Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Recon all hard failure,
by Vicente Ferrer 13 Nov '19

13 Nov '19

External Email - Use Caution Hello, I was runnning reconall in one of my images and it got stucked fixing surface defects, since i run it on a cluster it stopped when it runned out from cpu time. As you will see in the log the command started in SUNday 16 14:59:32 CEST 2019 and ended in Mon Jun 17 05:10:16 CEST 2019 which is more than usual for a recon-all duration. I have checked some of the previous images and there is clearly an alignment problem as you can check in this image: Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

3 5

Error "dyld: lazy symbol binding failed..." when some commands run via Matlab [system('fscmd')]
by hj23 13 Nov '19

13 Nov '19

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to run FreeSurfer commands via Matlab [system(‘fscmd’)]. Some of the commands work but some don’t, though all the commands work well when run in Terminal. Commands work in both Terminal and Matlab: When I run “tksurfer” in Terminal or system(’tksurfer’) in Matlab, I will get the help information for ’tksurfer'. Commands do not work in Matlab, but work in Terminal: For example, when I run “mri_info" in terminal, I will get the help information for “mri_info”. However, when I run system(‘mri_info’) in Matlab, I got the following error (screeshot also attached): =================================================================== dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer_6.0/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_6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mri_info: Aborted ans = 134 =================================================================== I randomly tried some FreeSurfer commands and the commands do not work in Matlab (but work in Terminal) are: ‘mri_info’ ‘mri_coreg’ Commands work in both terminal and Matlab are: ’tksurfer’ ‘mri_convert’ ‘mri_head’ I did search for the error in FreeSurfer Archive and found the recommendation of disable System Integrity Protection. Before doing that, I wonder if there is any other solution to this. Also, I tried to run these commands in both FreeSurfer 5.3-HCP and FreeSurfer 6.0 (on the same computer), and interestingly, the commands via Matlab work well in FS 5.3 (except that ‘mri_coreg’ cannot be found in FS 5.3) but the error will show in FS 6.0. Additional information: 1) FreeSurfer version: error show for freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but not for freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0-HCP 2) Platform: macOS Mojave (version 10.14.5) iMac Pro (2017) 3) uname -a Darwin ADUAED07785WKMX.local 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64 Please let me know if there is any other information will help. Thanks in advance, Haiyang

1 0

Postdoctoral Researcher Position in Neuropsychology/Imaging/Genetics at UCSD
by Andrews, Murray 12 Nov '19

12 Nov '19

External Email - Use Caution Postdoctoral Researcher in Neuropsychology/Imaging/Genetics The Human Memory Lab at UCSD is looking for an outstanding postdoctoral researcher to join the team as soon as possible. The researcher will work primarily with Dr. Sarah Banks on a study of sex differences in Alzheimer’s disease using preexisting data. The study utilizes cutting edge neuroimaging and analytic techniques involving tau PET and also MRI to assess cross-sectional and longitudinal patterns of sex differences in tau, and how they relate to cognition and genetics. In addition to Dr. Banks, the researcher will work extensively with collaborators, including Drs. Jim Brewer, Anders Dale, Linda McEvoy, Chun Chieh Fan and Steve Edland. The ideal candidate will hold a PhD in neuroscience, psychology or similar and have an interest in and experience with neurodegenerative disease, cognition, and neuroimaging. Background in research with Alzheimer’s disease is beneficial, but not mandatory. He or she will enjoy working in a multidisciplinary team, be productive and enjoy contributing to every stage of analysis and presentation. He or she will hit the ground running, working on already existing datasets to answer research questions related to those posed in the grant, and also develop their own projects. There will also be the opportunity to work on prospective data currently being collected using tau PET in participants with Alzheimer’s disease. In addition to image analysis and statistical knowledge and ability, great writing and communication skills will be important. UCSD provides a superlative environment to jump start an academic career, especially for those interested in Alzheimer’s and neuroimaging. There will be plenty of opportunities to broaden academic horizons through seminars across the campus, and the Banks Lab, while relatively new, has established multiple cross-disciplinary collaborations. The Banks Lab is housed within the Human Memory Lab, and thus benefits from being a new, growing lab within a more established infrastructure. Please send your CV to sbanks(a)ucsd.edu<mailto:sbanks@ucsd.edu>. If you have any questions regarding the position, please do not hesitate to contact Dr. Banks directly.

1 0

Question about how to create subjectname file during fMRI analysis
by 于倩倩 12 Nov '19

12 Nov '19

External Email - Use Caution Dear Developer, I am learning the FaFast to analyse the fMRI data. I have a question about the sunjectname file, I created a text file under the Sess06 file, like this: The content of the subjectname file is 'f06'. I created a file called fsl_bold including my anatomical data Then, I runned this preprocessing command: export SUBJECTS_DIR=/Users/qianqianyu/Desktop/fsl_bold cd /Users/qianqianyu/Desktop/preject_try preproc-sess -s Sess06 -vol-fwhm 4 -fsd bold -per-run There was a error!!! I do't know how to solve this error, so I hope I can get your help. Beat wishes to you! Looking forward to your reply！ qianqianyu 2019.11.12

2 1

4D multi-frame parcellation
by 曲岸 12 Nov '19

12 Nov '19

External Email - Use Caution Hi there, I am working with creating a surface parcellation from a volumetric parcellation and have some questions as follows: 1. If the volumetric parcellation is a labeled 4D multi-frame dataset, could I still use the mris_sample_parc? Or could mri_vol2surf get the sampled labels for every vertex? 2. For the 4D multi-frame dataset and mri_vol2surf output results, which GUI should I use to visualize it? I tried freeview for 4D multi-frame dataset but it looks weird. 3. Is there any command to separate multi-frame volume to single frame volumes? Many thanks! Best, An

3 3

Recon all hard failure,
by Vicente Ferrer 12 Nov '19

12 Nov '19

External Email - Use Caution Hello, I was runnning reconall in one of my images and it got stucked fixing surface defects, since i run it on a cluster it stopped when it runned out from cpu time. As you will see in the log the command started in SUNday 16 14:59:32 CEST 2019 and ended in Mon Jun 17 05:10:16 CEST 2019 which is more than usual for a recon-all duration. I have checked some of the previous images and there is clearly an alignment problem as you can check in this image: How can I solve this error? freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c OP:ubuntu 18 command: recon-all -all -s $SUBJ$session -i $T1 -sd $SUBJECTS_DIR \ -hippocampal-subfields-T1 -brainstem-structures -3T -openmp 1 thank you, Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

1 0

license error
by Francesca Strappini 12 Nov '19

12 Nov '19

External Email - Use Caution Dear FreeSurfer experts, I'm trying to convert FreeSurfer surfaces to afni format. I run this command line but I got an error message about the license although I've updated it. francesca-desktop:/opt/freesurfer/subjects/PP> @SUMA_Make_Spec_FS -NIFTI -sid PP FreeSurferEnv.csh (vers=13) requires csh/tcsh -- current shell: FreeSurferEnv.csh: CSURF_DIR reset to current dir ----------------------------------------------------------------------- csurf font changes: xset fp default (reset to default) xset +fp /opt/csurf/lib/fonts/75dpi-helvetica xset fp rehash ----------------------------------------------------------------------- csurf setenv changes: CSURF_DIR=/opt/csurf SUBJECTS_DIR=/opt/freesurfer/subjects FUNCTIONALS_DIR=/opt/csurf/sessions TCL_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tcl8.5 TK_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tk8.5 [dist=Ubuntu] pre-appended to LD_LIBRARY_PATH: + /opt/csurf/tcltktix/lib/Linux-x86_64 + /opt/csurf/gsl/lib/Linux-x86_64 + /opt/csurf/lib/Linux-x86_64 + /opt/csurf/afni/lib/Linux-x86_64 ----------------------------------------------------------------------- pre-appended to csh path: + /opt/csurf/afni/bin/Linux-x86_64 + /opt/csurf/mni_autoreg/bin/Linux-x86_64 + /opt/csurf/tcltktix/bin/Linux-x86_64 + /opt/csurf/bin/Linux-x86_64 + /opt/csurf/bin/noarch ----------------------------------------------------------------------- other setenv changes (mostly bak compat): FREESURFER_HOME=/opt/csurf (mri_surf2surf) AFNI_PLUGINPATH=/opt/csurf/afni/lib/Linux-x86_64 DIAG=0x4040 (surfer bins 2000) MRI_DIR=/opt/csurf (surfer bins 2000) PERL5LIB=/opt/csurf/mni_autoreg/perl (MNI) MNI_CONFIG_PATH=/opt/csurf/mni_autoreg/cfg (MNI) LANG=en_US (RH9) ----------------------------------------------------------------------- FreeSurfer0.8 from CSURF_DIR=/opt/csurf MGH freesurfer from FSURF_DIR=/opt/freesurfer surf directory found at './subjects/fsaverage-ADDITIONS/surf' consider running program from './subjects/fsaverage-ADDITIONS' program failure: exiting... francesca-desktop:/opt/freesurfer/subjects/PP> @SUMA_Make_Spec_FS -fspath /opt/freesurfer/subjects/PP -NIFTI -sid PP FreeSurferEnv.csh (vers=13) requires csh/tcsh -- current shell: FreeSurferEnv.csh: CSURF_DIR reset to current dir ----------------------------------------------------------------------- csurf font changes: xset fp default (reset to default) xset +fp /opt/csurf/lib/fonts/75dpi-helvetica xset fp rehash ----------------------------------------------------------------------- csurf setenv changes: CSURF_DIR=/opt/csurf SUBJECTS_DIR=/opt/freesurfer/subjects FUNCTIONALS_DIR=/opt/csurf/sessions TCL_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tcl8.5 TK_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tk8.5 [dist=Ubuntu] pre-appended to LD_LIBRARY_PATH: + /opt/csurf/tcltktix/lib/Linux-x86_64 + /opt/csurf/gsl/lib/Linux-x86_64 + /opt/csurf/lib/Linux-x86_64 + /opt/csurf/afni/lib/Linux-x86_64 ----------------------------------------------------------------------- pre-appended to csh path: + /opt/csurf/afni/bin/Linux-x86_64 + /opt/csurf/mni_autoreg/bin/Linux-x86_64 + /opt/csurf/tcltktix/bin/Linux-x86_64 + /opt/csurf/bin/Linux-x86_64 + /opt/csurf/bin/noarch ----------------------------------------------------------------------- other setenv changes (mostly bak compat): FREESURFER_HOME=/opt/csurf (mri_surf2surf) AFNI_PLUGINPATH=/opt/csurf/afni/lib/Linux-x86_64 DIAG=0x4040 (surfer bins 2000) MRI_DIR=/opt/csurf (surfer bins 2000) PERL5LIB=/opt/csurf/mni_autoreg/perl (MNI) MNI_CONFIG_PATH=/opt/csurf/mni_autoreg/cfg (MNI) LANG=en_US (RH9) ----------------------------------------------------------------------- FreeSurfer0.8 from CSURF_DIR=/opt/csurf MGH freesurfer from FSURF_DIR=/opt/freesurfer ++ creating directory './SUMA' for results... -- found 6 LH surfaces -- found 6 RH surfaces mri_convert -ot nii /opt/freesurfer/subjects/PP/mri/orig.mgz /opt/freesurfer/subjects/PP/./SUMA/orig.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /opt/freesurfer/subjects/PP/mri/orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/orig.nii... ++ created AFNI file './SUMA/PP_SurfVol.nii' Made roi label table for AFNI - fs_table.niml.lt mri_convert -ot nii mri/T1.mgz /opt/freesurfer/subjects/PP/./SUMA/T1.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/T1.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/T1.nii... mri_convert -ot nii mri/aparc+aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aparc+aseg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/aparc+aseg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/aparc+aseg.nii... ++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [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 + loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Program 3dmerge ++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [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_2011_12_21_1014 (Aug 28 2014) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_rank.nii + 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 -ot nii mri/aparc.a2009s+aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aparc.a2009s+aseg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/aparc.a2009s+aseg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/aparc.a2009s+aseg.nii... ++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [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 + 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_2011_12_21_1014 (Aug 28 2014) [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_2011_12_21_1014 (Aug 28 2014) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii + 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 -ot nii mri/aseg.auto.mgz /opt/freesurfer/subjects/PP/./SUMA/aseg.auto.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/aseg.auto.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/aseg.auto.nii... mri_convert -ot nii mri/aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aseg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/aseg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/aseg.nii... ++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [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 + 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_2011_12_21_1014 (Aug 28 2014) [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_2011_12_21_1014 (Aug 28 2014) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aseg_rank.nii + 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 -ot nii mri/brain.finalsurfs.mgz /opt/freesurfer/subjects/PP/./SUMA/brain.finalsurfs.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/brain.finalsurfs.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/brain.finalsurfs.nii... mri_convert -ot nii mri/brain.mgz /opt/freesurfer/subjects/PP/./SUMA/brain.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/brain.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/brain.nii... mri_convert -ot nii mri/brainmask.auto.mgz /opt/freesurfer/subjects/PP/./SUMA/brainmask.auto.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/brainmask.auto.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/brainmask.auto.nii... mri_convert -ot nii mri/brainmask.mgz /opt/freesurfer/subjects/PP/./SUMA/brainmask.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/brainmask.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/brainmask.nii... mri_convert -ot nii mri/norm.mgz /opt/freesurfer/subjects/PP/./SUMA/norm.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/norm.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/norm.nii... mri_convert -ot nii mri/nu.mgz /opt/freesurfer/subjects/PP/./SUMA/nu.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/nu.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/nu.nii... mri_convert -ot nii mri/lh.ribbon.mgz /opt/freesurfer/subjects/PP/./SUMA/lh.ribbon.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/lh.ribbon.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/lh.ribbon.nii... mri_convert -ot nii mri/rh.ribbon.mgz /opt/freesurfer/subjects/PP/./SUMA/rh.ribbon.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/rh.ribbon.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/rh.ribbon.nii... mri_convert -ot nii mri/wm.asegedit.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.asegedit.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/wm.asegedit.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/wm.asegedit.nii... mri_convert -ot nii mri/wm.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/wm.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/wm.nii... mri_convert -ot nii mri/wm.seg.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.seg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mri/wm.seg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 3.72529e-09) j_ras = (0, -1.16415e-10, -1) k_ras = (0, 1, -1.22236e-09) writing to /opt/freesurfer/subjects/PP/./SUMA/wm.seg.nii... -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' -------------------------------------------------------------------------- GNU libc version: 2.27 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- Reading lh.smoothwm.asc ... Performing affine transform... Writing surface... -- running 'mris_convert lh.pial lh.pial.asc' -------------------------------------------------------------------------- GNU libc version: 2.27 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- -- Error ConvertSurface (SUMA_ConvertSurface.c:589): if_name lh.pial.asc not found. failure: could not create surface lh.pial.gii --> is your FreeSurfer license installed? program failure: exiting... Thanks for the help Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

2 1

FSGD file formatting for Xhemi
by Jose Graterol 11 Nov '19

11 Nov '19

External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y file was created as previously explained in another discussion ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html) That is, mris_preproc with --xhemi and no --fsgd flag. If I understood correctly, that would create a mgh file with the following order: sub01lh, sub01rh, sub02lh, sub02rh... Then the FSGD file while running mri_glmfit would be: GroupDescriptorFile 1 Title xxx Class sub Variables var1 Input sub01lh sub var1_lh_sub01 Input sub01rh sub var1_rh_sub01 Input sub02lh sub var1_lh_sub02 Input sub02rh sub var1_rh_sub02 Would this be correct? If so, what would be the best case for specifying a variable like age? Just repeating the value 2 times? As always, thanks in advance Kind Regards José

2 11

how to compute geodesic distance and intensity
by chenyang jiang 11 Nov '19

11 Nov '19

External Email - Use Caution Dear fs developer Hello, I want to compute Geodesic distance and intensity contrast in all the vertices based on T1 image, and also could get the feature map to do the statistical analysis. Is there any code or toolbox could handle with it. It will be better if the input is from freesurfer output. thanks so much, chenyang

2 1

low snr with t1_mp2rage compared to MPRAGE
by Knut J Bjuland 11 Nov '19

11 Nov '19

External Email - Use Caution Dear freesurfer experts, I have some image that are in t1_mp2rage_sag. Are there anything I should be aware of when importing them into freesurfer from nifit? How can I detect what sequence that is used in the MRI dicoms? When I compare these images with MPRAGE dicom I get lower snr measured with wm-anat-snr with, what can cause this? Best regards Knut Jørgen Bjuland

2 1

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