Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

RE: make_average_surface
by antao＠itsa.ucsf.edu 13 Oct '05

13 Oct '05

Hi, I just installed the newest freesurfer and modified make_average_surface as suggestion by Nick and Brian. When I run make_average_surface, it stop with the following error. Did anyone meet the simialr probelm? Thanks [antao@freesurfer subjects]$ make_average_surface --subjects AD1293 AD1297 --out average_cn set VERSION = '$Id: make_average_surface,v 1.14 2005/09/27 19:42:14 greve Exp $' ; set VERSION = $Id: make_average_surface,v 1.14 2005/09/27 19:42:14 greve Exp $ set PrintHelp = 0 ; set PrintHelp = 0 if ( $?SUBJECTS ) then if ( 0 ) then if ( $?SUBJECTS_DIR ) then if ( 1 ) then set SUBJECTS_DIR= ( $SUBJECTS_DIR ) set SUBJECTS_DIR= ( /home/antao/freesurfer/subjects ) endif endif set average_subject=average set average_subject=average set ddir = ${SUBJECTS_DIR}/${average_subject} set ddir = /home/antao/freesurfer/subjects/average set transform_fname="" set transform_fname= set XFORM_FLAG="" set XFORM_FLAG= if ( $#argv == 0 ) then if ( 5 == 0 ) then set PWD = `getpwdcmd` ; set PWD = `getpwdcmd` getpwdcmd if ( $status ) exit 1 ; if ( 0 ) exit 1 goto parse_args ; goto parse_args set cmdline = ( $argv ) ; set cmdline = ( --subjects AD1293 AD1297 --out average_cn ) set getting_subjects = 0 ; set getting_subjects = 0 while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; set flag = --subjects if ( ! $getting_subjects ) then if ( ! 0 ) then shift ; shift endif endif switch ( $flag ) switch ( --subjects ) if ( $#argv == 0 ) goto arg1moreerr ; if ( 4 == 0 ) goto arg1moreerr set SUBJECTS = $argv[1] ; shift ; set SUBJECTS = AD1293 shift set getting_subjects = 1 ; set getting_subjects = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 3 != 0 ) set flag = $argv[1] ; set flag = AD1297 if ( ! $getting_subjects ) then if ( ! 1 ) then switch ( $flag ) switch ( AD1297 ) if ( $getting_subjects ) then if ( 1 ) then set SUBJECTS = "$SUBJECTS $argv[1]" ; shift ; set SUBJECTS = AD1293 AD1297 shift set getting_subjects = 1 ; set getting_subjects = 1 else else breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; set flag = --out if ( ! $getting_subjects ) then if ( ! 1 ) then switch ( $flag ) switch ( --out ) if ( $getting_subjects ) then if ( 1 ) then set getting_subjects = 0 ; set getting_subjects = 0 shift ; shift endif endif if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set average_subject = $argv[1] ; shift ; set average_subject = average_cn shift set ddir = ${SUBJECTS_DIR}/${average_subject} set ddir = /home/antao/freesurfer/subjects/average_cn breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( ! $?SUBJECTS ) then if ( ! 1 ) then if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /home/antao/freesurfer/subjects ) then if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then if ( ! -e $FREESURFER_HOME ) then if ( ! -e /home/antao/freesurfer ) then if ( x$transform_fname != x ) then if ( x != x ) then goto check_params_return ; goto check_params_return echo ==================== echo ==================== ==================== echo make_average_surface echo make_average_surface make_average_surface echo ==================== echo ==================== ==================== echo input subjects: ${SUBJECTS} echo input subjects: AD1293 AD1297 input subjects: AD1293 AD1297 echo output subject: ${average_subject} echo output subject: average_cn output subject: average_cn mkdir -p ${ddir} ${ddir}/surf ${ddir}/mri ${ddir}/mri/transforms ${ddir}/mri/T1 ${ddir}/mri/orig ${ddir}/mri/label mkdir -p /home/antao/freesurfer/subjects/average_cn /home/antao/freesurfer/subjects/average_cn/surf /home/antao/freesurfer/subjects/average_cn/mri /home/antao/freesurfer/subjects/average_cn/mri/transforms /home/antao/freesurfer/subjects/average_cn/mri/T1 /home/antao/freesurfer/subjects/average_cn/mri/orig /home/antao/freesurfer/subjects/average_cn/mri/label if ( -e ${SUBJECTS_DIR}/${average_subject} == 0 ) then if ( -e /home/antao/freesurfer/subjects/average_cn == 0 ) then mkdir -p ${SUBJECTS_DIR}/${average_subject}/surf mkdir -p /home/antao/freesurfer/subjects/average_cn/surf endif endif set tmp_subjects = ( $SUBJECTS ) set tmp_subjects = ( AD1293 AD1297 ) foreach hemi ( rh lh ) foreach hemi ( rh lh ) cd ${SUBJECTS_DIR}/${average_subject} cd /home/antao/freesurfer/subjects/average_cn foreach s ( orig white pial inflated ) foreach s ( orig white pial inflated ) echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from orig... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average orig_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.orig_avg mris_make_average_surface done end end echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o white rh white_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from white... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average white_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.white_avg mris_make_average_surface done end end echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o pial rh pial_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from pial... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average pial_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.pial_avg mris_make_average_surface done end end echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o inflated rh inflated_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from inflated... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average inflated_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.inflated_avg mris_make_average_surface done end end foreach c ( sulc curv thickness ) foreach c ( sulc curv thickness ) echo mris_average_curvature... echo mris_average_curvature... mris_average_curvature... mris_average_curvature $c ${hemi} sphere.reg $SUBJECTS $SUBJECTS_DIR/${average_subject}/surf/${hemi}.avg_${c} mris_average_curvature sulc rh sphere.reg AD1293 AD1297 /home/antao/freesurfer/subjects/average_cn/surf/rh.avg_sulc processing subject AD1293... processing subject AD1297... end end echo mris_average_curvature... echo mris_average_curvature... mris_average_curvature... mris_average_curvature $c ${hemi} sphere.reg $SUBJECTS $SUBJECTS_DIR/${average_subject}/surf/${hemi}.avg_${c} mris_average_curvature curv rh sphere.reg AD1293 AD1297 /home/antao/freesurfer/subjects/average_cn/surf/rh.avg_curv processing subject AD1293... processing subject AD1297... end end echo mris_average_curvature... echo mris_average_curvature... mris_average_curvature... mris_average_curvature $c ${hemi} sphere.reg $SUBJECTS $SUBJECTS_DIR/${average_subject}/surf/${hemi}.avg_${c} mris_average_curvature thickness rh sphere.reg AD1293 AD1297 /home/antao/freesurfer/subjects/average_cn/surf/rh.avg_thickness processing subject AD1293... processing subject AD1297... end end cd ${SUBJECTS_DIR}/${average_subject}/surf cd /home/antao/freesurfer/subjects/average_cn/surf pwd pwd /home/antao/freesurfer/subjects/average_cn/surf mris_smooth -n 5 ./${hemi}.white_avg ./${hemi}.smoothwm mris_smooth -n 5 ./rh.white_avg ./rh.smoothwm smoothing for 5 iterations smoothing surface tessellation for 5 iterations... smoothing complete - recomputing first and second fundamental forms... writing smoothed curvature to ./rh.curv writing smoothed area to ./rh.area mris_inflate ./${hemi}.smoothwm ./${hemi}.inflated mris_inflate ./rh.smoothwm ./rh.inflated avg radius = 48.1 mm, total surface area = 76079 mm^2 tol=1.0e-04, host=frees, nav=16, nbrs=2, l_spring_norm=1.000, l_dist=0.100 mom=0.90, dt=0.90 desired rms height=0.015 inflating to desired rms height = 0.015 000: dt: 0.0000, rms height=0.116, avgs=16 005: dt: 0.9000, rms height=0.081, avgs=16, l_dist=0.40 010: dt: 0.9000, rms height=0.068, avgs=16, l_dist=0.40 015: dt: 0.9000, rms height=0.057, avgs=8, l_dist=0.28 020: dt: 0.9000, rms height=0.047, avgs=8, l_dist=0.28 025: dt: 0.9000, rms height=0.040, avgs=4, l_dist=0.20 030: dt: 0.9000, rms height=0.033, avgs=4, l_dist=0.20 035: dt: 0.9000, rms height=0.028, avgs=2, l_dist=0.14 040: dt: 0.9000, rms height=0.024, avgs=2, l_dist=0.14 045: dt: 0.9000, rms height=0.021, avgs=1, l_dist=0.10 050: dt: 0.9000, rms height=0.018, avgs=1, l_dist=0.10 055: dt: 0.9000, rms height=0.017, avgs=0, l_dist=0.00 060: dt: 0.9000, rms height=0.015, avgs=0, l_dist=0.00 inflation complete. writing inflated surface to ./rh.inflated writing sulcal depths to ./rh.sulc writing curvature file ./rh.sulc inflation took 2.8 minutes mris_curvature -a 10 -w ./${hemi}.white_avg mris_curvature -a 10 -w ./rh.white_avg averaging curvature patterns 10 times. total integrated curvature = 165.547*4pi (2080.322) --> -165 handles ICI = 410.5, FI = 7165.7, variation=101079.032 writing Gaussian curvature to ./rh.white_avg.K...done. writing mean curvature to ./rh.white_avg.H...done. cp ${hemi}.white_avg.H ${hemi}.curv cp rh.white_avg.H rh.curv cp ${FREESURFER_HOME}/average/surf/${hemi}.sphere.reg . cp /home/antao/freesurfer/average/surf/rh.sphere.reg . cp: cannot stat `/home/antao/freesurfer/average/surf/rh.sphere.reg': No such file or directory [antao@freesurfer subjects]

1 0

"Failed to find brainstem" in monkey volume
by peggy christidis 13 Oct '05

13 Oct '05

I'm helping out an intern here who is working on monkey volumes in FreeSurfer. He has gotten to the point where he has a decent looking white matter segmentation, but when he tries to proceed with filling the white matter, he says he gets the following error: "Failed to find brain stem". At this point I don't have any additional information to give you (sorry), but has anyone ever encountered this problem? Any idea what "failed to find brain stem" might mean? Thanks, peggy

3 2

labeling question
by Erin.Slason＠UCHSC.edu 12 Oct '05

12 Oct '05

We are using the development version of freesurfer in our lab for segmenting brains. In the parcellation process, the superior temporal gyrus is labeled as a whole, but specific parts of the STG including the planum temporale (which we need) are not being labeled. The labeling process used is curvature.buckner40.filled.desikan_killany. If we use a different labeling process, such as atlas2005, will these structures be labeled? If not, is there another way to approach this problem? Thanks. Erin Slason Professional Research Assistant Neuromagnetic Imaging Center Department of Psychiatry University of Colorado Health Sciences Center 303-315-5459 Erin.Slason(a)uchsc.edu

2 1

hardware recommendations?
by L.Scheef＠uni-bonn.de 11 Oct '05

11 Oct '05

Dear list members! I wonder if anybody could recommend me hardware for a dedicated freesurfer PC. Any suggestion? Also, should I stick to Redhat 9 or is it worth to go for the new SUSE/Redhat distributions? Many thanks for your help and best wishes, Lukas _______________________________________________ Dr. Lukas Scheef, Dipl. Phys. FE: MRT/fMRI Dep. of Radiology University of Bonn 53105 Bonn Germany

4 4

invalid command name "PNG"
by xmeadow＠uchicago.edu 10 Oct '05

10 Oct '05

Hi, I've got a Mac box running OS X 10.3.9 and Freesurfer ,v 1.3 2003/08/05 19: 19:16, and just recently when I start up freesurfer I get an error. To reproduce the error I do: >source /Applications/Freesurfer/SetUpFreeSurfer.csh Setting up enviroment for FreeSurfer/FS-FAST $Id: FreeSurferEnv.csh,v 1.3 2003/08/05 19:19:16 kteich Exp $ FREESURFER_HOME /Applications/Freesurfer FSFAST_HOME /Applications/Freesurfer/fsfast AFNI_DIR /Applications/Freesurfer/afni FSL_DIR /Applications/Freesurfer/fsl SUBJECTS_DIR /Users/xmeadow/subjects >csurf & Application initialization failed: invalid command name "PNG" Then Freesurfer opens up normally. I was just wondering what this error message means. I've looked online and seen that PNG stands for 'Portable Network Graphics' (I think), but I don't know if I have it installed or if I need it installed. Is there something I can do to get Freesurfer to load without errors? Thanks very much. >Xander

3 5

aseg visualization
by Bruce Fischl 10 Oct '05

10 Oct '05

Hi All, if you are generating aseg volumes DON'T overlay them on the T1 volume. It is only for cortical processing, as the intensity normalization that creates it will erode the borders of the thalamus and the pallidum. Overlay the segmentation on the norm (or orig) volume in order to assess it's accuracy. cheers, Bruce

1 0

Subcortical questions
by Fornito, Alexander 09 Oct '05

09 Oct '05

Hi, Just wandering if there are any options for improving the results of the subcortical segmentation. It seems to label to large an area for many structures (eg., white matter gets included in the thalamus label). Also, are the surfaces through the midline of the subcortex (ie., the portion labelled as 'medial wall' bu the parcellation step) used during ther spherical registration for the cortex? I'm wandering if I need to pay attention to how the surfaces look in these areas or not. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito(a)wh.org.au

2 1

subcortseg with files processed with older version
by walhovd＠nmr.mgh.harvard.edu 07 Oct '05

07 Oct '05

Hi We've some data processed with the FS version prior to the dev version. Now we want to subcortically label these, but when recon-all -subcortseg -segstats -subjid <subject name> we get error:cannot find nu/COR-info understandably, since there is no nu for the old version. Is it possible to work around this so that it doesn't use that? It all works excellently if we do the preprocessing (autorecon1) again with the new version, but if possible it would be great to avoid that because the brain volumes of many of these have been edited for stuff like vessels and skullfragments. Thanks, - Kristine

2 1

difference between dev version and the final stable version?
by Renat Yakupov 07 Oct '05

07 Oct '05

Hi FreeSurfer community, I have a question about the current dev release - how different is the new 'stable' release going to be different from it? Is it mostly stability and compatibility between different platforms issue? Or are the actual processing or computational steps going to be different also? Can I start processing some brains using dev release and then continue processing using new 'stable' release? Or process half of my images with dev release and the other half with new 'stable' release and then do some inter-group comparisons? And another small question - should I also use Red Hat 9 download for Linux Fedora Core 3? Thank you. Regards, Renat.

2 1

PhD-Position; Medical Physics
by Uwe Pietrzyk 07 Oct '05

07 Oct '05

Dear Colleagues, please find attached to this eMail a Word-Document (german/english) describing a PhD-Project in the field of Medical Phyics / Polarized Light Imaging with the topic in brain research / connectivity. Feel free to forward this eMail to potentially interested colleagues. Many thanks, Uwe Pietrzyk /---------------------------------------------------------------------- Prof. Dr. Uwe Pietrzyk Diplom-Physiker Institut für Medizin Forschungszentrum Jülich GmbH 52425 Jülich Tel: +49-2461-61 4763 Fax: +49-2461-61 2820 + 8229 Mobil: +49-172-213-2155 eMail: U.Pietrzyk(a)fz-juelich.de http://www.fz-juelich.de/ime/ime_mitarbeiter_pietrzyk & Bergische Universität Wuppertal Fachbereich C - Physik / D.08.01 Gaußstr. 20 42097 Wuppertal Tel: +49-(0)202-439-3523 Fax: +49-(0)202-439-2811 eMail: Uwe.Pietrzyk(a)physik.uni-wuppertal.de http://www.physik.uni-wuppertal.de ----------------------------------------------------------------------/

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