Yeah - I would STRONGLY recommend that you just don't serve $FSLDIR
from a Mac server onto your Sun - you will find it much easier to
solve these problems if you just host it locally - plus there are
many problems with Apple's file server software that will probably
cause problems for you, unrelated to getting FSL running.
Cheers, Steve.
On 21 May 2007, at 18:48, Christian Beckmann wrote:
> Hi
>
> these are the GUI programs included in the MacOSX release (in
> general the uppercase versions are GUIs and the lowercase version
> are the CLIs)
> /usr/local/fsl/bin/ApplyXFM_gui
> /usr/local/fsl/bin/Glm_gui
> /usr/local/fsl/bin/Bet_gui
> /usr/local/fsl/bin/InvertXFM_gui
> /usr/local/fsl/bin/ConcatXFM_gui
> /usr/local/fsl/bin/Make_flobs_gui
> /usr/local/fsl/bin/Fast_gui
> /usr/local/fsl/bin/Melodic_gui
> /usr/local/fsl/bin/Fdt_gui
> /usr/local/fsl/bin/Nudge_gui
> /usr/local/fsl/bin/Feat_gui
> /usr/local/fsl/bin/Renderhighres_gui
> /usr/local/fsl/bin/Featquery_gui
> /usr/local/fsl/bin/Renderstats_gui
> /usr/local/fsl/bin/Featwatcher_gui
> /usr/local/fsl/bin/Susan_gui
> /usr/local/fsl/bin/Flirt_gui
> /usr/local/fsl/bin/fsl_gui
>
> You'd then call Feat_gui instead of feat - make sure that a call to
> 'feat' on the command line gets you a simple usage info and does
> not bring up any windows. It seems you don't have the 'feat' script
> in /FSLDIR/bin (it got lost when untarring on your non-case
> specific file system - you'll need to un-tar again and copy these
> files over (Maybe grab a macosx copy of FSL to see what your /bin
> should look like)
> cheers
> christian
>
>
>
>
> On 21 May 2007, at 17:22, Lokke Highstein wrote:
>
>> i don't know how to differentiate the GUI programs from the CLI
>> versions.
>>
>> here is the /bin directory:
>>
>> ApplyXFM convert
>> img2imgcoord runavw
>> ConcatXFM convert_xfm
>> img2stdcoord selfintersection
>> Fast convertb
>> imglob sigloss
>> Feat convertwarp
>> imln slicer
>> Featquery create_lut
>> immv slices
>> Featwatcher design_ttest2
>> imrm slicesdir
>> Flirt display
>> imtest slicetimer
>> Glm displayb
>> ip smoothest
>> InvertXFM distancemap
>> ip_16SI sphere
>> Make_flobs drawmesh
>> ip_16UI standard_space_roi
>> Melodic easythresh
>> ip_32R std2imgcoord
>> Nudge eqn2gif
>> ip_32SI susan_smooth
>> Renderhighres estnoise
>> ip_32UI susan_smooth_16SI
>> Renderstats extractfidparams
>> ip_8SI tbss_1_preproc
>> Runtcl extracttxt
>> ip_8UI tbss_2_reg
>> Susan fast_exe
>> makehtmeqns tbss_3_postreg
>> afni2avw fdr
>> makerot tbss_4_prestats
>> applywarp feat2afni
>> mccutup tbss_non_FA
>> applyxfm4D feat_model
>> mcflirt tbss_reg
>> avscale featregapply
>> mean tbss_skeleton
>> avw2afni film_gls
>> mfast tclsh
>> bet filmbabe
>> mfast_exe tclsh8.4
>> bet2 filmbabescript
>> midtrans tixindex
>> bet_16SI flame
>> mm tixwish8.1.8.4
>> bet_32R freqtest
>> morph_kernel tmpnam
>> bet_32SI fsl
>> overlay tsplot
>> bet_8UI fsl_gui
>> pairreg ttologp
>> betall fslerrorreport
>> perfusion_subtract ttoz
>> betfunc fslpres
>> pngappend updatefeatreg
>> betpremask ftoz
>> pointflirt vmapper
>> betsmallz fugue
>> prelude wish
>> betsurf gifmerge
>> prewhiten wish8.4
>> cluster gnuplot
>> ptoz wpng
>> cluster2html halfcosbasis
>> randomise ztop
>> connectedcomp hist2prob remove_ext
>> contrast_mgr imcp rmsdiff
>>
>> i edited the $FSLDIR/tcl/fslstart.tcl file to set the plain UNIX
>> settings to match the Darwin ones, but it still seems to be
>> opening a new FEAT window rather than starting analysis.
>>
>> here's the fslstart.tcl file:
>>
>> # test for whether we are in tclsh or wish
>> if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) ==
>> "wish" } {
>> package require Tk
>> package require Tix
>> tix configure -scheme TixGray
>> option add *AutoRepeat false
>> }
>>
>> set FSLDIR $env(FSLDIR)
>>
>> set FSLCONVERT $env(FSLCONVERT)
>> set FSLGNUPLOT $env(FSLGNUPLOT)
>> set FSLOUTPUTTYPE $env(FSLOUTPUTTYPE)
>> set FSLTCLSH $env(FSLTCLSH)
>> set FSLWISH $env(FSLWISH)
>> set FSLDISPLAY $env(FSLDISPLAY)
>> set FSLBROWSER $env(FSLBROWSER)
>>
>> set USER $env(USER)
>> set HOME [ exec sh -c " cd ; pwd " ]
>> set PWD [ exec sh -c " pwd " ]
>> set PROCID [ pid ]
>> set HOSTNAME [ exec hostname ]
>> set OS [ exec uname ]
>>
>> set auto_path [ linsert $auto_path 0 $FSLDIR/tcl ]
>>
>> if { ! [ info exists INGUI ] } {
>> source $FSLDIR/tcl/FSLFileDirBox.tcl
>> source $FSLDIR/tcl/FSLFileDirDlg.tcl
>> source $FSLDIR/tcl/FSLFileEntry.tcl
>> }
>>
>> # what type of OS?
>> set OSFLAVOUR unix
>> set gui_ext "_gui"
>> set FSLSLASH ""
>> set UNAME [ exec uname ]
>> if { $UNAME == "Darwin" } {
>> set OSFLAVOUR macos
>> set gui_ext "_gui"
>> } elseif { [ string compare CYGWIN [ string range $UNAME 0 5 ] ]
>> == 0 } {
>> set OSFLAVOUR cygwin
>> set gui_ext "_gui"
>> set FSLSLASH "C:/cygwin"
>> }
>>
>>
>> On May 19, 2007, at 3:50 PM, Christian Beckmann wrote:
>>
>>> Hi,
>>>
>>> I think it's as simple as (i) making sure that the GUI programs
>>> in $FSLDIR/bin have the _gui ending and (ii) changing the
>>> relevant lines 40+ in $FSLDIR/tcl/fslstart.tcl so that 'gui_ext'
>>> is set to _gui on your platform.
>>> hope this helps
>>> Christian
>>>
>>>
>>>
>>> On 19 May 2007, at 13:37, Lokke Highstein wrote:
>>>
>>>> that is quite possible.
>>>>
>>>> the files are being served off of an osx server, mounted on the
>>>> solaris 9 server via NFS.
>>>>
>>>> any idea on how we can convince FSL to use the mac filesystem
>>>> rules with the solaris operating system?
>>>>
>>>> On May 19, 2007, at 2:40 AM, Steve Smith wrote:
>>>>
>>>>> Hi - this sounds like upper/lower-case confusion - is your
>>>>> filesystem not case sensitive? If this is the case then you'll
>>>>> need to convince FSL that this follows the same rules as
>>>>> Windows and Mac, i.e. that the GUIs have "_gui" appended at the
>>>>> end to differentiate them from the command line
>>>>> programs.....sorry we can't add more detailed support for these
>>>>> other UNIX flavours that we haven't seen before.
>>>>>
>>>>> Cheers.
>>>>>
>>>>>
>>>>> On 18 May 2007, at 13:27, Lokke Highstein wrote:
>>>>>
>>>>>> i mean another copy of the main FEAT gui, i wish the
>>>>>> Featwatcher gui would come up, that would be the desired result.
>>>>>>
>>>>>> thanks for the reply
>>>>>>
>>>>>> On May 18, 2007, at 1:53 AM, Steve Smith wrote:
>>>>>>
>>>>>>> Hi - do you mean that another copy of the main FEAT GUI comes
>>>>>>> up, or the Featwatcher GUI?
>>>>>>> Cheers.
>>>>>>>
>>>>>>>
>>>>>>> On 17 May 2007, at 18:58, Lokke Highstein wrote:
>>>>>>>
>>>>>>>> hello -
>>>>>>>>
>>>>>>>> i am a systems admin at an fMRI research center and am
>>>>>>>> trying to get the latest version of FSL compiled and running
>>>>>>>> for my users.
>>>>>>>>
>>>>>>>> our system is running solaris 9 and we (finally after many
>>>>>>>> tries) managed to get FSL 3.3.11 to compile with no errors,
>>>>>>>> however we are
>>>>>>>> still seeing a bizzare error.
>>>>>>>>
>>>>>>>> when we launch FSL, the gui comes up just fine, and we can
>>>>>>>> launch the FEAT gui as well, but once a design.fsf file has
>>>>>>>> been loaded, and the "go" button is clicked, all that
>>>>>>>> happens is that another FEAT gui window comes up (and
>>>>>>>> nothing gets processed.)
>>>>>>>>
>>>>>>>> has anyone experienced this? i tried to search the archives
>>>>>>>> but found no reference to it.
>>>>>>>>
>>>>>>>> thanks!
>>>>>>>>
>>>>>>>> lokke highstein
>>>>>>>> systems admin
>>>>>>>> fmri research center
>>>>>>>> columbia university
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------
>>>>>>> -----------
>>>>>>> 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)
>>>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>>>>> ----------------------------------------------------------------
>>>>>>> -----------
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> ---------
>>>>> 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)
>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>>> ------------------------------------------------------------------
>>>>> ---------
>>>
>>> ____
>>> Christian F. Beckmann
>>> University Research Lecturer
>>> Oxford University Centre for Functional MRI of the Brain (FMRIB)
>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
>>> tel: +44 1865 222551 fax: +44 1865 222717
>
> ____
> Christian F. Beckmann
> University Research Lecturer
> Oxford University Centre for Functional MRI of the Brain (FMRIB)
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
> tel: +44 1865 222551 fax: +44 1865 222717
------------------------------------------------------------------------
---
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)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
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