tutorials

Vistasoft tutorials operate on sample data sets. Accessing the sample data sets is handled through the function mrtInstallSampleData, which depends on the Remote Data Toolbox. The tutorial code is organized in the vistasoft/tutorials directory.

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

This is a sequence of tutorials that goes through several steps of processing on a sample data set. It begins by getting anatomical files from Freesurfer, then initializes a vistasession, then precosseses the data, then runs a pRF model.

• t_initAnatomyFromFreeSurfer
  • get the anatomical files and create a volume nifti and a grey/white boundary nifti
• t_initVistaSession
  • initialize a mrVista session
• t_alignInplaneToVolume
  • align the inplanes to the volume anatomy
• functional preprocessiong
  • motion correction, clip time series, smoothing etc....
• install the segmentation as gray
  • some choices here
• transform timeseries from the inplanes to the volume/gray
• t_glmRun
  • fit a GLM
• fit the pRF model
• build a mesh and view the fits

Video tutorials

• A small but growing collection of video tutorials

Tutorials by category

• anatomy
  • for ubuntu version 14.04, mri_convert across multiple versions of freesurfer produces a segmentation fault as discussed here
• bold
• diffusion
• mesh

Additional directories (which may go away):

• fileFilters
• sdm
• xforms