External Email - Use Caution
On Sep 5, 2019, at 02:56, Minsun Park <vd.mpark@gmail.com> wrote:External Email - Use Caution
Hi_______________________________________________I've tried to run @SUMA_Make_Spec_FS in afni but I've kept getting this error message (which is written at the end of this email).I'm using Mac (high sierra 10.13.6), the latest afni, XQuartz(2.10.11).Using Freesurfer I made a flattened map by running recon-all and tksurfer without any problems.I disabled SIPs and updated Freesurfer (as recommended in this link: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-April/061591.html).I'd appreciate if you give any suggestions I can do!######bash-3.2$ @SUMA_Make_Spec_FS -fspath ./ -NIFTI -sid 060717KHW++ creating directory './SUMA' for results...-- found 8 LH surfaces-- found 8 RH surfacesmri_convert.bin -ot nii /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii...++ created AFNI file './SUMA/060717KHW_SurfVol.nii'Made roi label table for AFNI - fs_table.niml.ltmri_convert.bin -ot nii mri/T1.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/T1.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii...mri_convert.bin -ot nii mri/aparc+aseg..mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii$Id: mri_convert.c,v 1..226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aparc+aseg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii...++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32Warnings of this type will be muted for this session.Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.++ Processing AFNI dataset aparc+aseg.nii+ setting labeltable+ loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage)++ 3drefit processed 1 datasetsProgram 3dmerge++ 3dmerge: AFNI version=AFNI_19..2.21 (Aug 29 2019) [64-bit]3dmerge: edit and combine 3D datasets, by RW Cox++ default -1dindex = 0++ default -1tindex = 1++ editing input dataset in memory (64.0 MB).-- Wrote edited dataset: ./aparc+aseg_rank.nii++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox++ Processing AFNI dataset aparc+aseg_rank.nii+ setting labeltable+ loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank.mri_convert.bin -ot nii mri/aparc.a2009s+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aparc.a2009s+aseg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M..Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii...++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32Warnings of this type will be muted for this session.Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.++ Processing AFNI dataset aparc.a2009s+aseg.nii+ setting labeltable+ loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.Program 3dmerge++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]3dmerge: edit and combine 3D datasets, by RW Cox++ default -1dindex = 0++ default -1tindex = 1++ editing input dataset in memory (64.0 MB).-- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii+ setting labeltable+ loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank.mri_convert.bin -ot nii mri/aseg.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aseg.auto.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii...mri_convert.bin -ot nii mri/aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aseg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii...++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox** AFNI converts NIFTI_datatype=8 (INT32) in file aseg.nii to FLOAT32Warnings of this type will be muted for this session.Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.++ Processing AFNI dataset aseg.nii+ setting labeltable+ loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aseg.Program 3dmerge++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]3dmerge: edit and combine 3D datasets, by RW Cox++ default -1dindex = 0++ default -1tindex = 1++ editing input dataset in memory (64.0 MB).-- Wrote edited dataset: ./aseg_rank.nii++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox++ Processing AFNI dataset aseg_rank.nii+ setting labeltable+ loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aseg_rank.mri_convert.bin -ot nii mri/brain.finalsurfs.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brain.finalsurfs.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/../SUMA/brain.finalsurfs.nii...mri_convert.bin -ot nii mri/brain.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brain.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii...mri_convert.bin -ot nii mri/brainmask.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brainmask.auto.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii...mri_convert.bin -ot nii mri/brainmask.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brainmask.mgz....TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M..Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii...mri_convert.bin -ot nii mri/norm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/norm.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii...mri_convert.bin -ot nii mri/nu.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/nu.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7..27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii...mri_convert.bin -ot nii mri/lh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii$Id: mri_convert.c,v 1..226 2016/02/26 16:15:24 mreuter Exp $reading from mri/lh.ribbon.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii...mri_convert.bin -ot nii mri/rh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/rh.ribbon.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii...mri_convert.bin -ot nii mri/wm.asegedit.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/wm.asegedit.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii...mri_convert.bin -ot nii mri/wm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/wm.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii...mri_convert.bin -ot nii mri/wm.seg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/wm.seg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii...-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'Abortdyld: lazy symbol binding failed: Symbol not found: ___emutls_get_addressReferenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylibExpected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_addressReferenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylibExpected in: /usr/lib/libSystem.B.dylibdyld: lazy symbol binding failed: Symbol not found: ___emutls_get_addressReferenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylibExpected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_addressReferenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp..1.dylibExpected in: /usr/lib/libSystem.B.dylibAbortc_ras: Subscript out of range.c_ras: Subscript out of range.Thanks,Minsun
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