External Email - Use Caution
Hi
I've tried to run @SUMA_Make_Spec_FS in afni but I've kept getting this error message (which is written at the end of this email). I'm using Mac (high sierra 10.13.6), the latest afni, XQuartz(2.10.11). Using Freesurfer I made a flattened map by running recon-all and tksurfer without any problems. I disabled SIPs and updated Freesurfer (as recommended in this link: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-April/061591.html ).
I'd appreciate if you give any suggestions I can do!
######
bash-3.2$ @SUMA_Make_Spec_FS -fspath ./ -NIFTI -sid 060717KHW
++ creating directory './SUMA' for results...
-- found 8 LH surfaces
-- found 8 RH surfaces
mri_convert.bin -ot nii /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz...
TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00
i_ras = (-1, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii...
++ created AFNI file './SUMA/060717KHW_SurfVol.nii'
Made roi label table for AFNI - fs_table.niml.lt
mri_convert.bin -ot nii mri/T1.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii...
mri_convert.bin -ot nii mri/aparc+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii...
++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [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
+ setting labeltable
+ loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [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_19.2.21 (Aug 29 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_rank.nii
+ setting labeltable
+ 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 /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii...
++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [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
+ setting labeltable
+ 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_19.2.21 (Aug 29 2019) [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_19.2.21 (Aug 29 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii
+ setting labeltable
+ 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 /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii...
mri_convert.bin -ot nii mri/aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii...
++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [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
+ setting labeltable
+ 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_19.2.21 (Aug 29 2019) [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_19.2.21 (Aug 29 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aseg_rank.nii
+ setting labeltable
+ 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 /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii...
mri_convert.bin -ot nii mri/brain.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii...
mri_convert.bin -ot nii mri/brainmask.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii...
mri_convert.bin -ot nii mri/brainmask.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii...
mri_convert.bin -ot nii mri/norm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii...
mri_convert.bin -ot nii mri/nu.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii...
mri_convert.bin -ot nii mri/lh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii...
mri_convert.bin -ot nii mri/rh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii...
mri_convert.bin -ot nii mri/wm.asegedit.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii...
mri_convert.bin -ot nii mri/wm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii...
mri_convert.bin -ot nii mri/wm.seg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./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, 9.31323e-10, 0)
j_ras = (9.31323e-10, -1.45519e-11, -1)
k_ras = (0, 1, 7.27596e-12)
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
Abort
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
Abort
c_ras: Subscript out of range.
c_ras: Subscript out of range.
Thanks, Minsun