Hi, Jessica-
If you go into the distributed AFNI_data6/FT_analysis/ directory and type "ls", then you should see these items (some files, some directories; if you have run some scripts, there might be more items):
compare.s05.vs.ex6b README.txt s02.ap.align s07.ap.rest.11 s15.proc.FT.uber.NL
compare.s05.vs.NL results.clustsim.05 s03.ap.surface s09.cleanup s16.proc.FT.rest
FT results.QC_FT.05 s04.cmd.usubj s11.proc.FT s17.proc.FT.rest.11
index.html results.QC_FT.05.NL s05.ap.uber s12.proc.FT.align tutorial
PPI results.QC_FT.rest.11 s05.ap.uber.NL s13.proc.FT.surf
Qwarp s01.ap.simple s06.ap.rest s15.proc.FT.uber
If you aren't seeing all of these, I can only guess that there might have been an error in downloading or unpacking the CD.tgz directory. Perhaps you could move these directories that were unpacked by s2.* in CD/:
AFNI_data5
AFNI_data6
AFNI_demos
afni_handouts
std_meshes
suma_demo
... and then try re-downloading and extracting the files:
curl -O [afni.nimh.nih.gov]
tar xvzf CD.tgz
cd CD
tcsh s2.cp.files . ~
cd ..
--pt
