Hi Mattew,
After modifying the fslstart.tcl file when I click on the Bet button i get the following error:
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 BETHello,If you rename the symbolic links ( e.g Bet to Bet_gui ) and then copy, it should work.
Kind RegardsMatthew
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 argumentcp: cannot create regular file './fsl/extras/src/libgd/readme.txt': File existscp: cannot create symbolic link './fsl/bin/Renderhighres': File existscp: cannot create symbolic link './fsl/bin/Possum': File existscp: cannot create symbolic link './fsl/bin/Bet': File existscp: cannot create symbolic link './fsl/bin/Fsl_prepare_fieldmap': File existscp: cannot create symbolic link './fsl/bin/Flirt': File existscp: cannot create symbolic link './fsl/bin/Melodic': File existscp: cannot create symbolic link './fsl/bin/Fast': File existscp: cannot create symbolic link './fsl/bin/Susan': File existscp: cannot create symbolic link './fsl/bin/Featquery': File existscp: 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 BETHi - 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/Betperform-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 BETHello,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 Betwhich beton your system?
Kind RegardsMatthew
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 BETHi
"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