AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
January 11, 2023 04:23PM
Dear AFNI experts,
I'm trying to run realtime demo 1 in the directory: AFNI_data6/realtime.demos. When I launch the script from the demo_1_run1 directory like this:
./demo.1.run1

I get this output:
Precompiled binary linux_ubuntu_16_64: Jan 6 2023 (Version AFNI_23.0.00 'Commodus')

Thanks go to B Feige for advice and help

Initializing: X11[The X.Org Foundation v 12101003].. Widgets...... Input files:[Global]
** Searching subdirectories of './' for data
AFNI_GLOBAL_SESSION = /usr/local/afni/bin/ 77 datasets
image count = 77
Timeseries.1D = 0 files read
.[tc]sv data = 0 files read
Path(s) to be searched for plugins:
/usr/local/afni/bin
** RTM: clearing Mask_Vals setting from Motion_Only
as AFNI_REALTIME_MP_HOST_PORT is unset
-- no T2star_ref from env

Plugins = 49 libraries read
write compress= GZIP
RT: AFNI realtime plugin is active; cf. README.realtime document

++ NOTE: This version of AFNI was built Jan 6 2023 ++
++ NOTE: 'Define Markers' is hidden: right-click 'DataDir' to see it
++ NOTE: Use '-seehidden' option to see which plugins are hidden
++ AFNI is detached from terminal.
RT: starting to listen for control stream.
[1] + Done afni -rt


ready to run Dimon
press enter to proceed...

Dimon version 4.30 (November 2, 2022) running, use <ctrl-c> to quit...

RT:---------------------------------------
RT: connected to control stream 127.0.0.1
RT: version 23 Jan 2020: ROIs_and_data
RT: init RT input via control channel
Can't connect? tcp_connect[connect]: Connection refused
RT: waiting for data stream to become good.
ART: comm link to afni established at <localhost>
-- scanning for first volume

-- first volume found (34 slices)
RT: receiving image metadata=472 bytes
## PARSE RT Detrend: RT Options mode 0x0 polort -1 fwhm 0
-- scanning for additional volumes...
-- run 3: 1 2 RT: sending dataset rt.__001+orig with 2 bricks
to AFNI[A], session /usr/local/afni/bin/

Fatal Signal 11 (SIGSEGV) received
AFNI_autorange_label
AFNI_reset_func_range
AFNI_setup_viewing
AFNI_initialize_view
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_23.0.00 Compile date = Jan 6 2023
** [[Precompiled binary linux_ubuntu_16_64: Jan 6 2023]]
** 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 /home/wgraves/.afni.crashlog
3 ART: ** failed to transmit data to afni @ localhost
- closing afni connection
- iochan error: iochan_goodcheck: no longer alive
ART: exit: closing afni control channel
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 . . .

final run statistics:
volume info :
slices : 34
z_first : -43.93
z_last : 71.57
z_delta : 3.5
oblique : no
mos_nslices : 0

run # 3 : volumes = 67, first file (#0) = ../../EPI_run1/8HRBRAINAx2DGRE-00001.dcm

I'd appreciate any help you could give!

Best,
Will
Subject Author Posted

realtime demo crashes

wgraves January 11, 2023 04:23PM

Re: realtime demo crashes

rick reynolds January 11, 2023 07:25PM

Re: realtime demo crashes

wgraves January 11, 2023 09:32PM

Re: realtime demo crashes

rick reynolds January 11, 2023 10:47PM

Re: realtime demo crashes

wgraves January 12, 2023 01:21PM

Re: realtime demo crashes

rick reynolds January 12, 2023 05:49PM

Re: realtime demo crashes

wgraves January 13, 2023 12:13PM

Re: realtime demo crashes

rick reynolds January 13, 2023 01:41PM