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History of AFNI updates  

|
September 29, 2019 02:58AM
Hi

I'm trying to see results of retinoproc called @ShowResult, but when I click the menu 'object controller' it's suddenly terminated.
Below is the output. What should I do?

tcsh @ShowResult
[1] 32209

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/9(Local Domain Parent), loading ...
1
SUMA_niml_call: Contacting on tcp:127.0.0.1:53219 (6), maximum wait 300.000 sec
(You can change max. wait time with env. SUMA_DriveSumaMaxWait)

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #2/9 (mappable via Local Domain Parent), loading ...
.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #3/9 (mappable via Local Domain Parent), loading ...

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #4/9 (mappable via Local Domain Parent), loading ...
++ Notice SUMA_SurfaceMetrics_eng (SUMA_Load_Surface_Object.c:4492 @15:53:27):
(IGNORE for surface with cuts)
Cannot inherit Edge List
and First Neightbor.
Cause: Node number mismatch.
Independent lists will
be created.


vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #5/9 (mappable via Local Domain Parent), loading ...
++ Notice SUMA_SurfaceMetrics_eng (SUMA_Load_Surface_Object.c:4492 @15:53:27):
(IGNORE for surface with cuts)
Cannot inherit Edge List
and First Neightbor.
Cause: Node number mismatch.
Independent lists will
be created.

.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #6/9 (mappable via Local Domain Parent), loading ...

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #7/9 (mappable via Local Domain Parent), loading ...

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #8/9 (mappable via Local Domain Parent), loading ...

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #9/9 (mappable via Local Domain Parent), loading ...
SUMA_Engine: Starting to listen ...

++ Notice SUMA_niml_workproc (SUMA_niml.c:303 @15:53:27):
++ NIML connection opened from 127.0.0.1 on port 53219 (6th stream)

Waiting for SUMA to close stream .++ Notice SUMA_XtWarn_handler (SUMA_display.c:4114 @15:53:28):
X11 Warning 1:Cannot find callback list in XtAddCallback
Have 1 X11 warnings so far, see Help-->Message Log if curious.
This notice is shown once for each additional 10 warnings.

.SUMA_niml_hangup: stream index 6
.Done.
Minsunui-MacBook-Pro:retinoResult minsunpark$ Warning SUMA_Sphinx_DeRef:
No forward quote after ref! in Save the Drawn ROI to disk.
Choose the file format and what is to be
saved from the two menus ahead.

File format for saving ROI:
Format options are 1D and NIML.
The 1D format is the same one used in AFNI.
It is an ASCII file with 2 values per line. The first
value is a node index, the second is the node's value.
Needless, to say, this format does not support the storage
of ROI auxiliary information such as Label and
Parent Surface, etc., nor does it preserve the order in which
nodes are traversed during a tracing. For that you'll have to use :term:NIML.
NIML is a whole different story which will be documented
(if necessary) in the future. Suffice it to say that in NIML
format you can store all the auxiliary information about
each ROI, unlike with the .1D format.
But more importantly, the NIML format allows you to preserve
-------------------- the order in which you traced the ROI.
This information can be later used for the purpose of sampling
cortical activity along a particular path. This would be accomplished
with the aid of ROI2dataset's -nodelist* options, along with
ConvertDset's -node_select_1D option.

Which ROIs to save?
This: saves the current ROI.
All: saves all ROIs on surfaces related to the Parent
surface of the current ROI.
Warning SUMA_Sphinx_DeRef:
No forward quote after ref! in File format for saving ROI:
Format options are 1D and NIML.
The 1D format is the same one used in AFNI.
It is an ASCII file with 2 values per line. The first
value is a node index, the second is the node's value.
Needless, to say, this format does not support the storage
of ROI auxiliary information such as Label and
Parent Surface, etc., nor does it preserve the order in which
nodes are traversed during a tracing. For that you'll have to use :term:NIML.
NIML is a whole different story which will be documented
(if necessary) in the future. Suffice it to say that in NIML
format you can store all the auxiliary information about
each ROI, unlike with the .1D format.
But more importantly, the NIML format allows you to preserve
-------------------- the order in which you traced the ROI.
This information can be later used for the purpose of sampling
cortical activity along a particular path. This would be accomplished
with the aid of ROI2dataset's -nodelist* options, along with
ConvertDset's -node_select_1D option.

xp_import_surface: assertion failed: s == NULL
error: xp_import_surface returned: 2
xp_destroy_surface: assertion failed: s != NULL
xp_destroy_surface error: 3
oo Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++ Notice SUMA_XErrHandler (SUMA_display.c:4148 @15:53:42):
Trace At Xerr
SUMA_XErrHandler
SUMA_glXMakeCurrent
SUMA_cmap_wid_graphicsInit
SUMA_BringUpSurfContTLS
SUMA_viewSurfaceCont
SUMA_cb_viewSurfaceCont
suma
Bottom of Debug Stack
-- Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
-- Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
SUMA_glXMakeCurrent
SUMA_cmap_wid_graphicsInit
SUMA_BringUpSurfContTLS
SUMA_viewSurfaceCont
SUMA_cb_viewSurfaceCont
suma
Bottom of Debug Stack
Error SUMA_cmap_wid_graphicsInit: Failed in SUMA_glXMakeCurrent.
Continuing ...
SUMA_cmap_wid_graphicsInit (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_cmap_wid_graphicsInit: No errors found.
xp_import_surface: assertion failed: s == NULL
error: xp_import_surface returned: 2
xp_destroy_surface: assertion failed: s != NULL
xp_destroy_surface error: 3
oo Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++ Notice SUMA_XErrHandler (SUMA_display.c:4148 @15:53:42):
Trace At Xerr
SUMA_XErrHandler
SUMA_glXMakeCurrent
SUMA_cmap_wid_handleRedisplay
SUMA_InitializeColPlaneShell_SO
SUMA_viewSurfaceCont
SUMA_cb_viewSurfaceCont
suma
Bottom of Debug Stack
-- Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
-- Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
SUMA_glXMakeCurrent
SUMA_cmap_wid_handleRedisplay
SUMA_InitializeColPlaneShell_SO
SUMA_viewSurfaceCont
SUMA_cb_viewSurfaceCont
suma
Bottom of Debug Stack
-- Error SUMA_cmap_wid_handleRedisplay (SUMA_xColBar.c:381):
Failed in SUMA_glXMakeCurrent.
Continuing ...

Fatal Signal 11 (SIGSEGV) received
SUMA_cmap_wid_display
SUMA_cmap_wid_handleRedisplay
SUMA_InitializeColPlaneShell_SO
SUMA_viewSurfaceCont
SUMA_cb_viewSurfaceCont
suma
Bottom of Debug Stack
** AFNI version = AFNI_19.2.21 Compile date = Aug 29 2019
** [[Precompiled binary macos_10.12_local: Aug 29 2019]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/minsunpark/.afni.crashlog
Subject Author Posted

SUMA crash when opening object controller

Mpark September 29, 2019 02:58AM

Re: SUMA crash when opening object controller

Daniel Glen September 30, 2019 06:45PM

[SOLVED]Re: SUMA crash when opening object controller

Mpark October 01, 2019 12:18AM