Hello list,
a few quick questions about the format of coords_for_fdt_matrix* and fdt_matrix3.dot:
1) The file looks something like
57 69 27 0 1
57 70 27 0 2....
Are these the X/Y/Z coords of voxel number n, while n is in the 5th column? Is the 4th column always 0?
first 3 numbers are coordinates in SEED space. 4th is your ROI id (if you only have one roi then it's always 0 - this is useful when your roi, in this case target3, is composed of several combinations of surface and volume rois). the 5th column is the index of the different locations, i.e. vertices or voxels, within each roi).
2) is n the same number/reference which is in the 1st and 2nd column of "fdt_matrix3.dot" (i.e. a unique voxel identifier)?
yes
3) What are the origin and space of this coordinate system? Is it diffusion space (same space as fdt_paths.nii.gz), and is the origin (0,0,0) or (1,1,1)?
see (1). if your roi is a volume roi, then the coordinates are the same are those shown in fslview (voxels).
Cheers
Saad
Thanks a lot,
Nicola