Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

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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

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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

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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.

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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

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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

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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

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PALM Analysis
by Harikumar, Amritha 04 Sep '19

04 Sep '19

Hello, Thanks for letting me know regarding running fsPalm in your previous message. My next question is - what command can we use in Freesurfer that can run multiple comparison testing for subcortical regions? If not fsPalm, is there another function that will perform this? Thanks, Amritha Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283 > On Sep 3, 2019, at 6:06 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. OHBM International Mentoring Programme Sign-up {Disarmed} > (Meena M. Makary) > 2. PALM Analysis (Harikumar, Amritha) > 3. Re: PALM Analysis (Greve, Douglas N.,Ph.D.) > 4. Discrepancy between thresholded surface and cluster labels > (Bronwyn Overs) > 5. Reconall with no-MPRAGE T1w image? (Rovai Antonin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Sep 2019 12:19:45 -0400 > From: "Meena M. Makary" <meena.magharious(a)gmail.com> > Subject: [Freesurfer] OHBM International Mentoring Programme Sign-up > {Disarmed} > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAF4GKtcDD7AdkJFUhQ9KTq_ypOhEo+5Z_Qn+wz6u4kFrvjv=+Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi all, > > Between September 1st and September 31st 2019, registration for the fourth > round of the Online International Mentoring Programme organized and > coordinated by the OHBM Student and Postdoc Special Interest Group > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > will take place. In the programme, every OHBM member can become an (online) > mentor or a mentee to another OHBM member(s) for a period of approximately > one year (October-June). During this time, the mentor can support the > mentee to grow in academia by providing advice on topics such as?but not > limited to?personal development, grant writing, and work-life balance. In > response to the feedback from previous participants and the increased > interest of mentees in industry, we have also invited a number of mentors > from industry to join us for this new round. > > If you are interested in being a mentor and/or mentee, please fill out this > short registration form > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > and > you will be contacted with further details. > > If you participated in any of the previous rounds and would like to further > take part in the programme, you have two possible ways (It is possible to > choose both options): > > 1. If you would like to continue being paired with your current > mentors/mentees, please first discuss this with your mentoring partner. In > this case, please do not re-subscribe for the programme and please delegate > the mentee to fill in this feedback form > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > for us. > 2. If you would like to apply for new mentors/mentees, you will be able > to do so using the registration link above. > > Please feel free to forward this message to your colleagues. Please also > forward this email to former researchers working in industry, if you know > any, as we are still looking for more industry representatives to join the > programme as mentors this year. > > We would like to thank all the OHBM mentors and mentees who participated in > the previous three rounds of the programme! The third round of the > programme is now ending. We hope that most of you had an opportunity to > meet in person during the OHBM Annual Meeting in Rome. If you have feedback > for us, please contact us at ohbmtrainees(a)gmail.com > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. > Please share any comments which might help to further improve our > programme! > > > To find out more about the programme, please visit the OHBM Student and > Postdoc SIG website > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > and check our previous publication > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. > If you have any questions about the programme, please contact us at > ohbmtrainees(a)gmail.com > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > . > > > We hope to welcome you in the programme very soon! > > Best regards, > ? > *Meena M. Makary, Ph.D.* > Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> > Postdoctoral Fellow | Radiology, Harvard Medical School > <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> > Postdoctoral Fellow | Athinoula A. Martinos Center, MGH > <https://www.nmr.mgh.harvard.edu/user/4550386> > Career Development and Mentoring Manager | OHBM Student and Postdoc SIG > <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> >

2 1

FreeView : Tools : Volume Filter : Close
by Yasir Hadi 04 Sep '19

04 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the FreeView Version 2.0 Builed Jan 18 2017 16:48:55. I've searched the list and the wiki and I didn't find a similar information. Thanks :) Regards, Ysr H

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