FSnormals.py

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Return to Source Localization - SAM

Description

The FSnormals.py program will take a FreeSurfer surface, and output a list of all the vertices and their surface normals. Crucially, given an image in ortho/MEG space, as produced by AFNI's 3dTagAlign or orthohull.py, FSnormals.py will rotate the surface normals to MEG space. This program is required for use before sam_coreg can be run. Python must be installed. In addition, you must set the FREESURFER_HOME directory and, optionally, the SUBJECTS_DIR. Note that the default SUBJECTS_DIR is $FREESURFER_HOME/subjects, which is probably not where your images are. In addition to producing the surface normals, FSnormals.py will also preserve the annotation from freesurfer which gives the cortical parcel that any given vertice belongs to.

Usage

FSnormals.py

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