Freesurfer November 2019

freesurfer@nmr.mgh.harvard.edu

87 participants
122 discussions

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

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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

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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

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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

Inconsistent Morphology Output
by Chen, Christine 11 Nov '19

11 Nov '19

External Email - Use Caution Hello, My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all, autorecon, mris_volume and mris_wm_volume) then through run.r (pulls freesurfer.r and pedbirn.r) using the Desikan-Killiany atlas to output measures of cortical morphology. We've always gotten consistent output when rerunning data, however, lately when rerunning data using the exact same files as before, the output measures are different, sometimes significantly so, compared to when they were previously run. We recently installed the development version of FreeSurfer in a path different from $FREESURFER_HOME, which is still set to usr/local/freesurfer. We've also confirmed that all these runs have been using FreeSurfer v6.0 by looking at the /scripts/build-stamp.txt file. So the inconsistency in output might not be due to the FreeSurfer version used. Additionally, we are collecting a new dicom format, however when rerunning files collected in the previous dicom format through the pipeline and comparing this output to the output from when it was previously ran, the measures are still different, so the inconsistency in results might not be due to the dicom format. Do you have any ideas why this sudden change in outputs is being observed? Is there a flag we can add to the scripts to ensure results are identical and consistent with what they were previously, such as -norandomness or -seed 1234? Any help or guidance would be greatly appreciated. Thank you in advance. Best, CC ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 3

FDR for aseg
by Benjamin Ineichen 11 Nov '19

11 Nov '19

External Email - Use Caution Dear Freesurfer experts, I run the command mri_glmfit --table aseg.volume.stats.dat --fsgd GLM7.fsgd dods --C contrasts6.mtx --glmdir NFL.aseg.glmdir This gave me the output sig.table.dat. Is there a way to implement an FDR to this analysis in Freesurfer or do I have to use another statistical program for that? Many thanks for your support! Best regards, Ben

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Question about convert fsaverage to fsaverage5
by chenyang jiang 11 Nov '19

11 Nov '19

External Email - Use Caution Dear Fs Developers Hi, I am new to freesurfer, after I ran the recon-all command, I want to align the individual surface to fsaverage5 space. and then extracted the cortical thickness of each vertex. Should I use mri_surf2surf to do it, What's the specific parameter I should set up? like srcsurfval , trgsurfval and so on. would it be possible to give me entire command setting. Thank you so much! Chenyang

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Freesurfer November 2019