Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

tksurfer/suse 10.1 troubles
by Sebastian Moeller 02 Jul '06

02 Jul '06

Hi List, running freesurfer (centos 4 x86_64 3.0.2 pub full under SuSE 10.1 (had to upgrade from 9.3 because of stability issues)) I get the following Error while trying to run surf-sess (over ssh tunneled X11): surfer: ### GL window already open: can't open second % freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glitInit'. Interestingly both SuSE 9.3 and 10.1 use libglut.so.3.8.0 (freeglut). The exact command I ran from the mystudy directory is: surf-sess -sf sf -df df -analysis a3 -contrast c1_2 -hemi lh -surf inflated This exact command worked with SuSE 9.3 (all OSs 64bit linux). I am downloading 3.0.3 ATM to see whether this was fixed. If any of you have any advise I am keen to hear it ;). Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_segstats only generated values for index 0-82
by Nguyen, Thang Q 30 Jun '06

30 Jun '06

Hello all, I was able to generate statistics on functional overlays but for some reason, the statistics do not have values after the structure name "Right-non-WM-hypointensities." Everything after this region listed has values of zero for the Mean, StdDev, Min, Max, and Range. The command I used is listed below: mri_segstats --brain-vol-from-seg --in subbj1.img --seg aseg-in-subj1.img --ctab-default --sum -subj1.output.txt Is this a problem with the registration, the command line, or something else? Thank you for your help, -Thang Nguyen

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Aseg.stats measurements
by Goradia, Dhruman D 30 Jun '06

30 Jun '06

Hi all, Can anyone tell me how freesurfer defines Intracranial volume, Brain segmentation volume and Brain mask volume? What is the difference between the 3 measures? -Dhruman

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help: freesurfer on debian amd64 (problem with libtiff)
by Davide Anchisi 30 Jun '06

30 Jun '06

Hi, I have an amd64 machine with a Debian GNU/Linux (v. testing) system. I'd like to use freeSurfer but I got some problem. I installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz When I run tkmedit (or tksurf) I get the following message: tkmedit: error while loading shared libraries: libtiff.so.3: cannot open shared obj ect file: No such file or directory On my system I have libtiff4. Any suggestion? Thanks, Davide

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surface area
by Sasha Wolosin 29 Jun '06

29 Jun '06

Dear all, Are the regional surface areas computed by mris_anatomical_stats using the ?h.white surface or the ?h.pial surface? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your 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.

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mri_watershed
by dasoscia＠buffalo.edu 29 Jun '06

29 Jun '06

I am having trouble with one of my skull strips, and getting very extreme results. When I re-run the skullstrip using different watershed values, anything at 56% or below takes 75%+ of the brain out, and as soon as I jump to 57% or higher, it leaves on almost all of the skull, except for maybe 5% of it. Is this indicative of a more complicated problem, and what is my next step (other than manually taking off the skull), if any? Thanks

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RE: [Freesurfer] FreeSurfer Newbie can't get working with FSL onMac OS 10.4
by Don.Rojas＠UCHSC.edu 29 Jun '06

29 Jun '06

Marc, Or you can set the path to your own, newer fsl with something like setenv FSL_DIR /usr/local/fsl if you'd rather not use the fsl distro that comes with freesurfer. Don > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of > Nick Schmansky > Sent: Thursday, June 29, 2006 11:05 AM > To: Marc D. Yelle > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] FreeSurfer Newbie can't get working > with FSL onMac OS 10.4 > > > Marc, > > After sourcing the $FREESURFER_HOME/SetUpFreeSurfer.csh file, add this > line: > > unsetenv TCLLIBPATH > > This is what is causing the conflict with FSL's TCL libs. > > Nick > > > On Thu, 2006-06-29 at 12:26 -0400, Marc D. Yelle wrote: > > Hello, I am in need of some help. I have spent the last two days > > trying to get fsl and freesurfer to play well together. I have the > > newest version of FSL installed and it works perfectly. I then > > installed freesurfer per the instructions listed in the wiki. After > > these steps, freesurfer works, but fsl won't open. I get > this error > > message: > > > > MINC_LIB_DIR /usr/local/freesurfer/mni/lib > > PERL5LIB > > /usr/local/freesurfer/mni/lib/../System/Library/Perl/5.8.6:/sw/l > > ib/perl5:/sw/lib/perl5/darwin > > GSL_DIR /usr/local/freesurfer/lib/gsl > > TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib > > MISC_LIB /usr/local/freesurfer/lib/misc/lib > > FSL_DIR /usr/local/freesurfer/fsl > > > > Marc-Yelles-Computer 1% echo $FSLDIR > > /usr/local/fsl > > > > Marc-Yelles-Computer 2% fsl > > Error in startup script: no suitable image found. Did find: > > /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: > > unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 > > 0x3E 0x0A > > /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: > > unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 > > 0x3E 0x0A > > while executing > > "load /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" > > ("package ifneeded" script) > > invoked from within > > "package require Tix" > > invoked from within > > "if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) > == "wish" } { > > package require Tk > > package require Tix > > tix configure -scheme TixGr..." > > (file "/usr/local/fsl/tcl/fslstart.tcl" line 3) > > invoked from within > > "source [ file dirname [ info script ] ]/fslstart.tcl" > > (file "/usr/local/fsl/tcl/fsl.tcl" line 71) > > invoked from within > > "source ${FSLDIR}/tcl/${origname}.tcl" > > (file "/usr/local/fsl/bin/fsl" line 21 > > > > > > I tinkered with the setupfreesurfer.csh and the freesurferenv.csh > > files and got it to list FSL_DIR as usr/local/fsl but the program > > still wouldn't work. > > > > If I comment out the two freesurfer lines in my .cshrc > file, fsl works > > perfectly once again. My only guess is that there is a > problem with > > both fsl and freesurfer having tktcl libraries. But my > understanding > > of UNIX, etc is somewhat limited. Below I have also attached my > > .cshrc : > > > > #!/bin/tcsh > > set path = (/usr/X11R6/bin $path /sw/sbin /sw/bin > > /Users/marcyelle/bin) set prompt="`hostname -s` \!% " source > > /sw/bin/init.csh source /usr/local/rsi/idl_5.6/bin/idl_setup > > setenv IDL_PATH "<IDL_DEFAULT>:+/usr/local/rsi/idl_5.6/local_lib" > > setenv FREESURFER_HOME /usr/local/freesurfer > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > setenv FSLDIR /usr/local/fsl > > source ${FSLDIR}/etc/fslconf/fsl.csh > > setenv PATH ${FSLDIR}/bin:${PATH} > > unsetenv LANG > > > > > > Thank you in advance for your assistance, I need it! Sorry for the > > long email, I simply wanted to give you as much info as I > could. Take > > care. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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FreeSurfer Newbie can't get working with FSL on Mac OS 10.4
by Marc D. Yelle 29 Jun '06

29 Jun '06

Hello, I am in need of some help. I have spent the last two days trying to get fsl and freesurfer to play well together. I have the newest version of FSL installed and it works perfectly. I then installed freesurfer per the instructions listed in the wiki. After these steps, freesurfer works, but fsl won't open. I get this error message: MINC_LIB_DIR /usr/local/freesurfer/mni/lib PERL5LIB /usr/local/freesurfer/mni/lib/../System/Library/Perl/5.8.6:/sw/l ib/perl5:/sw/lib/perl5/darwin GSL_DIR /usr/local/freesurfer/lib/gsl TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib MISC_LIB /usr/local/freesurfer/lib/misc/lib FSL_DIR /usr/local/freesurfer/fsl Marc-Yelles-Computer 1% echo $FSLDIR /usr/local/fsl Marc-Yelles-Computer 2% fsl Error in startup script: no suitable image found. Did find: /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) == "wish" } { package require Tk package require Tix tix configure -scheme TixGr..." (file "/usr/local/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/usr/local/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/usr/local/fsl/bin/fsl" line 21 I tinkered with the setupfreesurfer.csh and the freesurferenv.csh files and got it to list FSL_DIR as usr/local/fsl but the program still wouldn't work. If I comment out the two freesurfer lines in my .cshrc file, fsl works perfectly once again. My only guess is that there is a problem with both fsl and freesurfer having tktcl libraries. But my understanding of UNIX, etc is somewhat limited. Below I have also attached my .cshrc : #!/bin/tcsh set path = (/usr/X11R6/bin $path /sw/sbin /sw/bin /Users/marcyelle/bin) set prompt="`hostname -s` \!% " source /sw/bin/init.csh source /usr/local/rsi/idl_5.6/bin/idl_setup setenv IDL_PATH "<IDL_DEFAULT>:+/usr/local/rsi/idl_5.6/local_lib" setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} unsetenv LANG Thank you in advance for your assistance, I need it! Sorry for the long email, I simply wanted to give you as much info as I could. Take care. -- Sláinte, -m Marc D. Yelle Dept. Neurobiology and Anatomy Wake Forest School of Medicine Medical Center Blvd. Winston-Salem, NC 27157 myelle(a)wfubmc.edu

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Anatomical Stats
by Anil Roy 29 Jun '06

29 Jun '06

Hi Everyone, Is there a way to process the minc files I have and only obtain the anatomical stats without the entire recon-all process. I have a large number of brains and it would take a couple of weeks if I was to take every minc file and run recon-all. Thanks - Anil.

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mri_normalize -conform question
by Sebastian Moeller 29 Jun '06

29 Jun '06

Hi List, as the subject line says I am having problems running mri_normalize (on suse 9.3 x86_64, freesurfer centos4 x86_64 3.0.2 release). When feeding in slightly unconformed volumes (like 1mm isotropic 256 by 256 by 256 of type 3 (float)) mri_normalize's "-conform" argument fails (fully unconformed volumes are no problem). The error message boils down to MRInormGentlyFindControlPoints: unsupported src format 3" followed by "MRI3dGentleNormalize failure! mri_ctrl=Null". I just work around this by running a full mri_convert --conform on my input file before running mri_normalize. Just a nit, specifying "-v" some where else than at the end of the commandline easily produces segmentation faults (probably because -v is "overloaded" to also expect Gx Gy Gz arguments? the help is a bit terse) Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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