Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

Interruption during data processing
by Троицкий Антон Александрович 05 Sep '19

05 Sep '19

External Email - Use Caution Dear freesurfer users, I encountered a problem when data processing suddenly interrupted. Is there any way to continue procession of patient data and don't repeat previous steps and don't waste the time? Best regards, Anton Troitskii.

2 1

Re: [Freesurfer] Problem with lazy symbol binding failed
by fsbuild 05 Sep '19

05 Sep '19

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_GMUSh… R. On Sep 5, 2019, at 02:56, Minsun Park <vd.mpark(a)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…'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 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

1 0

Problem with lazy symbol binding failed
by Minsun Park 05 Sep '19

05 Sep '19

External Email - Use Caution Hi I've tried to run @SUMA_Make_Spec_FS in afni but I've kept getting this error message (which is written at the end of this email). I'm using Mac (high sierra 10.13.6), the latest afni, XQuartz(2.10.11). Using Freesurfer I made a flattened map by running recon-all and tksurfer without any problems. I disabled SIPs and updated Freesurfer (as recommended in this link: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-April/061591.html ). I'd appreciate if you give any suggestions I can do! ###### bash-3.2$ @SUMA_Make_Spec_FS -fspath ./ -NIFTI -sid 060717KHW ++ creating directory './SUMA' for results... -- found 8 LH surfaces -- found 8 RH surfaces mri_convert.bin -ot nii /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii... ++ created AFNI file './SUMA/060717KHW_SurfVol.nii' Made roi label table for AFNI - fs_table.niml.lt mri_convert.bin -ot nii mri/T1.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/T1.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii... mri_convert.bin -ot nii mri/aparc+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aparc+aseg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii... ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aparc+aseg.nii + setting labeltable + loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] 3dmerge: edit and combine 3D datasets, by RW Cox ++ default -1dindex = 0 ++ default -1tindex = 1 ++ editing input dataset in memory (64.0 MB) . -- Wrote edited dataset: ./aparc+aseg_rank.nii ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_rank.nii + setting labeltable + loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank. mri_convert.bin -ot nii mri/aparc.a2009s+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aparc.a2009s+aseg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii... ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aparc.a2009s+aseg.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg. Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] 3dmerge: edit and combine 3D datasets, by RW Cox ++ default -1dindex = 0 ++ default -1tindex = 1 ++ editing input dataset in memory (64.0 MB) . -- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank. mri_convert.bin -ot nii mri/aseg.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aseg.auto.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii... mri_convert.bin -ot nii mri/aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aseg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii... ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aseg.nii + setting labeltable + loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aseg. Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] 3dmerge: edit and combine 3D datasets, by RW Cox ++ default -1dindex = 0 ++ default -1tindex = 1 ++ editing input dataset in memory (64.0 MB) . -- Wrote edited dataset: ./aseg_rank.nii ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aseg_rank.nii + setting labeltable + loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aseg_rank. mri_convert.bin -ot nii mri/brain.finalsurfs.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brain.finalsurfs.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii... mri_convert.bin -ot nii mri/brain.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brain.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii... mri_convert.bin -ot nii mri/brainmask.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brainmask.auto.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii... mri_convert.bin -ot nii mri/brainmask.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brainmask.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii... mri_convert.bin -ot nii mri/norm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/norm.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii... mri_convert.bin -ot nii mri/nu.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/nu.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii... mri_convert.bin -ot nii mri/lh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/lh.ribbon.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii... mri_convert.bin -ot nii mri/rh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/rh.ribbon.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii... mri_convert.bin -ot nii mri/wm.asegedit.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.asegedit.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii... mri_convert.bin -ot nii mri/wm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii... mri_convert.bin -ot nii mri/wm.seg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.seg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii... -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' Abort dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort c_ras: Subscript out of range. c_ras: Subscript out of range. Thanks, Minsun

1 0

Re: [Freesurfer] Invaild Key Error for Freesurfer 5.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello An, Try taking the attached file “license_5” and rename it to “.license”   Then put it under $FREESURFER_HOME so that you see it when you issue the command, $ ls $FREESURFER_HOME/.license - R. On Sep 4, 2019, at 22:50, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello An,My understanding is that in Freesurfer 5 you need to have a file called “.license” and it should be placed in the directory where you installed freesurfer.  That directory is also the path the variable $FREESURFER_HOME points to.So if there was no “.license” file there to begin with, then this command would have reported there was no such file,$ ls  $FRESSURFER_HOME/.licenseNewer versions of Freesurfer look for “license.txt”.   Did you rename the newly generated “license.txt” file and copy it to live under $FREESURFER_HOME to be “.license” ?, e..g., from wherever “license.txt” maybe you did something like,$ cp license.txt  $FREESURFER_HOME/.licenseI was going to suggest you try doing that copy to create what freesurfer 5 is looking for, but from your output below, it looks like you already did that and it is finding $FREESURFER_HOME/.license but saying the key is incorrect to run version 5..I don’t know how to change/re-generate a key to work with version 5, but we can look into it.    - R.On Sep 4, 2019, at 20:56, An Lijun <lijun.an(a)hotmail.com> wrote:        External Email - Use Caution        Dear Freesurfer experts,Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before..May I ask how to get the licnese of 5.1.0?The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1.New License I get(call license.txt):xxxxxxxx@gmail.com43508 *CRBDdLNbgmws FSOkaDD5AxOQkOld License(call .license):xxxxxxxx@gmail.com39689*1PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------Best Regards,An Lijun_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Invaild Key Error for Freesurfer 5.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello An, My understanding is that in Freesurfer 5 you need to have a file called “.license” and it should be placed in the directory where you installed freesurfer.  That directory is also the path the variable $FREESURFER_HOME points to. So if there was no “.license” file there to begin with, then this command would have reported there was no such file, $ ls  $FRESSURFER_HOME/.license Newer versions of Freesurfer look for “license.txt”.   Did you rename the newly generated “license.txt” file and copy it to live under $FREESURFER_HOME to be “.license” ?, e.g., from wherever “license.txt” maybe you did something like, $ cp license.txt  $FREESURFER_HOME/.license I was going to suggest you try doing that copy to create what freesurfer 5 is looking for, but from your output below, it looks like you already did that and it is finding $FREESURFER_HOME/.license but saying the key is incorrect to run version 5. I don’t know how to change/re-generate a key to work with version 5, but we can look into it.     - R. On Sep 4, 2019, at 20:56, An Lijun <lijun.an(a)hotmail.com> wrote:        External Email - Use Caution        Dear Freesurfer experts,Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before.May I ask how to get the licnese of 5.1.0?The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1.New License I get(call license.txt):xxxxxxxx@gmail.com43508 *CRBDdLNbgmws FSOkaDD5AxOQkOld License(call .license):xxxxxxxx@gmail.com39689*1PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------Best Regards,An Lijun_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Invaild Key Error for Freesurfer 5.1
by An Lijun 04 Sep '19

04 Sep '19

External Email - Use Caution Dear Freesurfer experts, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before. May I ask how to get the licnese of 5.1.0? The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1. New License I get(call license.txt): xxxxxxxx(a)gmail.com<mailto:xxxxxxxx@gmail.com> 43508 *CRBDdLNbgmws FSOkaDD5AxOQk Old License(call .license): xxxxxxxx(a)gmail.com<mailto:xxxxxxxx@gmail.com> 39689 *1 PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------ Best Regards, An Lijun

1 0

Siemens Enhanced DICOM
by Funk, Quentin 04 Sep '19

04 Sep '19

External Email - Use Caution Hey all- Freesurfer's recon-all fails if I try to give it a dicom from the new Siemens Enhanced format. Are there any workarounds that don't involve converting to nifti with a different software first? Thanks! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

Scale Option for mris_convert
by rockj5＠netzero.net 04 Sep '19

04 Sep '19

External Email - Use Caution Hello, I normally use mris_convert --combinesurfs for generating STL files from the lh.pial and rh.pial. When running Freesurfer on my local computer, there are no problems with this approach and everything is perfect. However, the lh.pial and rh.pial files I get when running Freesurfer through fMRIPrep are much larger (about 3-4x bigger than the ones I get locally). This makes the STL file I get through mris_convert also much larger. The file size is too big for me to use. I discovered that mris_convert has a scale option using -s. I tried putting -s 0.1, expecting the file size to be reduced 90%. But no matter how little I set the scale to be, the file size is only reduced 1 to 2%. Does anyone know how to properly reduce the STL size using mris_convert? I would really like to avoid having to install a third party software to do this. Thanks a lot! ____________________________________________________________ Beverly Hills Housekeeper Shocks Doctors: Avoid Botox antiaging-breakthrough.com http://thirdpartyoffers.netzero.net/TGL3231/5d700780cb78f7805c97st01duc

2 1

Re: [Freesurfer] recon_all cuda 9.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello Vasudev, I think in January of 2018 it was possible to build the development branch of the freesurfer tree using cuda 5.  But I believe that was the last version we tried building the source with.  We no longer support building with cuda and instead favor using OpenMP..  Part of this is because of cuda’s dependencies on the Nvidia graphics hardware which is a moving target.  Some vendors have essentially stopped supporting Nvidia graphics card drivers, e.g., Apple as of Mac OS 10.14 onward.  The Freesurfer dev branch source is now compiled with C++ compilers, and I don’t know that anyone has tried building with cuda since we changed the compilers for freesurfer. - R. On Aug 30, 2019, at 11:39, Dev vasu <vasudevamurthy.devulapally(a)gmail.com> wrote:        External Email - Use Caution        Dear all,Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1.ThanksVasudev_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

paired t-test for pet surface analysis
by miracle ozzoude 04 Sep '19

04 Sep '19

External Email - Use Caution Hello Freesurfer, I am trying to run a surface based paired ttest for pet. I started by running mri_vol2surf for each pet longitudinal subject. However, when i use mri_concat with --f, --prune, and --paired-diff i get an error " --paired-xxx specified but there are an odd number of frames". I have 4 subjects, 3 has 3 timepoints and 1 has 2 timepoints (total of 11 frames). Below are my commands and full errors. How do I solve this problem? best, Paul *COMMANDS* mri_vol2surf --mov $in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg $in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 \ --o $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage { echo $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz; } >> $lhmgxctx #concatenate the surface pets mri_concat --f "$lhmgxctxgm" --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune --paired-diff session=subject_basline.long.baseid (e.g. 001_baseline.long.001, 001_12mon.long.001 etc) lhmgxctx = text file containing the pet volumes mapped to the surface for each timepoints. (e.g. /Analysis/001_baseline.long.001/lh.mgx.ctxgm.001_baseline.long.001.fsaverage.sm00.nii.gz /Analysis/001_12mon.long.001/lh.mgx.ctxgm.001_12mon.long.001.fsaverage.sm00.nii.gz etc.) *ERRORS* + mri_concat --f Analysis/lh_hemi_ctxgm.txt --o Analysis/results/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune --paired-diff-norm1 ninputs = 11 Checking inputs nframestot = 11 ERROR: --paired-xxx specified but there are an odd number of frames

2 1

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Freesurfer September 2019