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 vertex belongs to.
FSnormals.py subject [surface]
The subject argument corresponds to the FreeSurfer subject designation, and denotes a directory under $SUBJECTS_DIR. The surface argument denotes the surface to use: pial, white, or smoothwm. Other options:
|-q||Operate quietly, default is verbose|
|-a annotation||Restrict the output to a single annotation region, denoted by its number (see the corresponding ctab for a list of numbers and regions in the label/ directory of each subject's FreeSurfer directory). To select multiple regions, repeat this command. Note that positive numbers denote the left hemisphere, and negative numbers denote the right.|
|-t ortho+orig||Rotate the output vertices and surface normals into the space defined by the ortho+orig space, in order to use this, ortho+orig must have been generated using the 3dTagAlign command.|
|-i fac||Inflate each vertex according to v' = v + fac * n (-I .001 is 1mm)|
|-r thresh||Use this option to filter out vertices which have near radial normals. The threshold is the absolute value of the dot product of the vertex's position vector (relative to the centroid) with the normal vector, so it ranges from 0 to 1. Large values allow more radial normals, small values (e.g. -r 0.2) pass only more tangential normals.|
|-L, -R, -B||-L or -R means just output the left or right hemisphere, respectively. The default is -B, which will output both.|
|-o outputfule||Specify an output prefix to use. Otherwise, the output defaults to aparc.a2009s.norm, or whatever parcellation is specified by -p.|
The output of FSnormals.py is a single text file, stored in the label subdirectory of the subject's FreeSurfer directory. Each line of the file is a single vertex, and contains seven columns: vx, vy, vz, nx, ny, nz, annot. v x, y, and z are the coordinates in meters. nx, ny, and nz denote the normal vectors. The last number is the annotation or region number, negative for left hemisphere and positive for right.