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IDProjectCategoryView StatusLast Update
0000083Slicer3GUIpublic2020-03-12 10:51
Reporteruser49Assigned Topieper  
PrioritynormalSeverityfeatureReproducibilityalways
Status closedResolutionfixed 
PlatformMac Intel OSDarwinOS Version 10.4
Summary0000083: X11 DISPLAY environment required, thus preventing easy and reliable batch processing.
Description

Can not run Slicer without a valid display. If the DISPLAY variable is not set, even the “Slicer3 –help” command does not work. Trying to run items in batch mode (i.e. no gui at all with the expectation of running a 1000 data sets in a batch process through condor) requires that a valid display is available to place the “Slicer3 starting up” screen. Even when the –no_splash and –f flags are given.

Even the Slicer3 --help command requires the DISPLAY to be set. The program displays "Slicer3 starting up" gui display, and after about 3 seconds displays the valid command line options.

If the DISPLAY is not set, the error messages to a "Slicer3 --help" are cryptic and it is unclear how to resolve the problem.

Steps To Reproduce

unset DISPLAY;
Slicer3 --help

Additional Information

[hjohnson@HJMBP hjohnson]$ unset DISPLAY
[hjohnson@HJMBP hjohnson]$ ./src/Slicer3-build/Slicer3 --help
no display name and no $DISPLAY environment variable
while executing
"load /Users/hjohnson/src/Slicer3-build/Slicer3/lib/tk8.4/libtk8.4.dylib Tk"
invoked from within
"if {[lsearch -exact [info loaded] {{} Tk}] >= 0} {
load "" Tk
} else {
load /Users/hjohnson/src/Slicer3-build/Slicer3/lib/tk8.4/libtk8.4.dyl..."
("package ifneeded" script)
invoked from within
"package require Tk"
(procedure "launch_SplashScreen" line 3)
invoked from within
"launch_SplashScreen"
(file "/Users/hjohnson/src/Slicer3-build/lib/launch.tcl" line 518)
invoked from within
"source $env(SLICER_HOME)/lib/launch.tcl"
(file "/Users/hjohnson/src/Slicer3-build/Slicer3/main.tcl" line 26)

[hjohnson@HJMBP hjohnson]$ export DISPLAY=localhost:0
[hjohnson@HJMBP hjohnson]$ ./src/Slicer3-build/Slicer3 --help

USAGE:

/Users/hjohnson/src/Slicer3-build/bin/Slicer3-real
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--vtk_debug] [-i] [-o] [-3] [-a]
[-v <std::string>] [-e
<std::string>] [-p <std::string>]
[-f <std::string>] [-x
<std::string>] [-q <std::string>]
[-n <std::string>] [-s
<std::string>] [-m <std::string>]
[-l <std::string>] [-y
<std::string>] [-d <std::string>]
[-k] [--daemon] [--no_modules]
[--no_splash] [-t] [--] [--version]
[-h] <std::vector<std::string>>
...

Where:

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--vtk_debug
Turn on vtk's debug macros (lots of output) (default: 0)

-i, --immediate_mode
Turn on immediate mode rendering (slower) (default: 0)

-o, --old_voxel_shift
start slicer with voxel coords in corner not center of image pixel
(default: 0)

-3, --stereo
Set the flag to allow use of frame sequential stereo (default: 0)

-a, --all_info
Print out all of the version info and continue (default: 0)

-v <std::string>, --eval <std::string>
Like --exec, but doesn't load slicer first

-e <std::string>, --exec <std::string>
Some code to execute after slicer loads. (note: cannot specify scene
after --exec) (note: use ,. instead of ; between tcl statements)

-p <std::string>, --script <std::string>
Script to execute after slicer loads

-f <std::string>, --file <std::string>
Script to execute instead of loading slicer

-x <std::string>, --load_bxh <std::string>
Read bxh file

-q <std::string>, --load_freesurfer_qa <std::string>
Read freesurfer QA subjects.csh file

-n <std::string>, --load_freesurfer_annot <std::string>
Read freesurfer annotation file

-s <std::string>, --load_freesurfer_scalar <std::string>
Read freesurfer scalar file

-m <std::string>, --load_freesurfer_model <std::string>
Read freesurfer model file

-l <std::string>, --load_freesurfer_label_volume <std::string>
Read freesurfer label file

-y <std::string>, --load_freesurfer_volume <std::string>
Read freesurfer file

-d <std::string>, --load_dicom <std::string>
Read dicom files from dir

-k, --tkcon
Brings up just the tk console (default: 0)

--daemon
Turns on the Slicer Daemon (open listening socket port) (default: 0)

--no_modules
Disables the loading of Command Line Modules (default: 0)

--no_splash
Disables the startup splash screen (default: 0)

-t, --no_threads
Disables multi threading (default: 0)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::vector<std::string>> (accepted multiple times)
Remaining arguments to be passed to scripts (-f or -p)

Description: The ultimate 3D Segmentation, Registration and
Visualization System

Author(s): NA-MIC

TagsNo tags attached.

Activities

jcfr

jcfr

2020-03-12 10:51

administrator   ~0016367

Closing. Slicer3 is not being developed anymore.

Issue History

Date Modified Username Field Change
2007-07-08 07:34 user49 New Issue
2007-09-14 11:42 pieper Assigned To => pieper
2007-09-14 11:42 pieper Status new => assigned
2007-11-26 13:02 pieper Status assigned => resolved
2007-11-26 13:02 pieper Resolution open => fixed
2020-03-12 10:51 jcfr Status resolved => closed
2020-03-12 10:51 jcfr Note Added: 0016367