as ROIs the volume label files created by Noah's docker (wang atlas and benson areas) as vistasoft ROIs. For the volume data files (benson angle data and eccentricity data), loadParameter map can already do what we need.
• 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