Dear AFNI team,

I am trying to create spec files to use with SUMA from freesurfer files (generated with recon-all), using @SUMA_Make_Spec_FS. The code seems to run fine, except at the end it produces a bunch of errors and the surfaces look really weird when viewed in SUMA - squashed into a corner and not at all brain-like. I've tried this on 5 different subjects, and the outcome it the same.

So, currently I'm doing:
@SUMA_Make_Spec_FS -sid 003 -fspath 003

where 003 is the directory name containing the /surf/ folder.

I've pasted below the last part of the terminal output where the errors start to appear. Any ideas? Is there something really obvious I'm doing wrong?

AFNI version is AFNI_2011_12_21_1014. Updated in January 2014.

Thanks!

_____________

++ Notice FSread_annot (SUMA_FSread_annot.c:298 @16:14:07):
Guessed FS annot version of 2009
++ Notice FSread_annot (SUMA_FSread_annot.c:310 @16:14:07):
Guessed left hemisphere
++ Notice FSread_annot (SUMA_FSread_annot.c:332 @16:14:07):
Using /usr/local/freesurfer//FreeSurferColorLUT.txt
++ Notice FSread_annot (SUMA_FSread_annot.c:343 @16:14:07):
Setting -FScmaprange to [13100 13199]
++ Notice FSread_annot (SUMA_FSread_annot.c:298 @16:14:07):
Guessed FS annot version of 2009
++ Notice FSread_annot (SUMA_FSread_annot.c:312 @16:14:07):
Guessed right hemisphere
++ Notice FSread_annot (SUMA_FSread_annot.c:332 @16:14:07):
Using /usr/local/freesurfer//FreeSurferColorLUT.txt
++ Notice FSread_annot (SUMA_FSread_annot.c:348 @16:14:07):
Setting -FScmaprange to [14100 14199]
++ created spec file'./SUMA/003_lh.spec'
++ created spec file'./SUMA/003_rh.spec'
++ created spec file'./SUMA/003_both.spec'

------------------------------------------------------------------
Running MapIcosahedron for both hemispheres at ld values of 141 60
++ Notice SUMA_LoadSpec_eng (SUMA_Load_Surface_Object.c:4066 @16:14:21):
Have 0 DOs to load
++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:789 @16:14:21):
Adding -NN_dset_map ./lh.aparc.a2009s.annot.niml.dset


** **
To view in SUMA, run:
suma -spec std.141.003_lh.spec
** **

-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
++ Notice SUMA_LoadSpec_eng (SUMA_Load_Surface_Object.c:4066 @16:15:02):
Have 0 DOs to load
++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:789 @16:15:02):
Adding -NN_dset_map ./rh.aparc.a2009s.annot.niml.dset


** **
To view in SUMA, run:
suma -spec std.141.003_rh.spec
** **

-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
++ Notice SUMA_LoadSpec_eng (SUMA_Load_Surface_Object.c:4066 @16:15:53):
Have 0 DOs to load
++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:789 @16:15:53):
Adding -NN_dset_map ./lh.aparc.a2009s.annot.niml.dset


** **
To view in SUMA, run:
suma -spec std.60.003_lh.spec
** **

-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
++ Notice SUMA_LoadSpec_eng (SUMA_Load_Surface_Object.c:4066 @16:16:03):
Have 0 DOs to load
++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:789 @16:16:03):
Adding -NN_dset_map ./rh.aparc.a2009s.annot.niml.dset


** **
To view in SUMA, run:
suma -spec std.60.003_rh.spec
** **

-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V
-- Error SUMA_SetOverlay_Vecs (SUMA_Color.c:2543):
NULL input
-- Error SUMA_FreeOverlayPointer (SUMA_Color.c:6260):
Failed to clear T/V

------------------------------------------------------------------
Please verify that the datasets are aligned properly in both
afni and suma. You may do this by running the following commands:

cd ./SUMA
afni -niml &
suma -spec 003_both.spec -sv 003_SurfVol+orig

@SUMA_Make_Spec_FS ... finished