External Email - Use Caution
Hello Minsun, You can try downloading this link to a zip file with an updated version of 6.0.0 freeview for the Mac. Follow the instructions in README.patch.https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=s... R. On Sep 5, 2019, at 02:56, Minsun Park <vd.mpark@gmail.com> wrote: External Email - Use Caution HiI'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... 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 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 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 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 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 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 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_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylibdyld: 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.dylibdyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylibAbortc_ras: Subscript out of range.c_ras: Subscript out of range.Thanks,Minsun_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer