I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer?
[Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/Cliff/Imaging/freesurfer FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5 .8.6 GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib FSL_DIR /users/cliff/fsl [Clifford-Smiths-Computer:~] Cliff% fsl Error in startup script: no suitable image found. Did find: /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] != 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/users/cliff/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/users/cliff/fsl/bin/fsl" line 19) [Clifford-Smiths-Computer:~] Cliff%
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Hi - I suspect that the simplest solution is to source the FreeSurfer setup _before_ the FSl setup. Cheers, Steve.
On 21 Mar 2006, at 16:36, Clifford A. Smith, PhD wrote:
I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer?
[Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/Cliff/Imaging/freesurfer FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/ Library/Perl/5 .8.6 GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib FSL_DIR /users/cliff/fsl [Clifford-Smiths-Computer:~] Cliff% fsl Error in startup script: no suitable image found. Did find: /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] != 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/users/cliff/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/users/cliff/fsl/bin/fsl" line 19) [Clifford-Smiths-Computer:~] Cliff%
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---
Clifford,
After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
unsetenv TCLLIBPATH
This should take care of the problem you are seeing. You may want to include that line in your SetUpFreeSurfer.csh file.
Nick
On Tue, 2006-03-21 at 10:36 -0600, Clifford A. Smith, PhD wrote:
I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer?
[Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/Cliff/Imaging/freesurfer FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5 .8.6 GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib FSL_DIR /users/cliff/fsl [Clifford-Smiths-Computer:~] Cliff% fsl Error in startup script: no suitable image found. Did find: /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/users/cliff/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/users/cliff/fsl/bin/fsl" line 19) [Clifford-Smiths-Computer:~] Cliff%
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That was it. Thanks so much. Just added the unsetenv line to my .cshrc file.
Cliff
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
From: Nick Schmansky nicks@nmr.mgh.harvard.edu Date: Tue, 21 Mar 2006 12:28:43 -0500 To: "Clifford A. Smith, PhD" csmith13@rush.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSL/Freesurfer
Clifford,
After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
unsetenv TCLLIBPATH
This should take care of the problem you are seeing. You may want to include that line in your SetUpFreeSurfer.csh file.
Nick
On Tue, 2006-03-21 at 10:36 -0600, Clifford A. Smith, PhD wrote:
I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer?
[Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/Cliff/Imaging/freesurfer FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5 .8.6 GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib FSL_DIR /users/cliff/fsl [Clifford-Smiths-Computer:~] Cliff% fsl Error in startup script: no suitable image found. Did find: /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/users/cliff/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/users/cliff/fsl/bin/fsl" line 19) [Clifford-Smiths-Computer:~] Cliff%
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Clifford A. Smith, PhD -
Nick Schmansky -
Steve Smith