MOpt3d
mopt3d.m - Matlab 3D-reconstruction of OPTical imaging data
Copyright (c) 2014 All Right Reserved Dr. Kyle Mathewson, Postdoctoral Fellow, Beckman Institute kylemath@gmail.com April 24/2014 - University of Illinios
Translated to matlab based on original fortran 90 code opt3d_fast_v2.f90 by Dr. Gabriele Gratton
mopt3d.m is a wrapper function that sets the paramaters and calls the fucntions to:
Run the code by running '''mopt3d''' in the command line. Change settings inside the mopt3d script. You will at least have to change the experiment name and data path.
- Load in location information from .mtg and .rol/.tol files -readloc_new.m - no longer needs a .loc text file, finds files based on parameters
- Create photon density maps (banana paths) for each "channel", for each subject -slices.m, look_slice.m, setuplook.m, in_lookup.m
- Plots these maps on individual and common space anatomy -plot_banans.m, -load_anat.m
- Saves these photon density maps as .nii briks for plottin in outside programs (freesurfer) -write_freesurer_nii.m
- Convert this information to a voxel lookup table -convert2vox.m
- Loads in pc##-##/.avm or pc##-##.00# files created by PPOD -import_avm.m, -import_ppod.m
- Analyzes the continuous or averaged data -anal_avm.m, -anal_retinotopy.m
- Plots the results of the analysis on individual and group anatomy -plot_anal_avm.m, -plot_anal.m
- Saves a .nii brik of the data for plotting in outside programs (freesurfer) -write_freesurer_nii.m
All of the parameters, as well as steps 1 and 2 are direct translations of the algorithm used in opt3d_fast_v2.f90, with some computations converted to vector computations to speed up the code. However, this code differs in that it cycles through EVERY SLICE to make a 3D brik of the data
Please see Documentation/html/opt3dmat_functions_variables.html for more detailed information