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
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