AFNI program: plugout_drive
Output of -help
Usage: plugout_drive [-host name] [-v]
This program connects to AFNI and sends commands
that the user specifies interactively or on command line
over to AFNI to be executed.
If you quit plugout_drive and then re-start it immediately
(as in a script), you might run into problems re-connecting
to AFNI. The reason is that the TCP/IP system doesn't hang
up a socket instantly when commanded to do so; the socket
takes about a second to close down completely. If you are
writing a script that starts plugout_drive repeatedly, you
should insert a command 'sleep 1' between each start, to
give the operating system time to clean the socket up.
Otherwise, AFNI might not be able to open the socket,
and plugout_drive will output an error message:
** AFNI didn't like control information!
-host name Means to connect to AFNI running on the computer
'name' using TCP/IP. The default is to connect
on the current host 'localhost' using TCP/IP.
-shm Means to connect to the current host using shared
memory. There is no reason to do this unless
you are transferring huge quantities of data.
N.B.: '-host .' is equivalent to '-shm'.
-v Verbose mode.
-port pp Use TCP/IP port number 'pp'. The default is
8099, but if two plugouts are running on the
same computer, they must use different ports.
For a list of currently used ports use afni -list_ports
-maxwait t Wait a maximum of 't' seconds for AFNI to connect;
if the connection doesn't happen in that time, exit.
[default wait time is 9 seconds]
-name sss Use the string 'sss' for the name that AFNI assigns
to this plugout. The default is something stupid.
-com 'ACTION DATA' Execute the following command. For example:
-com 'SET_FUNCTION SomeFunction'
will switch AFNI's function (overlay) to
dataset with prefix SomeFunction.
Make sure ACTION and DATA are together enclosed
in one pair of single quotes.
There are numerous actions listed in AFNI's
You can use the option -com repeatedly.
-quit Quit after you are done with all the -com commands.
The default is for the program to wait for more
commands to be typed at the terminal's prompt.
You will need to turn plugouts on in AFNI using one of the
1. Including '-yesplugouts' as an option on AFNI's command line
2. From AFNI GUI: Define Datamode->Misc->Start Plugouts
3. From AFNI GUI: Press the 'NIML+PO' button (near 'Overlay')
4. Set environment variable AFNI_YESPLUGOUTS to YES in .afnirc
Otherwise, AFNI won't be listening for a plugout connection.
[AFNI does't listen for socket connections, unless]
[it is told to, in order to avoid the overhead of]
[checking for incoming data every few milliseconds]
This program's exit status will be 1 if it couldn't connect
to AFNI at all. Otherwise, the exit status will be 0.
You could use this feature in a script to check if a copy of
AFNI is ready to rumble, and if not then start one, as in the
following csh fragment:
plugout_drive -maxwait 1 -com 'OPEN_WINDOW axialimage'
if( $status == 1 )then
afni -yesplugouts &
sleep 2 ; plugout_drive -com 'OPEN_WINDOW axialimage'
To have different plugout_* programs talking to different
AFNI, use the -np* options below
-np PORT_OFFSET: Provide a port offset to allow multiple instances of
AFNI <--> SUMA, AFNI <--> 3dGroupIncorr, or any other
programs that communicate together to operate on the same
All ports are assigned numbers relative to PORT_OFFSET.
The same PORT_OFFSET value must be used on all programs
that are to talk together. PORT_OFFSET is an integer in
the inclusive range [1025 to 65500].
When you want to use multiple instances of communicating programs,
be sure the PORT_OFFSETS you use differ by about 50 or you may
still have port conflicts. A BETTER approach is to use -npb below.
-npq PORT_OFFSET: Like -np, but more quiet in the face of adversity.
-npb PORT_OFFSET_BLOC: Similar to -np, except it is easier to use.
PORT_OFFSET_BLOC is an integer between 0 and
MAX_BLOC. MAX_BLOC is around 4000 for now, but
it might decrease as we use up more ports in AFNI.
You should be safe for the next 10 years if you
stay under 2000.
Using this function reduces your chances of causing
See also afni and suma options: -list_ports and -port_number for
information about port number assignments.
You can also provide a port offset with the environment variable
AFNI_PORT_OFFSET. Using -np overrides AFNI_PORT_OFFSET.
-max_port_bloc: Print the current value of MAX_BLOC and exit.
Remember this value can get smaller with future releases.
Stay under 2000.
-max_port_bloc_quiet: Spit MAX_BLOC value only and exit.
-num_assigned_ports: Print the number of assigned ports used by AFNI
-num_assigned_ports_quiet: Do it quietly.
Port Handling Examples:
Say you want to run three instances of AFNI <--> SUMA.
For the first you just do:
suma -niml -spec ... -sv ... &
afni -niml &
Then for the second instance pick an offset bloc, say 1 and run
suma -niml -npb 1 -spec ... -sv ... &
afni -niml -npb 1 &
And for yet another instance:
suma -niml -npb 2 -spec ... -sv ... &
afni -niml -npb 2 &
Since you can launch many instances of communicating programs now,
you need to know wich SUMA window, say, is talking to which AFNI.
To sort this out, the titlebars now show the number of the bloc
of ports they are using. When the bloc is set either via
environment variables AFNI_PORT_OFFSET or AFNI_PORT_BLOC, or
with one of the -np* options, window title bars change from
[A] to [A#] with # being the resultant bloc number.
In the examples above, both AFNI and SUMA windows will show [A2]
when -npb is 2.
Global Options (available to all AFNI/SUMA programs)
-h: Mini help, at time, same as -help in many cases.
-help: The entire help output
-HELP: Extreme help, same as -help in majority of cases.
-h_view: Open help in text editor. AFNI will try to find a GUI editor
-hview : on your machine. You can control which it should use by
setting environment variable AFNI_GUI_EDITOR.
-h_web: Open help in web browser. AFNI will try to find a browser.
-hweb : on your machine. You can control which it should use by
setting environment variable AFNI_GUI_EDITOR.
-h_find WORD: Look for lines in this programs's -help output that match
-h_raw: Help string unedited
-h_spx: Help string in sphinx loveliness, but do not try to autoformat
-h_aspx: Help string in sphinx with autoformatting of options, etc.
-all_opts: Try to identify all options for the program from the
output of its -help option. Some options might be missed
and others misidentified. Use this output for hints only.
-overwrite: Overwrite existing output dataset.
Equivalent to setting env. AFNI_DECONFLICT=OVERWRITE
-ok_1D_text: Zero out uncommented text in 1D file.
Equivalent to setting env. AFNI_1D_ZERO_TEXT=YES
-Dname=val: Set environment variable 'name' to value 'val'
For example: -DAFNI_1D_ZERO_TEXT=YES
-Vname=: Print value of environment variable 'name' to stdout and quit.
This is more reliable that the shell's env query because it would
include envs set in .afnirc files and .sumarc files for SUMA
For example: -VAFNI_1D_ZERO_TEXT=
-skip_afnirc: Do not read the afni resource (like ~/.afnirc) file.
-pad_to_node NODE: Output a full dset from node 0 to MAX_NODE-1
** Instead of directly setting NODE to an integer you
can set NODE to something like:
ld120 (or rd17) which sets NODE to be the maximum
node index on an Icosahedron with -ld 120. See
CreateIcosahedron for details.
d:DSET.niml.dset which sets NODE to the maximum node found
in dataset DSET.niml.dset.
** This option is for surface-based datasets only.
Some programs may not heed it, so check the output if
you are not sure.
-pif SOMETHING: Does absolutely nothing but provide for a convenient
way to tag a process and find it in the output of ps -a
-echo_edu: Echos the entire command line to stdout (without -echo_edu)
for edification purposes
SPECIAL PURPOSE ARGUMENTS TO ADD *MORE* ARGUMENTS TO THE COMMAND LINE
Arguments of the following form can be used to create MORE command
line arguments -- the principal reason for using these type of arguments
is to create program command lines that are beyond the limit of
practicable scripting. (For one thing, Unix command lines have an
upper limit on their length.) This type of expanding argument makes
it possible to input thousands of files into an AFNI program command line.
The generic form of these arguments is (quotes, 'single' or "double",
are required for this type of argument):
where X = I for Include (include strings from file)
or X = G for Glob (wildcard expansion)
where Y = M for Multi-string (create multiple arguments from multiple strings)
or Y = 1 for One-string (all strings created are put into one argument)
Following the XY modifiers, a list of strings is given, separated by spaces.
* For X=I, each string in the list is a filename to be read in and
included on the command line.
* For X=G, each string in the list is a Unix style filename wildcard
expression to be expanded and the resulting filenames included
on the command line.
In each case, the '<<XY list' command line argument will be removed and
replaced by the results of the expansion.
* '<<GM wildcards'
Each wildcard string will be 'globbed' -- expanded from the names of
files -- and the list of files found this way will be stored in a
sequence of new arguments that replace this argument:
'<<GM ~/Alice/*.nii ~/Bob/*.nii'
might expand into a list of hundreds of separate datasets.
* Why use this instead of just putting the wildcards on the command
line? Mostly to get around limits on the length of Unix command lines.
* '<<G1 wildcards'
The difference from the above case is that after the wildcard expansion
strings are found, they are catenated with separating spaces into one
big string. The only use for this in AFNI is for auto-catenation of
multiple datasets into one big dataset.
* '<<IM filenames'
Each filename string will result in the contents of that text file being
read in, broken at whitespace into separate strings, and the resulting
collection of strings will be stored in a sequence of new arguments
that replace this argument. This type of argument can be used to input
large numbers of files which are listed in an external file:
which could in principle result in reading in thousands of datasets
(if you've got the RAM).
* This type of argument is in essence an internal form of doing something
like `cat filename` using the back-quote shell operator on the command
line. The only reason this argument (or the others) was implemented is
to get around the length limits on the Unix command line.
* '<<I1 filenames'
The difference from the above case is that after the files are read
and their strings are found, they are catenated with separating spaces
into one big string. The only use for this in AFNI is for auto-catenation
of multiple datasets into one big dataset.
* 'G', 'M', and 'I' can be lower case, as in '<<gm'.
* 'glob' is Unix jargon for wildcard expansion:
* If you set environment variable AFNI_GLOB_SELECTORS to YES,
then the wildcard expansion with '<<g' will not use the '[...]'
construction as a Unix wildcard. Instead, it will expand the rest
of the wildcard and then append the '[...]' to the results:
would expand to something like
fred/A.nii[1..100] fred/B.nii[1..100] fred/C.nii[1..100]
This technique is a way to preserve AFNI-style sub-brick selectors
and have them apply to a lot of files at once.
3dttest++ -DAFNI_GLOB_SELECTORS=YES -brickwise -prefix Junk.nii \
-setA '<<gm sub-*/func/*rest_bold.nii.gz[0..100]'
* However, if you want to put sub-brick selectors on the '<<im' type
of input, you will have to do that in the input text file itself
(for each input filename in that file).
* BE CAREFUL OUT THERE!
plugout_drive -com 'SWITCH_SESSION A.afni' \
-com 'OPEN_WINDOW A.axialimage geom=600x600+416+44 \
ifrac=0.8 opacity=9' \
-com 'OPEN_WINDOW A.sagittalimage geom=+45+430 \
ifrac=0.8 opacity=9' \
-com 'SWITCH_UNDERLAY anat' \
-com 'SWITCH_OVERLAY strip' \
-com 'SEE_OVERLAY +' \
-com 'SET_DICOM_XYZ 7 12 2' \
-com 'OPEN_WINDOW A.axialimage keypress=v' \
More help in: README.driver
More Demos is: @DriveAfni
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Fri Dec 2 21:09:20 EST 2022