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
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