Folks:
Regarding SUMA's import of FS data using @SUMA_Make_Spec_FS.
I'm 99% certain there's a documentation error in the main SUMA instructions page at:
afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_do1.htm
Section I.D.1.b.i "Creating the specs file for FreeSurfer" says:
[...] "we assume that the .COR images are in LSP order".
This is probably incorrect. FS .COR image data is stored in (R-L, S-I, P-A) order, which I think is RSP in AFNI lingo.
For a visualization:
wideman-one.com/gw/brain/fs/coords/fscoords.htm
The actual script says:
if ( $neuro_ori == 1 ) then
to3d -prefix $afni_prefix -xSLAB 127.5L-R -ySLAB 127.5S-I -zSLAB 127.5P-A $cor_files
else
to3d -prefix $afni_prefix -xSLAB 127.5R-L -ySLAB 127.5S-I -zSLAB 127.5P-A $cor_files
endif
... which appears to have it correct, and contradicts the description in the instructions page.
Graham
