Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

RE: [Freesurfer] GNU GPL source?
by Kirk, Gregory 01 May '06

01 May '06

It would be nice whatever could be available for having a detailed look At what some of the code does. Also for persons anticipating trying To do some algorithm work a bit of perusing the code to having a working Understanding would be interesting. Also maybe feedback on what parts of the Code are most in need of a bit of explaining might help with allocating the limited Amount of resources you will be able to devote to such efforts. Cheerio Greg. -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 01, 2006 1:02 PM To: Nick Schmansky Cc: Darren.Weber(a)radiology.ucsf.edu; Freesurfer Mailing List Subject: Re: [Freesurfer] GNU GPL source? p.s. we can't use GPL because of various MGH restrictions (which also unfortunately means we can't use any other GPL code). We could conceivably post an incomplete (and thus unbuildable version) - would that be helpful? We're working towards a make/configure type open source, but aren't there yet. cheers, Bruce On Mon, 1 May 2006, Nick Schmansky wrote: > Darren, > > The freesurfer source code is not ready to be posted for download just > yet. We are currently replacing some code that we cannot distribute > as open-source. > > About your problem with libtiff, I suppose a hacky solution is to try > symlinking libtiff.so.3 to libtiff.so.4. I'll also check if we have a > Debian build on our network. > > Maybe you can answer a question for me. Do you know how to make an > application build against the .so library, instead of the .so.# > version? In other words, I don't know why our build chooses to build > against libtiff.so.3 instead of libtiff.so, since we don't rely on > anything special in the tiff library. > > Nick > > > > On Mon, 2006-05-01 at 08:09 -0700, Darren Weber wrote: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Dear Bruce et al., >> >> I don't see the GNU source download on the wiki. Have you withdrawn >> that download? >> >> I have a Debian testing (etch) system, running in UNICODE mode. The >> rh9 version of tksurfer requires libtiff3, but libtiff4 is now >> available, ie: >> >> dnlweber:~/bin/cpp> ls -l /usr/lib/libtiff* >> - -rw-r--r-- 1 root root 412842 2006-03-28 18:49 /usr/lib/libtiff.a >> - -rw-r--r-- 1 root root 971 2006-03-28 18:49 /usr/lib/libtiff.la >> lrwxrwxrwx 1 root root 16 2006-04-19 23:30 /usr/lib/libtiff.so -> >> libtiff.so.4.2.1 >> lrwxrwxrwx 1 root root 16 2006-04-17 16:38 /usr/lib/libtiff.so.4 -> >> libtiff.so.4.2.1 >> - -rw-r--r-- 1 root root 341988 2006-03-28 18:49 /usr/lib/libtiff.so.4.2.1 >> - -rw-r--r-- 1 root root 6322 2006-03-28 18:49 /usr/lib/libtiffxx.a >> - -rw-r--r-- 1 root root 997 2006-03-28 18:49 /usr/lib/libtiffxx.la >> lrwxrwxrwx 1 root root 18 2006-04-19 23:30 /usr/lib/libtiffxx.so -> >> libtiffxx.so.0.0.6 >> lrwxrwxrwx 1 root root 18 2006-04-19 23:30 /usr/lib/libtiffxx.so.0 >> - -> libtiffxx.so.0.0.6 >> - -rw-r--r-- 1 root root 7528 2006-03-28 18:49 /usr/lib/libtiffxx.so.0.0.6 >> >> >> Anyhow, I'm interested in compiling freesurfer. I recall there was a >> download and instructions for this. >> >> Thanks, Darren >> >> >> - -- >> >> Darren L. Weber, Ph.D. >> Postdoctoral Scholar >> >> Dynamic Neuroimaging Laboratory, >> UCSF Department of Radiology, >> 185 Berry Street, Suite 350, Box 0946, >> San Francisco, CA 94107, USA. >> >> Tel: +1 415 353-9444 >> Fax: +1 415 353-9421 >> www: http://dnl.ucsf.edu/users/dweber >> >> "To explicate the uses of the brain seems as difficult >> a task as to paint the soul, of which it is commonly >> said, that it understands all things but itself." >> Thomas Willis (The Anatomy of the Brain and Nerves, 1664) >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.2.2 (GNU/Linux) >> Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org >> >> iD8DBQFEViSOxaCYN7qs0v4RAss0AJ0RWUQmcWzxntNrexGtnSSOPQGC8wCfcfn1 >> Kc7NW/rZrZdK3zrkhWRcKHI= >> =jXET >> -----END PGP SIGNATURE----- >> >> _______________________________________________ >> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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3T problems
by Fornito, Alexander 30 Apr '06

30 Apr '06

Hi, I'm trying to segment some Siemens 3T images (200x200x256; 1mm3) and have encountered some problems at autorecon1 - the normalization seems to label some of the background as white matter. Needless to say, the skullstrip fails spectacularly. I've attached a snapshot of the T1 image showing the problem.Any ideas as to why this might occur? I'm running recon-all version 1.104 Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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Skullstripping
by Joao Pereira 29 Apr '06

29 Apr '06

Can someone explain me why my the recon-all skull stripping option is writting a file named brainmask.mgz instead of brain.mgz? This is a problem because the subsequent procedures do not recognize the file. Thank you! JP

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Surface intersections
by rhaynes＠neuro.gatech.edu 28 Apr '06

28 Apr '06

After running the final processing stage of recon-all, I viewed the results in tkmedit and noticed several places where the wm and pial surfaces intersect (see attachment). This mostly happens on the medial and temporal areas, but I have seen it elsewhere. Doesn't this cause problems with the cortical thickness estimation? Is there anything else I should be doing to correct this? Thanks. Ryan

2 1

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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