Hello,
If you have renamed the symlinks to be Bet_gui etc, then you can try modifying the line in
$FSLDIR/tcl/fslstart.tcl
reading:
set gui_ext “”
to
set gui_ext “_gui"
and the buttons in the main FSL gui should start to work.
Kind Regards
Matthew
> On 26 Jan 2017, at 18:49, Thomas Beaudry <[log in to unmask]> wrote:
>
> Hi Matthew,
>
> I renamed the all of the symlinks and it fixes the problem for the command line commands (i.e. bet, flirt, fast, etc), but the the GUI button's don't work anymore. When i click on the Bet button i can see that the bet commandline command is called, so no window opens.
>
> Is there a quick fix?
>
> Thanks!
> Thomas
> From: FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>> on behalf of Matthew Webster <[log in to unmask] <mailto:[log in to unmask]>>
> Sent: Thursday, January 26, 2017 12:00 PM
> To: [log in to unmask] <mailto:[log in to unmask]>
> Subject: Re: [FSL] issues with BET
>
> Hello,
> If you rename the symbolic links ( e.g Bet to Bet_gui ) and then copy, it should work.
>
> Kind Regards
> Matthew
>
>> On 25 Jan 2017, at 15:20, Thomas Beaudry <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>>
>> Thanks Steve, you are correct, my filesystem didn't distinguish uppercase from lowercase files, so the install wasn't working. When I installed it locally (not on the NFS share) it worked. I tried copying the local install to my NFS share I got these errors:
>>
>> perform-admin@perf-hpc01:/util/packages/FSL$ cp -r /home/perform-admin/fsl .
>> cp: cannot create regular file './fsl/extras/man/mann/pkg::create.n': Invalid argument
>> cp: cannot create regular file './fsl/extras/src/libgd/readme.txt': File exists
>> cp: cannot create symbolic link './fsl/bin/Renderhighres': File exists
>> cp: cannot create symbolic link './fsl/bin/Possum': File exists
>> cp: cannot create symbolic link './fsl/bin/Bet': File exists
>> cp: cannot create symbolic link './fsl/bin/Fsl_prepare_fieldmap': File exists
>> cp: cannot create symbolic link './fsl/bin/Flirt': File exists
>> cp: cannot create symbolic link './fsl/bin/Melodic': File exists
>> cp: cannot create symbolic link './fsl/bin/Fast': File exists
>> cp: cannot create symbolic link './fsl/bin/Susan': File exists
>> cp: cannot create symbolic link './fsl/bin/Featquery': File exists
>> cp: cannot create symbolic link './fsl/bin/Feat': File exists
>>
>>
>> Has anyone had to deal with this and knows a solution? Could i change modify some code and change the uppercase File names i.e. replace Bet with Bet_gui or something along those lines (or is it a big headache?)
>>
>> Thanks for your help guys!
>> Thomas
>>
>> From: FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>> on behalf of Stephen Smith <[log in to unmask] <mailto:[log in to unmask]>>
>> Sent: Wednesday, January 25, 2017 10:07 AM
>> To: [log in to unmask] <mailto:[log in to unmask]>
>> Subject: Re: [FSL] issues with BET
>>
>> If your file system doesn't distinguish, you won't even have two distinct files - Ubuntu can't fix that.
>> Steve.
>>
>>
>>> On 25 Jan 2017, at 15:04, Thomas Beaudry <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>
>>> Hi Steve,
>>>
>>> But I invoke it from unbuntu command line, so I'm calling the correct file.
>>>
>>> Thomas
>>> From: FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>> on behalf of Stephen Smith <[log in to unmask] <mailto:[log in to unmask]>>
>>> Sent: Wednesday, January 25, 2017 10:03 AM
>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>> Subject: Re: [FSL] issues with BET
>>>
>>> Hi - maybe your filesystem you're installing on doesn't distinguish between uppercase and lowercase filenames.
>>> Steve.
>>>
>>>
>>>> On 25 Jan 2017, at 14:54, Thomas Beaudry <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>>
>>>> Hi Matthew,
>>>>
>>>> Thanks a lot for answering. Here are my results:
>>>>
>>>> perform-admin@perf-hpc01:~$ which Bet
>>>> /util/packages/FSL/5.0.9/bin/Bet
>>>> perform-admin@perf-hpc01:~$ which bet
>>>> /util/packages/FSL/5.0.9/bin/bet
>>>>
>>>> Something that I noticed is that when i look at the file contents of bet, it looks identical to fsl, which definitely seems wrong:
>>>>
>>>> perform-admin@perf-hpc01:~$ cat /util/packages/FSL/5.0.9/bin/bet
>>>> #!/bin/sh
>>>>
>>>> # Check for display being set \
>>>> if [ _$DISPLAY = _ ] ; then echo "DISPLAY is not set. Please set your DISPLAY environment variable!" ; exit 1 ; fi
>>>> # Check for FSLDIR being set \
>>>> if [ -z "$FSLDIR" ]; then echo "You need to set the FSLDIR environment variable to point to the FSL installation directory before you can run anything." ; exit 1; fi
>>>> # Check for FSLDIR being valid \
>>>> if [ ! -f $FSLDIR/etc/fslconf/fsl.sh ]; then echo "You need to set the FSLDIR environment variable to point to the FSL installation directory before you can run anything." ; exit 1; fi
>>>>
>>>> # the next line restarts using wish \
>>>> if [ _$FSLWISH = _ ] ; then echo "You need to source an FSL setup file - either fsl.sh or fsl.csh in \$FSLDIR/etc/fslconf !" ; exit 1 ; else exec $FSLWISH "$0" -- "$@" ; fi
>>>>
>>>> set FSLDIR $env(FSLDIR)
>>>>
>>>> set origname [ string tolower [ file tail [ info script ] ] ]
>>>>
>>>> set UNAME [ exec uname ]
>>>> if { $UNAME == "Darwin" || [ string compare CYGWIN [ string range $UNAME 0 5 ] ] == 0 } {
>>>> regsub "_gui" $origname "" origname
>>>> }
>>>>
>>>> source ${FSLDIR}/tcl/${origname}.tcl
>>>>
>>>> exit
>>>>
>>>>
>>>>
>>>> One of the first things I tried was installing the package again, and I got the same results. I used the fsl-5.0.9-centos6_64.tar.gz package since a system admin running ubuntu 14.04 at a nearby university uses it without having any issues (i'm running ubuntu 16.04).
>>>>
>>>> Also, I don't know if it's important, but I installed FSL on a windows NFS share that doesn't allow hard links, so while untaring i got a few errors like:
>>>>
>>>> tar: fsl/extras/man/man3/Tcl_ChannelWideSeekProc.3: Cannot hard link to ‘fsl/extras/man/man3/Tcl_GetChannelType.3’: Operation not permitted
>>>> tar: fsl/extras/man/man3/Tk_DestroyWindow.3: Cannot hard link to ‘fsl/extras/man/man3/Tk_CreateWindow.3’: Operation not permitted
>>>>
>>>> But all of these errors were in the man directory so I wasn't really worried about them.
>>>>
>>>> Thank you so much for your help,
>>>> Thomas
>>>>
>>>> From: FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>> on behalf of Matthew Webster <[log in to unmask] <mailto:[log in to unmask]>>
>>>> Sent: Wednesday, January 25, 2017 6:00 AM
>>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>>> Subject: Re: [FSL] issues with BET
>>>>
>>>> Hello,
>>>> I have just installed FSL on a fresh Ubuntu system and Bet/bet are working correctly. Can you let me know the results of running
>>>>
>>>> which Bet
>>>> which bet
>>>> on your system?
>>>>
>>>> Kind Regards
>>>> Matthew
>>>>
>>>>> On 23 Jan 2017, at 18:52, Thomas Beaudry <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Bet and bet produce the sam result - they open the GUI.
>>>>>
>>>>> How can i fix this? Thanks!
>>>>> Thomas
>>>>> From: FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>> on behalf of Stephen Smith <[log in to unmask] <mailto:[log in to unmask]>>
>>>>> Sent: Monday, January 23, 2017 1:49 PM
>>>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>>>> Subject: Re: [FSL] issues with BET
>>>>>
>>>>> Hi
>>>>>
>>>>> "Bet" (capitalised) should open the GUI
>>>>> "bet" (lowercase) should run the non-GUI command-line program.
>>>>>
>>>>> If that's not happening then I guess the Debian implementation is wrong?
>>>>> Cheers.
>>>>>
>>>>>
>>>>>
>>>>>> On 23 Jan 2017, at 18:26, Thomas Beaudry <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>>>>
>>>>>> Hi All,
>>>>>>
>>>>>> I am running into a strange problem with BET (using FSL 5.0.9 on ubuntu). In the command line, when I type BET it opens a gui (instead of being a command line command). Also within the FSL gui, if i click on BET button followed by the go button, it open up another bet gui.
>>>>>>
>>>>>> Any help would be greatly appreciated!
>>>>>> Thomas
>>>>>
>>>>>
>>>>> ---------------------------------------------------------------------------
>>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>>> Head of Analysis, Oxford University FMRIB Centre
>>>>>
>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>>> +44 (0) 1865 222726 (fax 222717)
>>>>> [log in to unmask] <mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve>
>>>>> ---------------------------------------------------------------------------
>>>>>
>>>>> Stop the cultural destruction of Tibet <http://smithinks.net/>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Head of Analysis, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] <mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve>
>>> ---------------------------------------------------------------------------
>>>
>>> Stop the cultural destruction of Tibet <http://smithinks.net/>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Head of Analysis, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] <mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve>
>> ---------------------------------------------------------------------------
>>
>> Stop the cultural destruction of Tibet <http://smithinks.net/>
>>
>>
>>
>>
>>
>>
>
>
