Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

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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retinotopy
by Nurunisa Neyzi 28 Jun '06

28 Jun '06

Hi, during retinotopic mapping, still at the beginning, when I run the analysis (with the command sfa-sess), I get the error: ERROR: meanimg for mean image failed meanimg -i rtopy/eccen/h-offset -i rtopy/polar/h-offset -o rtopy/h-offset and I have h.bdhr and omnibus in my eccen and polar folders... and no h volume folder. (I have f.bhdr, fmc.bhdr, fmc.mcdat, my 32 f-stem and fmc-stem data, rtopy.par, inorm.log and mcparams2extreg.log in 001, 002, etc.) what can be going wrong? Thanks! Nurunisa

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Scale Bar
by Reza Rajimehr 28 Jun '06

28 Jun '06

Hi, Does anybody have any idea what the scale bar shows in Tksurfer? I have heard that the scalebar is 10mm for the human brain. I am working with the monkey brain. Is the length of the scale bar 1cm for the monkey brain as well? Thanks, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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Re: Re: [Freesurfer] Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

Thank you for the response. I may be overly forthcoming here, but when will the next stable release be available. Aju On Thu, 29 Jun 2006 Doug Greve wrote : > >We are still evaluating it, but it should be ready by our next stable release. > >doug > > > >Bruce Fischl wrote: > >>Doug put together a white matter parcellation that does this kind of thing, but I'm not sure what the status of it is. Doug? >>On Wed, 28 Jun 2006, Ajith Kumar U wrote: >> >>>What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work. >>> >>>Aju. >>> >>> >>>On Thu, 29 Jun 2006 Bruce Fischl wrote : >>> >>>>what would the white matter volume of a cortical region mean? >>>>On Wed, 28 Jun 2006, Ajith Kumar U wrote: >>>> >>>>>Hello All, >>>>> >>>>>How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? >>>>> >>>>>Thanks, >>>>> >>>>>Aju. >>>>> >>>>> >>>>>************************************************** >>>>>Mr.Ajith Kumar U >>>>>Junior Research Fellow, >>>>>Department of Audiology, >>>>>All India Institute of Speech and Hearing, Naimisham Camppus, >>>>>Manasagangothri, >>>>>Mysore,570006 >>>>>INDIA. >>>>>Ph: +91 821 2514449 Ext 186 (O) >>>>> +91 821 2514449 Ext 224 (R) >>>>>Fax: +91 821 2510515 >>>>>Email: ajithajitkumar18(a)rediffmail.com >>>>>************************************************** >>>> >>>>_______________________________________________ >>>>Freesurfer mailing list >>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>>************************************************** >>>Mr.Ajith Kumar U >>>Junior Research Fellow, >>>Department of Audiology, >>>All India Institute of Speech and Hearing, Naimisham Camppus, >>>Manasagangothri, >>>Mysore,570006 >>>INDIA. >>>Ph: +91 821 2514449 Ext 186 (O) >>> +91 821 2514449 Ext 224 (R) >>>Fax: +91 821 2510515 >>>Email: ajithajitkumar18(a)rediffmail.com >>>************************************************** >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- 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 ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. **************************************************

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Re: Re: [Freesurfer] Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work. Aju. On Thu, 29 Jun 2006 Bruce Fischl wrote : >what would the white matter volume of a cortical region mean? >On Wed, 28 Jun 2006, Ajith Kumar U wrote: > >>Hello All, >> >>How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? >> >>Thanks, >> >>Aju. >> >> >>************************************************** >>Mr.Ajith Kumar U >>Junior Research Fellow, >>Department of Audiology, >>All India Institute of Speech and Hearing, Naimisham Camppus, >>Manasagangothri, >>Mysore,570006 >>INDIA. >>Ph: +91 821 2514449 Ext 186 (O) >> +91 821 2514449 Ext 224 (R) >>Fax: +91 821 2510515 >>Email: ajithajitkumar18(a)rediffmail.com >>************************************************** >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

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Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

Hello All, How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? Thanks, Aju. ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

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Freesurfer June 2006