Failure with @SUMA_Make_Spec_FS

AFNI Message Board
1

Hi all,

I’m trying to run @SUMA_Make_Spec_FS after processing with Freesurfer.
But when I ran the command, error message poped up like ‘failure: could not create surface lh.smoothwm.asc’.
I already made csrutil enabled but the problem happened.
Also, in the reply for latest post relevant to my issue, Daniel recommended fs_update (sudo -E fs_update) and then sourcing the freesurfer.
I did it but the same error still happened.

My mac OS is OS X El Capitan 10.11.3.
Any advise will be helpful to me. Thank you very much!

Below is terminal message:

++ creating directory ‘./SUMA’ for results…
– found 8 LH surfaces
– found 8 RH surfaces

Notice: Found COR files and mri/orig.mgz
******** Will use COR files.

++ to3d: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ Counting images: total=256 2D slices
++ Each 2D slice is 256 X 256 pixels
++ Image data type = byte
++ Reading images: …
++ 3D dataset written to disk
++ created AFNI file ‘./SUMA/sbj1_SurfVol+orig.HEAD’
++ created AFNI file ‘./SUMA/sbj1_SurfVol+orig.BRIK’
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…
++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./T1.nii

  • loading and re-writing dataset ./T1.nii (./T1.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ** 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.
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 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
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ 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_17.2.00 (Jul 5 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_17.2.00 (Jul 5 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…
** 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.
++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 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
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ 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_17.2.00 (Jul 5 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_17.2.00 (Jul 5 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…
++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./aseg.auto.nii

  • loading and re-writing dataset ./aseg.auto.nii (./aseg.auto.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ** 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.
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 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
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ 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_17.2.00 (Jul 5 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_17.2.00 (Jul 5 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…
++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./brain.finalsurfs.nii

  • loading and re-writing dataset ./brain.finalsurfs.nii (./brain.finalsurfs.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./brain.nii
  • loading and re-writing dataset ./brain.nii (./brain.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./brainmask.auto.nii
  • loading and re-writing dataset ./brainmask.auto.nii (./brainmask.auto.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./brainmask.nii
  • loading and re-writing dataset ./brainmask.nii (./brainmask.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./norm.nii
  • loading and re-writing dataset ./norm.nii (./norm.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./nu.nii
  • loading and re-writing dataset ./nu.nii (./nu.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./lh.ribbon.nii
  • loading and re-writing dataset ./lh.ribbon.nii (./lh.ribbon.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./rh.ribbon.nii
  • loading and re-writing dataset ./rh.ribbon.nii (./rh.ribbon.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./wm.asegedit.nii
  • loading and re-writing dataset ./wm.asegedit.nii (./wm.asegedit.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./wm.nii
  • loading and re-writing dataset ./wm.nii (./wm.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    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…
    ++ 3drefit: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
    ++ Authored by: RW Cox
    ++ Processing AFNI dataset ./wm.seg.nii
  • loading and re-writing dataset ./wm.seg.nii (./wm.seg.nii in NIFTI storage)
    ++ 3drefit processed 1 datasets
    – 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

failure: could not create surface lh.smoothwm.asc

→ is your FreeSurfer license installed?
program failure: exiting…

2

Hi-

That appears to be related to a known error that FreeSurfer itself has on Sierra; please see this earlier discussion when someone queried this on the MB:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,154067,154112#msg-154112
… which has a link to solving it.

Also, when you use @SUMA_Make_Spec_FS, are you using the “-NIFTI” option? You probably should be. (Unrelated to this matter, but it is commented on in the help, and just checking.)

–pt

3

Can you run the mris_convert command by itself? Did you add the FreeSurfer environment variable script call by editing the @SUMA_Make_Spec_FS script as a test?

4

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.

5

Dear Daniel,

I did mris_convert itself, as your advised, like ‘mris_convert ./surf/lh.smoothwm lh.smoothwm.asc’ (which was error line when running the script), then the lh.smoothwm.asc file was made.
Would you please check my script whether there is something to make this error?

Thank you!

SCRIPT:

#!/bin/bash
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

@SUMA_Make_Spec_FS
-fspath ~/Desktop/MAE_fMRI/data_sbj/1_LHS/T1_MPRAGE_SAG_1_0ISO_0017/lhs
-NIFTI
-sid sbj1

6

Hi-

For those kinds of library errors, I wonder if you are using the AFNI “local” version install for Macs? Rick developed that build so that those kinds of linking errors shouldn’t happen. What is the output of “afni -ver” on your computer?

If you see the installation instructions here for Macs:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html
… it directs installing the “local” Mac version. If your current AFNI version is different, you could move your present “abin/” directory and then just download as described there in Step 2.

–pt

7

Hi ptaylor

I think the version of afni might be the cause!
The output of ‘afni -ver’ is “Precompiled binary macosx_10.7_Intel_64: Aug 4 2017 (Version AFNI_17.2.06)”, but my mac osx is 10.11.3 (El Capitan).
I’m not sure what is the ‘local’ mac version, but if that means 10.11+ mac osx, do I just download new afni following the step 2?
In command lines of step 2,
---- cd
---- curl -O https ://afni.nimh.nih.gov/pub/dist/bin/macosx_10.7_local/@update.afni.binaries
---- tcsh @update.afni.binaries -defaults
there is written as 10.7 (red mark), so I wonder if I need to re-download 10.11+ version of afni,does above command lines work?

Thank you very much!!!

***** Waiting for your answer, I just installed with above command lines but the previous error did not fixed. If there is wrong thing, I’ll wait for your advice!

8

That version should still work fine on 10.11; that is what everyone would use.

What is your current output for “afni -ver”? And also for “afni_system_check.py -check_all”?

–pt

9

Here are the outputs:

afni -ver

Precompiled binary macosx_10.7_local: Aug 9 2017 (Version AFNI_17.2.07)

afni_system_check.py -check_all

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.3.0
version: Darwin Kernel Version 15.3.0: Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64
distribution: 10.11.3 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/minsunpark/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 9 2017
: AFNI_17.2.07
AFNI_version.txt : AFNI_17.2.07, macosx_10.7_local, Aug 09 2017
which python : /sw/bin/python
python version : 2.7.13
which R : /usr/local/bin/R
R version : R version 3.3.1 (2016-06-21) – “Bug in Your Hair”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/minsunpark/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
/sw/bin/python2.7
/usr/bin/python
python2 : 0
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /sw/lib/qt4-mac/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7

-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/minsunpark/abin

PYTHONPATH = /sw/lib/qt4-mac/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/minsunpark/abin

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.41.1
which brew : /usr/local/bin/brew
brew version : Homebrew 0.9.5 (git revision d700; last commit 2016-03-28)

++ found ‘brew’ at /usr/local/bin/brew

========================= summary, please fix: =========================

  • AFNI programs show FAILURE
  • insufficient data for AFNI bootcamp

Thank you.

10

So, did you try removing the SUMA/ directory made by the initial @SUMA_Make_Spec_FS run, and try again with your new install? Again, the “local Mac 10.7” version should be fine on 10.11. In the afni_system_check.py output, I believe the one error/failure shouldn’t affect @SUMA_Make_Spec_FS (or very many other programs, either).

–pt

11

Was this problem resolved? Because I’m running into the exact same error.

Thanks!

Catherine

12

Hi, Catherine-

What is your specific error? There are a couple different things discussed here.

–pt

13

Hello,

When I run the commands:

I/O path, same as above, following earlier steps

set path_P_ss = data_proc/S01

ID of individual subj from “tail” of path, above

set ss_id = $path_P_ss:t

AFNI-SUMA function: convert FS output

@SUMA_Make_Spec_FS
-NIFTI
-fspath $path_P_ss/anat_02
-sid $ss_id

This is the entire readout with the error:

++ creating directory ‘./SUMA’ for results…
– found 6 LH surfaces
– found 6 RH surfaces
mri_convert.bin -ot nii /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/mri/orig.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/orig.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/mri/orig.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/orig.nii…
++ created AFNI file ‘./SUMA/S01_SurfVol.nii’
Made roi label table for AFNI - fs_table.niml.lt
mri_convert.bin -ot nii mri/T1.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/T1.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/T1.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/T1.nii…
mri_convert.bin -ot nii mri/aparc+aseg.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/aparc+aseg.nii…
++ 3drefit: AFNI version=AFNI_18.1.16 (May 21 2018) [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_18.1.16 (May 21 2018) [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_18.1.16 (May 21 2018) [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 /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/aparc.a2009s+aseg.nii…
++ 3drefit: AFNI version=AFNI_18.1.16 (May 21 2018) [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_18.1.16 (May 21 2018) [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_18.1.16 (May 21 2018) [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 /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/aseg.auto.nii…
mri_convert.bin -ot nii mri/aseg.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/aseg.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/aseg.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/aseg.nii…
++ 3drefit: AFNI version=AFNI_18.1.16 (May 21 2018) [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_18.1.16 (May 21 2018) [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_18.1.16 (May 21 2018) [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 /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/brain.finalsurfs.nii…
mri_convert.bin -ot nii mri/brain.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/brain.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/brain.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/brain.nii…
mri_convert.bin -ot nii mri/brainmask.auto.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/brainmask.auto.nii…
mri_convert.bin -ot nii mri/brainmask.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/brainmask.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/brainmask.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/brainmask.nii…
mri_convert.bin -ot nii mri/norm.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/norm.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/norm.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/norm.nii…
mri_convert.bin -ot nii mri/nu.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/nu.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/nu.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/nu.nii…
mri_convert.bin -ot nii mri/lh.ribbon.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/lh.ribbon.nii…
mri_convert.bin -ot nii mri/rh.ribbon.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/rh.ribbon.nii…
mri_convert.bin -ot nii mri/wm.asegedit.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/wm.asegedit.nii…
mri_convert.bin -ot nii mri/wm.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/wm.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/wm.mgz…
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./SUMA/wm.nii…
mri_convert.bin -ot nii mri/wm.seg.mgz /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/cunninghamca2/Desktop/DTI/data_proc/S01/anat_02/./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.

I’d appreciate any help! Thanks!

Catherine

14

Hi Catherine,

It seems possible that the AFNI setup is not being kind
to freesurfer. Since you seem to be in the same building,
it might be easier to meet about this. I will send you a
message.

  • rick
15

In a previous case of a user having this problem, what happened was that @SUMA_Make_Spec_FS got part way through its run and failed, and a specific “xmatras.1D” file got made badly – on rerunning, it wouldn’t get regenerated and this caused issues. If you remove the SUMA/ dir for that subject, which FreeSurfer is creating, does it work?

(and there may be other issues with the computer setup that need to be resolved-- I am sure as Rick noted those could be resolved more easily meeting).

–pt