Hi Mattew,


After modifying the fslstart.tcl file when I click on the Bet button i get the following error:


Error in startup script: couldn't read file "/util/packages/FSL/5.0.9/tcl/bet_gui.tcl": no such file or directory
    while executing
"source ${FSLDIR}/tcl/${origname}.tcl"
    (file "/util/packages/FSL/5.0.9/bin/Bet_gui" line 22)


I tried 2 things.

1.  I renamed /util/packages/FSL/5.0.9/tcl/bet.tcl  to   /util/packages/FSL/5.0.9/tcl/bet_gui.tcl
After which when I load fsl, the Bet button no longer appears on the gui.

2.  I made a symlink,  so bet_gui.tcl calls bet.tcl.  That appears to work now - is that what I should be doing, ro will i run into a problem later on?  Should i do something else?

Thanks so much for your help!
Thomas



From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Matthew Webster <[log in to unmask]>
Sent: Wednesday, February 1, 2017 9:58 AM
To: [log in to unmask]
Subject: Re: [FSL] issues with BET
 
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]> on behalf of Matthew Webster <[log in to unmask]>
Sent: Thursday, January 26, 2017 12:00 PM
To: [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]> 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]> on behalf of Stephen Smith <[log in to unmask]>
Sent: Wednesday, January 25, 2017 10:07 AM
To: [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]> 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]> on behalf of Stephen Smith <[log in to unmask]>
Sent: Wednesday, January 25, 2017 10:03 AM
To: [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]> 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]> on behalf of Matthew Webster <[log in to unmask]>
Sent: Wednesday, January 25, 2017 6:00 AM
To: [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]> 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]> on behalf of Stephen Smith <[log in to unmask]>
Sent: Monday, January 23, 2017 1:49 PM
To: [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]> 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]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

Stop the cultural destruction of Tibet










---------------------------------------------------------------------------
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]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

Stop the cultural destruction of Tibet








---------------------------------------------------------------------------
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]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

Stop the cultural destruction of Tibet