Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

display conventions
by adam walczak 27 Apr '06

27 Apr '06

Hello, I was wondering if FreeSurfer needed the data to be in a specific display convention (neurological or radiological). I have to do some manipulation of our images in order to get them in the correct space and was wondering if the program needed the data in a specific display type to work properly. I noticed that tkmedit displays in the radiological convention. Thank you, Adam adam --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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csurf porblem
by Joao Pereira 27 Apr '06

27 Apr '06

Hello, I have just installed FreeSurfer and I can't run csurf. The GUI appears but it is useless, giving an error at the beginning saying it can't find the paint file in the bin directory. Even when I select the bert subject, nothing happens, requiring COR files to exist. Could you please help me qith this? Thank you, Joao Pereira

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selxavg-sess: 2 errors
by Kathryn Devaney 27 Apr '06

27 Apr '06

Hello all, I'm running into two errors running selxavg-sess, and I haven't seen them anywhere in the archives. I get the same errors in the stable and the dev enviroments. I don't know if this is significant, but I have two versions of this data, one version was projfrac'd and the other was not. The non-projfrac data does not return the errors - I re-ran projfrac but got the same errors again. Please let me know if you have any suggestions. Thanks very much! Kathryn The command that I used for projrac was: cd <run_dir> mris_volsmooth --i fmc.bhdr --o fmc_vs.bhdr --projfrac-avg 0 1 .1 --fwhm 0 --reg ../register.dat And here's the output for mkanalysis and selxavg: whatever:color_orientation_20060403/mystudy% pwd /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy whatever:color_orientation_20060403/mystudy% mkanalysis-sess.new -sf sessid -df sesspar -motioncor -fsd bold -paradigm paradigm_color.par -dt blocked -mcextreg -polyfit 2 -gammafit 2.25 1.25 -TR 5.8 -nconditions 2 -timewindow 23.6 -funcstem fmc_vs -analysis subj27_color_volsmooth -force INFO: analysis subj27_color_volsmooth exists, but overwrite forced by user. /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403 Completed successfully whatever:color_orientation_20060403/mystudy% selxavg-sess -sf sessid -df sesspar -a subj27_color_volsmooth -noomnibus INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/log/selxavg-sess-bold-subj27_color_volsmooth-060427102037.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403 Thu Apr 27 10:20:39 EDT 2006 INFO (color_orientation_20060403): RunList = 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047 -------------------------------------------------------- /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/bold selxavg2 -TR 5.8 -parname paradigm_color.par -o subj27_color_volsmooth/h -i 005/fmc_vs -i 006/fmc_vs -i 007/fmc_vs -i 008/fmc_vs -i 009/fmc_vs -i 010/fmc_vs -i 011/fmc_vs -i 012/fmc_vs -i 013/fmc_vs -i 014/fmc_vs -i 015/fmc_vs -i 016/fmc_vs -i 017/fmc_vs -i 018/fmc_vs -i 019/fmc_vs -i 020/fmc_vs -i 021/fmc_vs -i 022/fmc_vs -i 023/fmc_vs -i 024/fmc_vs -i 025/fmc_vs -i 026/fmc_vs -i 027/fmc_vs -i 028/fmc_vs -i 029/fmc_vs -i 030/fmc_vs -i 031/fmc_vs -i 032/fmc_vs -i 033/fmc_vs -i 034/fmc_vs -i 035/fmc_vs -i 036/fmc_vs -i 037/fmc_vs -i 038/fmc_vs -i 039/fmc_vs -i 040/fmc_vs -i 041/fmc_vs -i 042/fmc_vs -i 043/fmc_vs -i 044/fmc_vs -i 045/fmc_vs -i 046/fmc_vs -i 047/fmc_vs -cfg /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/subj27_color_volsmooth/analysis.cfg -ipr 0.89690721666667 -------------------------------------------------------- cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory --- Parsing Config File: /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/subj27_color_volsmooth/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 23.2 -prestim 0 -polyfit 2 -TER 5.8 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 Logfile is subj27_color_volsmooth/h_sxa.log matlab file is /tmp/sxa_17501.m ----------- Matlab file -------------- % Matlab file for selxavg2 Thu Apr 27 10:21:05 EDT 2006 % This file may be deleted % /tmp/sxa_17501.m global QuitOnError; QuitOnError = 1; r = fast_selxavg( '-TR', '5.8', '-parname', 'paradigm_color.par', '-o', 'subj27_color_volsmooth/h', '-i', '005/fmc_vs', '-i', '006/fmc_vs', '-i', '007/fmc_vs', '-i', '008/fmc_vs', '-i', '009/fmc_vs', '-i', '010/fmc_vs', '-i', '011/fmc_vs', '-i', '012/fmc_vs', '-i', '013/fmc_vs', '-i', '014/fmc_vs', '-i', '015/fmc_vs', '-i', '016/fmc_vs', '-i', '017/fmc_vs', '-i', '018/fmc_vs', '-i', '019/fmc_vs', '-i', '020/fmc_vs', '-i', '021/fmc_vs', '-i', '022/fmc_vs', '-i', '023/fmc_vs', '-i', '024/fmc_vs', '-i', '025/fmc_vs', '-i', '026/fmc_vs', '-i', '027/fmc_vs', '-i', '028/fmc_vs', '-i', '029/fmc_vs', '-i', '030/fmc_vs', '-i', '031/fmc_vs', '-i', '032/fmc_vs', '-i', '033/fmc_vs', '-i', '034/fmc_vs', '-i', '035/fmc_vs', '-i', '036/fmc_vs', '-i', '037/fmc_vs', '-i', '038/fmc_vs', '-i', '039/fmc_vs', '-i', '040/fmc_vs', '-i', '041/fmc_vs', '-i', '042/fmc_vs', '-i', '043/fmc_vs', '-i', '044/fmc_vs', '-i', '045/fmc_vs', '-i', '046/fmc_vs', '-i', '047/fmc_vs', '-cfg', '/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/subj27_color_volsmooth/analysis.cfg', '-ipr', '0.89690721666667'); if(r==0) fmri_touch('/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/bold/subj27_color_volsmooth/selxavg.ok.17501'); end qoe; ----------------------------------- ------------------------------------------ ------- matlab output -------------------- < M A T L A B > Copyright 1984-2003 The MathWorks, Inc. Version 6.5.1.199709 Release 13 (Service Pack 1) Aug 4 2003 Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspblks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmasks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmex. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspdemos. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.22.2.1 2006/04/06 22:31:16 greve Exp $ Parsing Arguments Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 43 Input Volume List 1 005/fmc_vs 2 006/fmc_vs 3 007/fmc_vs 4 008/fmc_vs 5 009/fmc_vs 6 010/fmc_vs 7 011/fmc_vs 8 012/fmc_vs 9 013/fmc_vs 10 014/fmc_vs 11 015/fmc_vs 12 016/fmc_vs 13 017/fmc_vs 14 018/fmc_vs 15 019/fmc_vs 16 020/fmc_vs 17 021/fmc_vs 18 022/fmc_vs 19 023/fmc_vs 20 024/fmc_vs 21 025/fmc_vs 22 026/fmc_vs 23 027/fmc_vs 24 028/fmc_vs 25 029/fmc_vs 26 030/fmc_vs 27 031/fmc_vs 28 032/fmc_vs 29 033/fmc_vs 30 034/fmc_vs 31 035/fmc_vs 32 036/fmc_vs 33 037/fmc_vs 34 038/fmc_vs 35 039/fmc_vs 36 040/fmc_vs 37 041/fmc_vs 38 042/fmc_vs 39 043/fmc_vs 40 044/fmc_vs 41 045/fmc_vs 42 046/fmc_vs 43 047/fmc_vs Input Pardigm File List 1 005/paradigm_color.par 2 006/paradigm_color.par 3 007/paradigm_color.par 4 008/paradigm_color.par 5 009/paradigm_color.par 6 010/paradigm_color.par 7 011/paradigm_color.par 8 012/paradigm_color.par 9 013/paradigm_color.par 10 014/paradigm_color.par 11 015/paradigm_color.par 12 016/paradigm_color.par 13 017/paradigm_color.par 14 018/paradigm_color.par 15 019/paradigm_color.par 16 020/paradigm_color.par 17 021/paradigm_color.par 18 022/paradigm_color.par 19 023/paradigm_color.par 20 024/paradigm_color.par 21 025/paradigm_color.par 22 026/paradigm_color.par 23 027/paradigm_color.par 24 028/paradigm_color.par 25 029/paradigm_color.par 26 030/paradigm_color.par 27 031/paradigm_color.par 28 032/paradigm_color.par 29 033/paradigm_color.par 30 034/paradigm_color.par 31 035/paradigm_color.par 32 036/paradigm_color.par 33 037/paradigm_color.par 34 038/paradigm_color.par 35 039/paradigm_color.par 36 040/paradigm_color.par 37 041/paradigm_color.par 38 042/paradigm_color.par 39 043/paradigm_color.par 40 044/paradigm_color.par 41 045/paradigm_color.par 42 046/paradigm_color.par 43 047/paradigm_color.par Output Volume subj27_color_volsmooth/h TR 5.800000 TER 5.800000 Total Window 23.2 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 0 nSkip 0 InPlane Res 0.896907 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 1 1 2.25 1.25 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 ExtReg File mcextreg NExtReg 3 ExtRegOrthog 0 firstslice 0 nslices 26 nyqreg 0 SynthSeed = 0 Conditions Found (2): 1 2 Run 1: 8 7 Run 2: 8 7 Run 3: 8 7 Run 4: 8 7 Run 5: 8 8 Run 6: 8 8 Run 7: 8 8 Run 8: 8 8 Run 9: 8 8 Run 10: 8 8 Run 11: 8 8 Run 12: 8 8 Run 13: 8 8 Run 14: 8 8 Run 15: 8 8 Run 16: 8 8 Run 17: 8 8 Run 18: 8 8 Run 19: 8 8 Run 20: 8 8 Run 21: 8 8 Run 22: 8 8 Run 23: 8 8 Run 24: 8 8 Run 25: 8 8 Run 26: 8 8 Run 27: 8 8 Run 28: 8 8 Run 29: 8 8 Run 30: 8 8 Run 31: 8 8 Run 32: 8 8 Run 33: 8 8 Run 34: 8 8 Run 35: 8 8 Run 36: 8 8 Run 37: 8 8 Run 38: 8 8 Run 39: 8 8 Run 40: 8 8 Run 41: 8 8 Run 42: 8 8 Run 43: 8 8 Slice 0, 0.000334 -------------- First Pass (Accumulation), 0.006474 Run 1/43, 0.007439 Excluding 0 Points: Run 2/43, 1.23839 Excluding 0 Points: Run 3/43, 2.14573 Excluding 0 Points: Run 4/43, 3.051 Excluding 0 Points: Run 5/43, 3.97482 Excluding 0 Points: Warning: Matrix is singular to working precision. (Type "warning off MATLAB:singularMatrix" to suppress this warning.) > In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 35 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Divide by zero. (Type "warning off MATLAB:divideByZero" to suppress this warning.) > In /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/matlab/datafun/std.m at line 33 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 37 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Matrix is singular to working precision. (Type "warning off MATLAB:singularMatrix" to suppress this warning.) > In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 35 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Divide by zero. (Type "warning off MATLAB:divideByZero" to suppress this warning.) > In /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/matlab/datafun/std.m at line 33 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 37 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Matrix is singular to working precision. (Type "warning off MATLAB:singularMatrix" to suppress this warning.) > In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 47 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 ??? Index exceeds matrix dimensions. Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fmri_par2scm.m On line 112 ==> c1(1) = Pulses(1); Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 324 ==> Xfir = fmri_par2scm(par,Nc,SubSampRate*ntrs,TER,Nfir,TPS); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403): selxavg failed

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optic nerve
by Lars M. Rimol 26 Apr '06

26 Apr '06

Dear all, Do you recomend to routinely erase the optic nerve (regardless of how the wm surface looks), and where in the work flow do you recomend to do it? (We do it as part of the quality control after autorecon1 now.) -- yours, LMR

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Re: [Freesurfer] Help with Freesurfer Installation
by Binu Thomas 26 Apr '06

26 Apr '06

Thank you very much for your help. The configuration for FreeSurfer is done sucessfully. I have pasted the output during configuration: [root@localhost local]# setenv FREESURFER_HOME /usr/local/freesurfer [root@localhost local]# source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4-stable-pub-v3.0.2 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR /usr/local/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer/sessions MINC_BIN_DIR /usr/local/freesurfer/mni/bin MINC_LIB_DIR /usr/local/freesurfer/mni/lib PERL5LIB /usr/local/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /usr/local/freesurfer/lib/gsl QTDIR /usr/local/freesurfer/lib/qt TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib FSL_DIR /usr/local/freesurfer/fsl Now, I am having trouble with testing the software: I tried the first few commands on the Testing FreeSurfer page and here is the error I get: [root@localhost local]# tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory [root@localhost local]# cd freesurfer [root@localhost freesurfer]# tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory [root@localhost freesurfer]# I ran the "recon-all -s -bert -all" command and it stopped with the following error message: #@# Skull Stripping Wed Apr 26 15:40:43 CDT 2006 /usr/local/freesurfer/subjects/bert/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux localhost.localdomain 2.4.21-40.ELsmp #1 SMP Thu Feb 2 22:22:39 EST 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Apr 26 15:40:43 CDT 2006 I am installing the CentOS4 stable version of FreeSurfer on Red Hat Ent. Linux 3. Can this be a problem? Thanks again for any help possible, Binu. Binu Thomas, M.S. Computer Programmer III Department of Psychiatry UT Southwestern Medical Center Phone: 214-645-2792 >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 04/26/06 11:53 AM >>> Remove the angle brackets from the pathname, that is, the < and > chars. In Unix, these are the redirection commands, and not valid pathname characters. So, type this: setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh On Wed, 2006-04-26 at 11:42 -0500, Binu Thomas wrote: > Thanks for the reply! Here is a detail of all that I did. I downloaded > the RH9 version of the software to my /usr/local directory and installed > it with the "tar xzvf" command. I then changed the shell to tcsh and > then the rest of the output is as follows: > > [root@localhost ~]# set echo=1 > [root@localhost ~]# setenv FREESURFER_HOME </usr>/freesurfer > setenv FREESURFER_HOME > [root@localhost ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh > source /SetUpFreeSurfer.csh > /SetUpFreeSurfer.csh: No such file or directory. > [root@localhost ~]# > > I have followed all instructions provided on the freesurfer website. > > Thanks in advance for the help, > Binu. > > > Binu Thomas, M.S. > Computer Programmer III > Department of Psychiatry > UT Southwestern Medical Center > Phone: 214-645-2792 > > >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 04/26/06 11:33 AM >>> > Also, try enabling command echoing first, like this: > > set echo=1 > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > this will print-out details of the script as it runs. > > > On Wed, 2006-04-26 at 12:27 -0400, Bruce Fischl wrote: > > Hi Binu, > > > > can you send us the complete screen output from what you tried? > > > > thanks, > > Bruce > > On Wed, 26 > > Apr 2006, Binu Thomas wrote: > > > > > Dear all, > > > I posted a message yesterday regarding the same problem, > > > didn't get much help, hoping to get some help today. I am running > Red > > > Hat Enterprise Linux 3, tried to install Freesurfer CentOS4, when I > try > > > to access the SetUpFreeSurfer.csh file with the "source" command, I > get > > > the error: File or Directory not found. I had the feeling that > CentOS4 > > > version of FreeSurfer might not be compatible with my OS, so I tried > to > > > configure the RH9 version of the software and ended up with the same > > > error. I can see that the file exists in the "freesurfer" folder. I > > > would greatly appreciate any help. > > > > > > Thanks in advance, > > > Binu Thomas. > > > Univ. of TX Southwestern Medical Center. > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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orientation problems
by adam walczak 26 Apr '06

26 Apr '06

Hello, Our scanner outputs data so that the different orientations (sagittal, coronal) are not actually those orientations. For example: the "sagittal view" from our scanner is seen when using the horizontal view in tkmedit. And the sagittal view button produces the coronal view. How can this be fixed? Thanks Adam adam --------------------------------- Celebrate Earth Day everyday! Discover 10 things you can do to help slow climate change. Yahoo! Earth Day

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Re: [Freesurfer] Help with Freesurfer Installation
by Binu Thomas 26 Apr '06

26 Apr '06

Thanks for the reply! Here is a detail of all that I did. I downloaded the RH9 version of the software to my /usr/local directory and installed it with the "tar xzvf" command. I then changed the shell to tcsh and then the rest of the output is as follows: [root@localhost ~]# set echo=1 [root@localhost ~]# setenv FREESURFER_HOME </usr/local>/freesurfer setenv FREESURFER_HOME [root@localhost ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh source /SetUpFreeSurfer.csh /SetUpFreeSurfer.csh: No such file or directory. [root@localhost ~]# I have followed all instructions provided on the freesurfer website. Thanks in advance for the help, Binu. Binu Thomas, M.S. Computer Programmer III Department of Psychiatry UT Southwestern Medical Center Phone: 214-645-2792 >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 04/26/06 11:33 AM >>> Also, try enabling command echoing first, like this: set echo=1 source $FREESURFER_HOME/SetUpFreeSurfer.csh this will print-out details of the script as it runs. On Wed, 2006-04-26 at 12:27 -0400, Bruce Fischl wrote: > Hi Binu, > > can you send us the complete screen output from what you tried? > > thanks, > Bruce > On Wed, 26 > Apr 2006, Binu Thomas wrote: > > > Dear all, > > I posted a message yesterday regarding the same problem, > > didn't get much help, hoping to get some help today. I am running Red > > Hat Enterprise Linux 3, tried to install Freesurfer CentOS4, when I try > > to access the SetUpFreeSurfer.csh file with the "source" command, I get > > the error: File or Directory not found. I had the feeling that CentOS4 > > version of FreeSurfer might not be compatible with my OS, so I tried to > > configure the RH9 version of the software and ended up with the same > > error. I can see that the file exists in the "freesurfer" folder. I > > would greatly appreciate any help. > > > > Thanks in advance, > > Binu Thomas. > > Univ. of TX Southwestern Medical Center. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Help with Freesurfer Installation
by Binu Thomas 26 Apr '06

26 Apr '06

Dear all, I posted a message yesterday regarding the same problem, didn't get much help, hoping to get some help today. I am running Red Hat Enterprise Linux 3, tried to install Freesurfer CentOS4, when I try to access the SetUpFreeSurfer.csh file with the "source" command, I get the error: File or Directory not found. I had the feeling that CentOS4 version of FreeSurfer might not be compatible with my OS, so I tried to configure the RH9 version of the software and ended up with the same error. I can see that the file exists in the "freesurfer" folder. I would greatly appreciate any help. Thanks in advance, Binu Thomas. Univ. of TX Southwestern Medical Center.

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Freesurfer on FC5
by Glenn Lawyer 26 Apr '06

26 Apr '06

Hi, Saw some discussion last week regarding problems with FreeSurfer on a 64 bit FC5 system. I am planning on upgrading from 32-bit FC4 to 64-bit FC5 at the end of this week, and am wondering if the problem was an isolated incident or if I am in for alot of work? Heck, I started my career in medical research as a test-rabbit, one more time shouldn't hurt that much, right? -------------------------------------- The zipper displaces the button and a man lacks just that much time to think while dressing at dawn, a philosophical hour, and thus a mechanical hour. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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Re: [Freesurfer] fsfast "selxavg-sess" error
by Jenn Segawa 26 Apr '06

26 Apr '06

Hello all, I had the same error as this previous post, but after the suggested fix, I'm getting the following matlab output/error messages. Does anyone know what I'm doing wrong? Thanks so much, Jenn %------------------------------------------------- Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 014/fmc 2 016/fmc 3 017/fmc Input Pardigm File List 1 014/parfile.par 2 016/parfile.par 3 017/parfile.par Output Volume funcanal/h F Omnibus Volume funcanal/omnibus/f Sig Omnibus Volume funcanal/omnibus/fsig TR 2.870000 TER 2.870000 Total Window 0 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (6): 1 2 3 4 5 6 Run 1: 72 72 72 72 36 36 Run 2: 72 72 72 72 36 36 Run 3: 72 72 72 72 36 36 Slice 0, 0.000159 -------------- First Pass (Accumulation), 0.024409 Run 1/3, 0.024782 Excluding 0 Points: Run 2/3, 5.67758 Excluding 0 Points: Run 3/3, 11.2836 Excluding 0 Points: Second Pass (Residual Error Estimation), 16.6096 Paradigm Condition: 33.8741 Var Reduction Range: 65.7977 85.9199 97.4559 Computing hhat Run 1/3, 16.6695 Excluding 0 Points: Run 2/3, 17.4337 Excluding 0 Points: Run 3/3, 18.1927 Excluding 0 Points: Saving data to funcanal/h_000.bfloat Saving offset to funcanal/h-offset_000.bfloat ??? Error using ==> .* Matrix dimensions must agree. Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 657 ==> F = sign(qsum) .* Fnum ./ Fden; >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (<subject_dir>/<subject>): selxavg failed %---------------------------------------------------------- On 4/10/06, Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > Add the following lines to your startup.m file > > FSH = getenv('FREESURFER_HOME'); > fshmatlab = sprintf('%s/matlab',FSH); > path(path,fshmatlab); > clear fshmatlab; > > > Paymon Hosseini wrote: > > > hi > > > > i am going over the fsfast tutorial. i have completed all steps up to > > "FsFastTutorial/905 Average session-level data by condition" > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20…<https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://surfer.nm…> on_2dlevel_20data_20by_20condition > > > > > > > > when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", > > i get the following error: > > > > " > > ??? Undefined function or variable 'MRIread'. > > > > Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m > > On line 160 ==> rstd = MRIread(instem,1); > > > >>> ??? Undefined function or variable 'r'. > >> > > > >>> quiting matlab > >> > > ------------------------------------------ > > ERROR: fast_selxavg() failed\n > > ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg > > failed > > " > > > > can you please tell me why i am getting this error? > > > > thanks > > paymon hosseini > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.…> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.…> >

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