@SUMA_Make_Spec_Fs problem

swallowwly · April 10, 2019, 3:29pm

Hi,

I’m using @SUMA_Make _Spec_Fs to build surface model on my data and problems happens with some of my subjects. Interestingly enough, with few of my subjects, the function somehow overcome this problem while others are less fortunate. And I notice this problem has been posted before, changing afni version didn’t work for me.

Here are the output from running two subjects:

@SUMA_Make_Spec_Fs -NIFTI -sid AmpCon022
++ creating directory ‘./SUMA’ for results…
– found 6 LH surfaces
– found 6 RH surfaces
mri_convert.bin -ot nii /Applications/freesurfer/subjects/AmpCon022/mri/orig.mgz /Applications/freesurfer/subjects/AmpCon022/./SUMA/orig.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Applications/freesurfer/subjects/AmpCon022/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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/orig.nii…
++ created AFNI file ‘./SUMA/AmpCon022_SurfVol.nii’
Made roi label table for AFNI - fs_table.niml.lt
mri_convert.bin -ot nii mri/T1.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/T1.nii…
mri_convert.bin -ot nii mri/aparc+aseg.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/aparc+aseg.nii…
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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 /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/aparc.a2009s+aseg.nii…
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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 /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/aseg.auto.nii…
mri_convert.bin -ot nii mri/aseg.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/aseg.nii…
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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 /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/brain.finalsurfs.nii…
mri_convert.bin -ot nii mri/brain.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/brain.nii…
mri_convert.bin -ot nii mri/brainmask.auto.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/brainmask.auto.nii…
mri_convert.bin -ot nii mri/brainmask.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/brainmask.nii…
mri_convert.bin -ot nii mri/norm.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/norm.nii…
mri_convert.bin -ot nii mri/nu.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/nu.nii…
mri_convert.bin -ot nii mri/lh.ribbon.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/lh.ribbon.nii…
mri_convert.bin -ot nii mri/rh.ribbon.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/rh.ribbon.nii…
mri_convert.bin -ot nii mri/wm.asegedit.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/wm.asegedit.nii…
mri_convert.bin -ot nii mri/wm.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./SUMA/wm.nii…
mri_convert.bin -ot nii mri/wm.seg.mgz /Applications/freesurfer/subjects/AmpCon022/./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 /Applications/freesurfer/subjects/AmpCon022/./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

Reading lh.smoothwm.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert lh.pial lh.pial.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

Reading lh.pial.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert lh.inflated lh.inflated.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

Reading lh.inflated.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert lh.sphere lh.sphere.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

Reading lh.sphere.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert lh.white lh.white.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

Reading lh.white.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert lh.sphere.reg lh.sphere.reg.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

Reading lh.sphere.reg.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert rh.smoothwm rh.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

Reading rh.smoothwm.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert rh.pial rh.pial.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

Reading rh.pial.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert rh.inflated rh.inflated.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

Reading rh.inflated.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert rh.sphere rh.sphere.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

Reading rh.sphere.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert rh.white rh.white.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

Reading rh.white.asc …
Performing affine transform…
Writing surface…
– running ‘mris_convert rh.sphere.reg rh.sphere.reg.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

Reading rh.sphere.reg.asc …
Performing affine transform…
Writing surface…
++ Notice FSread_annot (SUMA_FSread_annot.c:298 @10:01:54):
Guessed FS annot version of 2009
++ Notice FSread_annot (SUMA_FSread_annot.c:310 @10:01:54):
Guessed left hemisphere
++ Notice FSread_annot (SUMA_FSread_annot.c:333 @10:01:54):
Using /Applications/freesurfer/FreeSurferColorLUT.txt
++ Notice FSread_annot (SUMA_FSread_annot.c:344 @10:01:54):
Setting -FScmaprange to [13100 13199]
++ Notice FSread_annot (SUMA_FSread_annot.c:298 @10:01:55):
Guessed FS annot version of 2009
++ Notice FSread_annot (SUMA_FSread_annot.c:312 @10:01:55):
Guessed right hemisphere
++ Notice FSread_annot (SUMA_FSread_annot.c:333 @10:01:55):
Using /Applications/freesurfer/FreeSurferColorLUT.txt
++ Notice FSread_annot (SUMA_FSread_annot.c:349 @10:01:55):
Setting -FScmaprange to [14100 14199]
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
mv: rename lh.thickness.gii to /Applications/freesurfer/subjects/AmpCon022/./SUMA/lh.thickness.gii.dset: No such file or directory
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
mv: rename lh.curv.gii to /Applications/freesurfer/subjects/AmpCon022/./SUMA/lh.curv.gii.dset: No such file or directory
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
mv: rename lh.sulc.gii to /Applications/freesurfer/subjects/AmpCon022/./SUMA/lh.sulc.gii.dset: No such file or directory
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
mv: rename rh.thickness.gii to /Applications/freesurfer/subjects/AmpCon022/./SUMA/rh.thickness.gii.dset: No such file or directory
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
mv: rename rh.curv.gii to /Applications/freesurfer/subjects/AmpCon022/./SUMA/rh.curv.gii.dset: No such file or directory
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
mv: rename rh.sulc.gii to /Applications/freesurfer/subjects/AmpCon022/./SUMA/rh.sulc.gii.dset: No such file or directory
++ created spec file’./SUMA/AmpCon022_lh.spec’
++ created spec file’./SUMA/AmpCon022_rh.spec’
++ created spec file’./SUMA/AmpCon022_both.spec’

Running MapIcosahedron for both hemispheres at ld values of 141 60
++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @10:02:05):
Adding -NN_dset_map ./lh.aparc.a2009s.annot.niml.dset

To view in SUMA, run:

suma -spec std.141.AmpCon022_lh.spec

++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @10:02:44):
Adding -NN_dset_map ./rh.aparc.a2009s.annot.niml.dset

To view in SUMA, run:

suma -spec std.141.AmpCon022_rh.spec

++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @10:03:22):
Adding -NN_dset_map ./lh.aparc.a2009s.annot.niml.dset

To view in SUMA, run:

suma -spec std.60.AmpCon022_lh.spec

++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @10:03:32):
Adding -NN_dset_map ./rh.aparc.a2009s.annot.niml.dset

To view in SUMA, run:

suma -spec std.60.AmpCon022_rh.spec

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 AmpCon022_both.spec -sv AmpCon022_SurfVol.nii

\n\n++ Going to make renumbered ROIs now.
→ done for colorbar and making tissue maps.
See ‘@SUMA_renumber_FS -help’ for description.\n\n
++ found .//aparc+aseg.nii
++ found .//aparc.a2009s+aseg.nii
++ Renumbering FS whole brain (.//aparc+aseg.nii).
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_all.nii.gz
++ … getting gm…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_gm.nii.gz
++ … getting wmat…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_wmat.nii.gz
++ … getting csf…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_csf.nii.gz
++ … getting vent…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_vent.nii.gz
++ … getting othr…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_othr.nii.gz
++ … getting unkn…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc+aseg_REN_unkn.nii.gz
\n++ Running checks now.\n
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_070.nii.gz
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_071.nii.gz
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_072.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_all.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_all.nii.gz

setting labeltable
loading and re-writing dataset aparc+aseg_REN_all.nii.gz (./aparc+aseg_REN_all.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc+aseg_REN_gm.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_gm.nii.gz
setting labeltable
loading and re-writing dataset aparc+aseg_REN_gm.nii.gz (./aparc+aseg_REN_gm.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc+aseg_REN_wmat.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_wmat.nii.gz
setting labeltable
loading and re-writing dataset aparc+aseg_REN_wmat.nii.gz (./aparc+aseg_REN_wmat.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc+aseg_REN_csf.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_csf.nii.gz
setting labeltable
loading and re-writing dataset aparc+aseg_REN_csf.nii.gz (./aparc+aseg_REN_csf.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc+aseg_REN_vent.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_vent.nii.gz
setting labeltable
loading and re-writing dataset aparc+aseg_REN_vent.nii.gz (./aparc+aseg_REN_vent.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc+aseg_REN_othr.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_othr.nii.gz
setting labeltable
loading and re-writing dataset aparc+aseg_REN_othr.nii.gz (./aparc+aseg_REN_othr.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc+aseg_REN_unkn.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_REN_unkn.nii.gz
setting labeltable
loading and re-writing dataset aparc+aseg_REN_unkn.nii.gz (./aparc+aseg_REN_unkn.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
\n\n++ OK through ‘2000’ dsets.\n\n
++ Renumbering FS whole brain (.//aparc.a2009s+aseg.nii).
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_all.nii.gz
++ … getting gm…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_gm.nii.gz
++ … getting wmat…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_wmat.nii.gz
++ … getting csf…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_csf.nii.gz
++ … getting vent…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_vent.nii.gz
++ … getting othr…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_othr.nii.gz
++ … getting unkn…
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aparc.a2009s+aseg_REN_unkn.nii.gz
\n++ Running checks now.\n
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_070.nii.gz
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_071.nii.gz
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_072.nii.gz
++ Attaching labeltable to: aparc.a2009s+aseg_REN_all.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_all.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_all.nii.gz (./aparc.a2009s+aseg_REN_all.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc.a2009s+aseg_REN_gm.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_gm.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_gm.nii.gz (./aparc.a2009s+aseg_REN_gm.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc.a2009s+aseg_REN_wmat.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_wmat.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_wmat.nii.gz (./aparc.a2009s+aseg_REN_wmat.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc.a2009s+aseg_REN_csf.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_csf.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_csf.nii.gz (./aparc.a2009s+aseg_REN_csf.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc.a2009s+aseg_REN_vent.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_vent.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_vent.nii.gz (./aparc.a2009s+aseg_REN_vent.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc.a2009s+aseg_REN_othr.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_othr.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_othr.nii.gz (./aparc.a2009s+aseg_REN_othr.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Attaching labeltable to: aparc.a2009s+aseg_REN_unkn.nii.gz
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_REN_unkn.nii.gz
setting labeltable
loading and re-writing dataset aparc.a2009s+aseg_REN_unkn.nii.gz (./aparc.a2009s+aseg_REN_unkn.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
\n\n++ OK through ‘2009’ dsets.\n\n

@SUMA_Make_Spec_Fs … finished

[b]This subject went till the end but still, a lot of ‘abort’ messages in the middle.

@SUMA_Make_Spec_Fs -NIFTI -sid 100307[/b]

++ creating directory ‘./SUMA’ for results…
– found 6 LH surfaces
– found 6 RH surfaces
mri_convert.bin -ot nii /Applications/freesurfer/subjects/100307/mri/orig.mgz /Applications/freesurfer/subjects/100307/./SUMA/orig.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Applications/freesurfer/subjects/100307/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 /Applications/freesurfer/subjects/100307/./SUMA/orig.nii…
++ created AFNI file ‘./SUMA/100307_SurfVol.nii’
Made roi label table for AFNI - fs_table.niml.lt
mri_convert.bin -ot nii mri/T1.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/T1.nii…
mri_convert.bin -ot nii mri/aparc+aseg.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/aparc+aseg.nii…
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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 /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/aparc.a2009s+aseg.nii…
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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 /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/aseg.auto.nii…
mri_convert.bin -ot nii mri/aseg.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/aseg.nii…
++ 3drefit: AFNI version=AFNI_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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_19.0.26 (Mar 20 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 /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/brain.finalsurfs.nii…
mri_convert.bin -ot nii mri/brain.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/brain.nii…
mri_convert.bin -ot nii mri/brainmask.auto.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/brainmask.auto.nii…
mri_convert.bin -ot nii mri/brainmask.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/brainmask.nii…
mri_convert.bin -ot nii mri/norm.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/norm.nii…
mri_convert.bin -ot nii mri/nu.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/nu.nii…
mri_convert.bin -ot nii mri/lh.ribbon.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/lh.ribbon.nii…
mri_convert.bin -ot nii mri/rh.ribbon.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/rh.ribbon.nii…
mri_convert.bin -ot nii mri/wm.asegedit.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/wm.asegedit.nii…
mri_convert.bin -ot nii mri/wm.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./SUMA/wm.nii…
mri_convert.bin -ot nii mri/wm.seg.mgz /Applications/freesurfer/subjects/100307/./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 /Applications/freesurfer/subjects/100307/./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.

With same abort messages, this subject stoped in the middle.

What is the reason and what can I do to fix this? Many thanks!

rickr · April 10, 2019, 3:42pm

Hello,

It is hard to tell where all of the errors are coming from, but it seems like there is a problem with the FreeSurfer setup. It is hard to tell whether there is a problem with AFNI. For example, try running FreeSurfer’s:

mris_convert -h

It looks like that is failing. It is possible that something needs to be adjusted in your dot files (e.g. .cshrc or .bashrc) to allow for both AFNI and FreeSurfer. What is the output of:

afni_system_check.py -check_all

rick

swallowwly · April 10, 2019, 4:02pm

Hi Rick,

Thanks. Here are the results:

mris_convert -h

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

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: bash (current shell is csh)
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/matthewcryer/abin/afni
afni version : Precompiled binary macos_10.12_local: Mar 20 2019
: AFNI_19.0.26 ‘Tiberius’
AFNI_version.txt : AFNI_19.0.26, macos_10.12_local, Mar 20 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.5.2 (2018-12-20) – “Eggshell Igloo”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/matthewcryer/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/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 : success
3dClustSim : success

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 -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/matthewcryer/abin:/Users/matthewcryer/abin:/Users/matthewcryer/abin:/Users/matthewcryer/abin:/Users/matthewcryer/abin:/Users/matthewcryer/abin

PYTHONPATH =
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/matthewcryer/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.0.6

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘csh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

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

login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
insufficient data for AFNI bootcamp

-Lingyan

rickr · April 10, 2019, 5:34pm

Hi Lingyan,

What is the output from:

find /Applications/freesurfer/lib -name libSystem.B*

If it finds something, then you might need to do a little more to set up FreeSurfer. Maybe you still need to source $FREESURFER_HOME/SetUpFreeSurfer.csh.

Also, I see that bash is your login shell, yet you are running csh now. Perhaps FreeSurfer is set up correctly in one shell but not the other. Why are you running a shell that differs from your login one?

rick

swallowwly · April 10, 2019, 6:56pm

Hi Rick,

There is nothing coming out of find /Applications/freesurfer/lib -name libSystem.B*

As for your other questions – I tried @SUMA_Make_Spec_Fs with both tcsh and bash, and the results are the same. And I always source freesurfer before using it with following lines:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Thanks!

-Lingyan

rickr · April 10, 2019, 7:11pm

So if FreeSurfer is not giving you that libSystem.B file, and your FreeSurfer binaries are complaining about the one on your system, it seems possible that you have a FreeSurfer package that is not appropriate for your system.

Is that a new FreeSurfer package or an old one? Have you recently updated the OS?

rick

swallowwly · April 11, 2019, 1:50pm

Hi Rick,

I’m using freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg, this is the one from freesurfer website.

And my OS is High Sierra 10.13.6. Could this be a problem for freesurfer? If so, is there any chance I can solve this problem?

Thanks!
-Lingyan

rickr · April 11, 2019, 2:37pm

Hi Lingyan,

If you cannot run “mris_convert -h”, then it would be good to directly contact the FreeSurfer folks.

Show them the mris_convert command, along with the text output (error message), and report your OS and the FreeSurfer package as you have done here.

rick

swallowwly · April 12, 2019, 2:08pm

Thanks Rick!

I’ll do that!