Thanks for the reply. Let me give some more details about my specific setup then.
Freesurfer version from build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Ran it with:
@SUMA_Make_Spec_FS -NIFTI -extra_annot_labels aparc.DKTatlas -sid sub-CSA006 -debug 2
I noticed these lines this time, that also mention the extra label...
++ have 1 extra labels, including as if -extra_fs_dsets
** missing surf input to mris_convert for -extra_fs_dsets
There are no surf files for the DTK atlas.
Output from it:
++ Running @SUMA_Make_Spec_FS version: 2.2.1
++ will track 1 extra annot labels
-- usage okay
-- using start_dir '/projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf'
-- all programs found
-- using surf directory '.'...
-- using orig directory '../mri/orig'...
++ creating directory './SUMA' for results...
-- found 6 LH surfaces
-- lh.smoothwm lh.pial lh.inflated lh.sphere lh.white lh.sphere.reg
-- found 6 RH surfaces
-- rh.smoothwm rh.pial rh.inflated rh.sphere rh.white rh.sphere.reg
mri_convert -ot nii /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/../mri/orig.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/orig.nii
reading from /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/../mri/orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/orig.nii...
++ created AFNI file './SUMA/sub-CSA006_SurfVol.nii'
Made roi label table for AFNI - fs_table.niml.lt
mri_convert -ot nii ../mri/T1.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/T1.nii
reading from ../mri/T1.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/T1.nii...
mri_convert -ot nii ../mri/aparc+aseg.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aparc+aseg.nii
reading from ../mri/aparc+aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aparc+aseg.nii...
mri_convert -ot nii ../mri/aparc.a2009s+aseg.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aparc.a2009s+aseg.nii
reading from ../mri/aparc.a2009s+aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aparc.a2009s+aseg.nii...
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.
mri_convert -ot nii ../mri/aseg.auto.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aseg.auto.nii
reading from ../mri/aseg.auto.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aseg.auto.nii...
mri_convert -ot nii ../mri/aseg.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aseg.nii
reading from ../mri/aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/aseg.nii...
Notice: SessionAtlases.niml already exists, appending to it aseg.
mri_convert -ot nii ../mri/brain.finalsurfs.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brain.finalsurfs.nii
reading from ../mri/brain.finalsurfs.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brain.finalsurfs.nii...
mri_convert -ot nii ../mri/brain.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brain.nii
reading from ../mri/brain.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brain.nii...
mri_convert -ot nii ../mri/brainmask.auto.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brainmask.auto.nii
reading from ../mri/brainmask.auto.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brainmask.auto.nii...
mri_convert -ot nii ../mri/brainmask.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brainmask.nii
reading from ../mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/brainmask.nii...
mri_convert -ot nii ../mri/norm.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/norm.nii
reading from ../mri/norm.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/norm.nii...
mri_convert -ot nii ../mri/nu.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/nu.nii
reading from ../mri/nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/nu.nii...
mri_convert -ot nii ../mri/lh.ribbon.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/lh.ribbon.nii
reading from ../mri/lh.ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/lh.ribbon.nii...
mri_convert -ot nii ../mri/rh.ribbon.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/rh.ribbon.nii
reading from ../mri/rh.ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/rh.ribbon.nii...
mri_convert -ot nii ../mri/wm.asegedit.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/wm.asegedit.nii
reading from ../mri/wm.asegedit.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/wm.asegedit.nii...
mri_convert -ot nii ../mri/wm.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/wm.nii
reading from ../mri/wm.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/wm.nii...
mri_convert -ot nii ../mri/wm.seg.mgz /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/wm.seg.nii
reading from ../mri/wm.seg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (1.86265e-09, 1, -5.82077e-11)
writing to /projectnb/onr/mcmains/razan/fs_data/sub-CSA006/surf/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
Saving lh.smoothwm.asc as a surface
Reading lh.smoothwm.asc ...
Performing affine transform...
Writing surface...
++ lh.smoothwm.gii created
-- running 'mris_convert lh.pial lh.pial.asc'
Saving lh.pial.asc as a surface
Reading lh.pial.asc ...
Performing affine transform...
Writing surface...
++ lh.pial.gii created
-- running 'mris_convert lh.inflated lh.inflated.asc'
Saving lh.inflated.asc as a surface
Reading lh.inflated.asc ...
Performing affine transform...
Writing surface...
++ lh.inflated.gii created
-- running 'mris_convert lh.sphere lh.sphere.asc'
Saving lh.sphere.asc as a surface
Reading lh.sphere.asc ...
Performing affine transform...
Writing surface...
++ lh.sphere.gii created
-- running 'mris_convert lh.white lh.white.asc'
Saving lh.white.asc as a surface
Reading lh.white.asc ...
Performing affine transform...
Writing surface...
++ lh.white.gii created
-- running 'mris_convert lh.sphere.reg lh.sphere.reg.asc'
Saving lh.sphere.reg.asc as a surface
Reading lh.sphere.reg.asc ...
Performing affine transform...
Writing surface...
++ lh.sphere.reg.gii created
-- running 'mris_convert rh.smoothwm rh.smoothwm.asc'
Saving rh.smoothwm.asc as a surface
Reading rh.smoothwm.asc ...
Performing affine transform...
Writing surface...
++ rh.smoothwm.gii created
-- running 'mris_convert rh.pial rh.pial.asc'
Saving rh.pial.asc as a surface
Reading rh.pial.asc ...
Performing affine transform...
Writing surface...
++ rh.pial.gii created
-- running 'mris_convert rh.inflated rh.inflated.asc'
Saving rh.inflated.asc as a surface
Reading rh.inflated.asc ...
Performing affine transform...
Writing surface...
++ rh.inflated.gii created
-- running 'mris_convert rh.sphere rh.sphere.asc'
Saving rh.sphere.asc as a surface
Reading rh.sphere.asc ...
Performing affine transform...
Writing surface...
++ rh.sphere.gii created
-- running 'mris_convert rh.white rh.white.asc'
Saving rh.white.asc as a surface
Reading rh.white.asc ...
Performing affine transform...
Writing surface...
++ rh.white.gii created
-- running 'mris_convert rh.sphere.reg rh.sphere.reg.asc'
Saving rh.sphere.reg.asc as a surface
Reading rh.sphere.reg.asc ...
Performing affine transform...
Writing surface...
++ rh.sphere.reg.gii created
++ have 1 extra labels, including as if -extra_fs_dsets
** missing surf input to mris_convert for -extra_fs_dsets
++ Converting surf dsets: lh.thickness
++ Converting surf dsets: lh.curv
++ Converting surf dsets: lh.sulc
++ Converting surf dsets: rh.thickness
++ Converting surf dsets: rh.curv
++ Converting surf dsets: rh.sulc
++ creating spec file 'sub-CSA006_lh.spec'...
++ created spec file'./SUMA/sub-CSA006_lh.spec'
++ creating spec file 'sub-CSA006_rh.spec'...
++ created spec file'./SUMA/sub-CSA006_rh.spec'
++ creating spec file 'sub-CSA006_both.spec'...
++ created spec file'./SUMA/sub-CSA006_both.spec'
------------------------------------------------------------------
Running MapIcosahedron for both hemispheres at ld values of 141 60
------------------------------------------------------------------
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 sub-CSA006_both.spec -sv sub-CSA006_SurfVol.nii
++ Going to make renumbered ROIs now.
--> done for colorbar and making tissue maps.
See '@SUMA_renumber_FS -help' for description.
++ Running @SUMA_renumber_FS version: 1.6
++ found ./aparc+aseg.nii
++ found ./aparc.a2009s+aseg.nii
++ Renumbering FS whole brain (./aparc+aseg.nii).
++ ... getting gm...
++ ... getting wmat...
++ ... getting csf...
++ ... getting vent...
++ ... getting othr...
++ ... getting unkn...
++ Running checks now.
++ Attaching labeltable to: aparc+aseg_REN_all.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_gm.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_gmrois.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_wmat.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_csf.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_vent.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_othr.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_unkn.nii.gz
++ OK through '2000' dsets.
++ Renumbering FS whole brain (./aparc.a2009s+aseg.nii).
++ ... getting gm...
++ ... getting wmat...
++ ... getting csf...
++ ... getting vent...
++ ... getting othr...
++ ... getting unkn...
++ Running checks now.
++ Attaching labeltable to: aparc.a2009s+aseg_REN_all.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_gm.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_gmrois.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_wmat.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_csf.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_vent.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_othr.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_unkn.nii.gz
++ OK through '2009' dsets.
++ Compressing all remaining .nii files, except for SurfVol.
@SUMA_Make_Spec_FS ... finished
