Hi,
Yes, I saw the link and I updated the fs by 'sudo -E fs_update', but still the same error happened.
Thanks for your another tip that '-NIFTI' should be included, I added that option.
Then a little changed error messages poped up.
If there is anything that I missed, please let me know.
Thank you.
Error messages after includeing '-NIFTI'
---------------------------------------------------------------
++ creating directory './SUMA' for results...
-- found 8 LH surfaces
-- found 8 RH surfaces
mri_convert.bin -ot nii /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/mri/orig.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/orig.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/mri/orig.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/orig.nii...
++ created AFNI file './SUMA/sbj1_SurfVol.nii'
Made roi label table for AFNI - fs_table.niml.lt
mri_convert.bin -ot nii mri/T1.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/T1.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/T1.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/T1.nii...
mri_convert.bin -ot nii mri/aparc+aseg.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aparc+aseg.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/aparc+aseg.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aparc+aseg.nii...
++ 3drefit: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc+aseg.nii
+ loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aparc+aseg_rank.nii
++ 3drefit: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_rank.nii
+ loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank.
mri_convert.bin -ot nii mri/aparc.a2009s+aseg.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aparc.a2009s+aseg.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/aparc.a2009s+aseg.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aparc.a2009s+aseg.nii...
++ 3drefit: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc.a2009s+aseg.nii
+ loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii
++ 3drefit: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii
+ loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank.
mri_convert.bin -ot nii mri/aseg.auto.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aseg.auto.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/aseg.auto.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aseg.auto.nii...
mri_convert.bin -ot nii mri/aseg.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aseg.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/aseg.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/aseg.nii...
++ 3drefit: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aseg.nii
+ loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aseg.
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aseg_rank.nii
++ 3drefit: AFNI version=AFNI_17.2.06 (Aug 4 2017) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aseg_rank.nii
+ loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aseg_rank.
mri_convert.bin -ot nii mri/brain.finalsurfs.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brain.finalsurfs.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/brain.finalsurfs.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brain.finalsurfs.nii...
mri_convert.bin -ot nii mri/brain.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brain.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/brain.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brain.nii...
mri_convert.bin -ot nii mri/brainmask.auto.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brainmask.auto.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/brainmask.auto.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brainmask.auto.nii...
mri_convert.bin -ot nii mri/brainmask.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brainmask.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/brainmask.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/brainmask.nii...
mri_convert.bin -ot nii mri/norm.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/norm.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/norm.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/norm.nii...
mri_convert.bin -ot nii mri/nu.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/nu.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/nu.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/nu.nii...
mri_convert.bin -ot nii mri/lh.ribbon.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/lh.ribbon.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/lh.ribbon.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/lh.ribbon.nii...
mri_convert.bin -ot nii mri/rh.ribbon.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/rh.ribbon.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/rh.ribbon.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/rh.ribbon.nii...
mri_convert.bin -ot nii mri/wm.asegedit.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/wm.asegedit.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/wm.asegedit.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/wm.asegedit.nii...
mri_convert.bin -ot nii mri/wm.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/wm.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/wm.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/wm.nii...
mri_convert.bin -ot nii mri/wm.seg.mgz /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/wm.seg.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/wm.seg.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 1.49012e-08, 1.86265e-09)
j_ras = (0, 2.32831e-10, -1)
k_ras = (0, 1, 0)
writing to /Users/minsunpark/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
Trace/BPT trap
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
Trace/BPT trap
c_ras: Subscript out of range.
c_ras: Subscript out of range.
