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getting_started:loreta [2017/08/17 11:21] (current)
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 +====== Getting started with LORETA ======
 +LORETA-KEY is a software program implemented by Roberto Pascual-Marqui that implements the LORETA source localization algorithm ("low resolution brain electromagnetic tomography"​). The software is available from the [[http://​www.unizh.ch/​keyinst/​NewLORETA/​LORETA01.htm|LORETA home page]]. Using LORETA-KEY, you can make a distributed source reconstruction for EEG data, using a three-shell spherical head model registered to a standardized stereotactic space (based on MNI brain). The source reconstruction is restricted to cortical gray matter.
 +The LORETA2FIELDTRIP function can be used to read in the resulting files (*.slor, *.lorb) from the LORETA-KEY software. The output of the LORETA2FIELDTRIP function is a matlab structure that is equivalent to the structures that result from the **[[reference:​ft_sourceanalysis]]** function in FieldTrip. Hence, you can use its output as input in the FieldTrip **[[reference:​ft_sourcegrandaverage]]** and/or **[[reference:​ft_sourcestatistics]]** functions. ​
 +Using sourcestatistics,​ you can perform a random-effect parametric or non-parametric statistical test based on a single-voxel statistic or based on a spatio-temporal cluster statistic (only non-parametric). Both the parametric and non-parametric statistical tests implemented in FieldTrip have support for correcting for the multiple comparison problem.
 +===== STEPS =====
 +To use sLORETA data in FieldTrip, you need to do the following steps.
 +==== Convert the sLORETA source to a text file ====
 +  - In the LORETA program, you go to main utilities > Format converter.
 +  - There you select: input binary file (sLORETA)
 +  - It does not matter which format for output you choose, the code will figure it out. In the text file, rows are the time points, columns are the volume-gridpoints (called voxels).
 +  - After using loreta2fieldtrip the data is in [[http://​fieldtrip.fcdonders.nl/​reference/​ft_datatype_volume| FieldTrip volume]] format in [[faq:​how_are_the_different_head_and_mri_coordinate_systems_defined?​s[]=mni#​details_of_the_mni_coordinate_system|MNI space]].
 +==== Hints on plotting the LORETA source ====
 +For use in **[[reference:​ft_sourceplot]]** with method //"​slice"//​ or //"​ortho"//​ you can use the MNI template as anatomy
 +  ​
 +  % Read in the MNI template from SPM:
 +  template = ft_read_mri([cur_path_FT,​ '​\external\spm8\templates\T1.nii'​]); ​
 +  ​
 +  % Interpolate your LORETA volume on the MNI template: ​
 +  [interp_mean] = ft_sourceinterpolate(cfg,​ GA_mean, template);
 +For method //"​surface"//​ you don't need to interpolate. However, you have to use a large sphereradius (15 for instance) to pull the source to plot nicely on the surface.
 +      ​
 +Also see the [[tutorial/​plotting#​plotting#​plotting_data_at_the_source_level|plotting tutorial]].