AFNI file: README.driver
=====================================================
*** Driving AFNI from a Plugout or a Startup Script ***
=====================================================
An external program (i.e., a "plugout") can control some aspects of AFNI.
This functionality is invoked by passing a command line of the form
DRIVE_AFNI command arguments ...
to AFNI (once the plugout connection is open, of course). The commands
available are described below.
The sample plugout plugout_drive.c can be used to test how things work
(highly recommended before you start writing your own code). For some
scripting purposes, the plugout_drive program (compiled with the usual
AFNI binaries) will be all you need.
It is also possible to drive AFNI from Matlab with the TellAfni.m function,
which uses plugout_drive to do the actual work.
A startup Script (file ".afni.startup_script") can also give a sequence
of commands to be run immediately after AFNI starts up. The file consists
of a sequence of command lines (without the "DRIVE_AFNI" prefix). It is
also possible to read in a Script file using the "Datamode->Misc->Run Script"
button from the AFNI controller. Some of the current state of AFNI can
be saved to ".afni.startup_script" using the "Datamode->Misc->Save Layout"
button (by giving a blank as the filename -- or any filename containing the
string "script" -- other filenames produce a 'layout' description which
is intended to be included in your .afnirc file).
You can also give commands to AFNI on the 'afni' command line, using the
'-com' option. For example:
afni -com 'OPEN_WINDOW A.axialimage' \
-com 'SWITCH_UNDERLAY anat' \
-com 'SAVE_JPEG A.axialimage sss.jpg' \
-com 'QUIT' \
somedirectory
could be used to create an image file 'sss.jpg' automatically. The AFNI GUI
would open up (and so X11 must be running), but no user interaction would
actually occur -- the image opens and gets saved, and then AFNI just ends.
N.B.: If the 'QUIT' command weren't included above, AFNI would remain open,
ready for user interaction after the image file was saved.
N.B.: If you are adroit, you could use the virtual X11 server program Xvfb
to create images as indicated above with no need for an actual X11 display.
A sample script is given later -- search forward to find the string 'Xvfb'.
Also see the script @snapshot_volreg for a practical example.
N.B.: The 'Render Dataset' plugin can be partially controlled by a script,
but not by the Driver functionality described here. Instead, see the
README.render_scripts file and the Help button in that plugin for more
information.
==============================================================================
Advanced AFNI Programming: Extending the AFNI Driver Functionality
------------------------------------------------------------------
A programmer of a plugin can register a command string and a callback function
to be called when that command string is 'driven' to AFNI. For example:
static int junkfun( char *cmd )
{
fprintf(stderr,"junkfun('%s')\n",cmd) ; return 0 ;
}
AFNI_driver_register( "JUNK" , junkfun ) ;
If the callback function return value is negative, a warning message will be
printed to stderr; otherwise, the return value is ignored. The string that
is passed to the callback function is everything AFTER the initial command
and the blank(s) that follows; in the above example, if "JUNK elvis lives"
were the driver command, then junkfun is called with the string "elvis lives".
In a plugin, the logical place to put the call to AFNI_driver_register() is
in the PLUGIN_init() function.
If you call AFNI_driver_register() with a new command name that duplicates
an existing one, then an error message is printed to stderr and this call
will be ignored. For this reason, you may want to prefix your commands
with some identifier; for example, a hypothetical diffusion tensor analysis
plugin could give command names starting with "DTI_". Or perhaps use your
institution's name or your initials as a prefix, as in "NIMH_" or "RWC_".
For the most part, driving AFNI is implemented in source code file
afni_driver.c, if you want to see how it works. (So far, no one outside
the AFNI team has looked at this, as far as I know.)
=============================================================================
AFNI DRIVING COMMANDS (in no coherent order)
--------------------------------------------
DO_NOTHING
This command does ... NOTHING :) -- it can be used as a placeholder
in a script, for example.
ADD_OVERLAY_COLOR colordef colorlab
Adds the color defined by the string "colordef" to the list of overlay
colors. It will appear in the menus with the label "colordef". Example:
ADD_OVERLAY_COLOR #ff5599 pinkish
SET_THRESHOLD [c.]val [dec]
Sets the threshold slider for controller index 'c' (default='A') to level
".val" (a number between .0000 and .9999, inclusive). If the optional
'dec' parameter is set, this is a number between 0 and 4 (inclusive) setting
the power-of-ten factor for the slider. Example:
SET_THRESHOLD A.3000 2
will set the '**' (decimal) level of the slider to 2 and the slider value to
30 (=0.3000*100).
++ You can also use "SET_FUNC_THRESH" for the command name.
++ The newer SET_THRESHNEW command is probably better for your needs;
this older command is left here for historical compatibility reasons.
SET_THRESHNEW [c] val [flags]
Sets the threshold slider for controller index 'c' (default='A') to the
numerical value 'val', which must be in the range [0..9999]. If the
optional 'flags' string contains the character '*', then the slider decimal
offset (i.e., the '**' setting) will be changed to match the size of 'val'.
If 'flags' contains the character 'p', then 'val will be interpreted as
a p-value (and so must be between 0.0 and 1.0). Examples:
SET_THRESHNEW A 9.2731
SET_THRESHNEW B 0.3971 *p
SET_PBAR_NUMBER [c.]num
Sets the number of panes in the color pbar to 'num' (currently must be between
2 and 20, inclusive). Example:
SET_PBAR_NUMBER A.10
SET_PBAR_SIGN [c.]+ or [c.]-
Sets the color pbar to be positive-only (+) or signed (-). Example:
SET_PBAR_SIGN A.+
SET_PBAR_ALL [c.]{+|-}num val=color val=color ...
Sets all color pbar parameters at once;
The initial string specifies the controller ('A', 'B', etc.), the sign
condition of the pbar ('+' or '-') and the number of panes to setup.
'num' equations of the form 'val=color' follow the initial string;
these set up the top levels and colors of each pane. Example:
SET_PBAR_ALL A.+5 2.0=yellow 1.5=green 1.0=blue 0.5=red 0.2=none
The top pane runs from 2.0-1.5 and is yellow; the second pane runs from
1.5-1.0 and is blue, etc. The 'color' values must be legal color labels.
SET_PBAR_ALL [c.]{+|-}99 topval colorscale_name [options]
Sets the color pbar for controller #c to be in "continuous" colorscale
mode. Again, '+' or '-' is used to specify if the colorscale should
be positive-only or signed. The special value of 99 panes is used
to indicate colorscale mode. The number 'topval' tells the scale
value to go at the top of the colorscale. The string 'colorscale_name'
tells which colorscale to use. For example:
SET_PBAR_ALL A.+99 1.0 Color_circle_AJJ
Please note that the '+' or '-' betfor the 99 is NOT optional -- you must
put one of these signs in before the number!
The 'options' available at this time only apply when in this "continuous"
colorscale case. They are
ROTA=n => after loading the colorscale, rotate it by 'n' steps
FLIP => after loading the colorscale, flip it upside down
These options are part of how the AFNI_PBAR_LOCK function works, and
probably aren't relevant for manual use.
PBAR_ROTATE [c.]{+|-}
Rotates the color pbar in the positive ('+') or negative ('-') direction:
PBAR_ROTATE A.+
++ You could use this to make fun movies, but otherwise it is hard to
see what value this command has.
PBAR_SAVEIM [c] filename [dim=dimstring]
Saves the current color pbar image into 'filename', which can end in
'.png', '.jpg', or '.ppm' for those 3 different formats. If you wish
to change the default size of the image (64 pixels wide, 512 tall),
you can add a 'dim=dimstring' value after the filename:
++ This dimension changing string starts with 'dim='
++ The 'dimstring' is of the format 'AxB', where
'A' is the number of pixels across the pbar
'B' is the number of pixels down the pbar
The default is '64x512'.
++ If you append 'H' to the 'dimstring', then the image will be
flipped to be horizontal, so that the color scale runs from
left-to-right rather than bottom-to-top.
++ To get the default 64x512 image but flipped to horizontal, you
can just use 'dim=H'.
++ NOTE: once you change 'dimstring', that becomes the default for
future 'PBAR_SAVEIM' commands in the same AFNI run; in other words,
setting 'dimstring' once will affect any future pbar saves the
same way unless a new 'dimstring' is provided.
DEFINE_COLORSCALE name number=color number=color ...
or
DEFINE_COLORSCALE name color color color
Defines a new colorscale with the given name. The format of the following
arguments is either like "1.0=#ffff00" or like "#ff00ff" (all must be in the
same format). See https://afni.nimh.nih.gov/afni/afni_colorscale.html for
more information about the format of color names and about how the colorscale
definition works.
++ You can also use "DEFINE_COLOR_SCALE" for the command name.
SET_FUNC_AUTORANGE [c.]{+|-}
Sets the function "autoRange" toggle to be on ('+') or off ('-'):
SET_FUNC_AUTORANGE A.+
SET_FUNC_PERCENTILE [c.]{+|-}
Sets the function "%" toggle to be on ('+') or off ('-'):
SET_FUNC_PERCENTILE A.+
SET_FUNC_RANGE [c.]value
Sets the functional range to 'value'. If value is 0, this turns autoRange
on; if value is positive, this turns autoRange off:
SET_FUNC_RANGE A.0.3333
SET_FUNC_VISIBLE [c.]{+|-}
Turns the "See Overlay" toggle on or off:
SET_FUNC_VISIBLE A.+
You can also use SEE_OVERLAY for this, which is closer to the label on
the GUI button.
SEE_OVERLAY
Same as SET_FUNC_VISIBLE
SET_FUNC_RESAM [c.]{NN|Li|Cu|Bk}[.{NN|Li|Cu|Bk}]
Sets the functional resampling mode:
SET_FUNC_RESAM A.Li.Li
sets the func and threshold resampling modes both to Linear interpolation.
SET_FUNC_ALPHA [c.]{Off|On|No|Yes}
Set the functional overlay Alpha mode, to Off (or No), or On (or Yes).
For example
SET_FUNC_ALPHA A.Yes
This command is equivalent to controlling Alpha with the 'A' button
on top of the threshold slider. You can also set the initial status
of Alpha by setting environment variable AFNI_FUNC_ALPHA to Yes or No.
[28 Jun 2021]
You can now do
SET_FUNC_ALPHA A.Linear
SET_FUNC_ALPHA A.Quadratic
to turn Alpha fading on and at the same time choose linear or quadratic
fading style -- this is the same as choosing the style from the right-
click popup menu attached to the 'Thr' label (left of 'A' button).
The default style is Quadratic.
SET_FUNC_BOXED [c.]{Off|On|No|Yes}
Set the functional overlay Boxed mode, to Off (or No), or On (or Yes).
For example
SET_FUNC_BOXED A.Yes
This command is equivalent to controlling Boxed with the 'B' button
on top of the threshold slider. You can also set the initial status
of Boxed by setting environment variable AFNI_FUNC_BOXED to Yes or No.
OPEN_PANEL [c.]Panel_Name
Opens the specified controller panel, where 'Panel_Name' is one of
'Define_Overlay', 'Define_Datamode', 'Define_Markers', or 'Etc'.
(Panel name is not case-sensitive.)
CLOSE_PANEL [c.]Panel_Name
Closes the specified controller panel, where 'Panel_Name' is one of
'Define_Overlay', 'Define_Datamode', 'Define_Markers', or 'Etc'.
(Panel name is not case-sensitive.)
SYSTEM command string
Executes "command string" using the system() library function; for
example, "SYSTEM mkdir aaa".
CHDIR newdirectory
Changes the current directory; for example, "CHDIR aaa". This is the
directory into which saved files (e.g., images) will be written.
RESCAN_THIS [c]
rescans the current session directory for controller 'c', where 'c'
is one of 'A', 'B', 'C', 'D', or 'E'. If 'c' is absent, the 'A'
controller's current session is scanned.
SET_SESSION [c.]directoryname
Switches controller 'c' to be looking at the named directory. The
match on directory names is done by a sub-string match - that is,
directoryname = "fred" will match an AFNI session directory named
"wilhelm/frederick/von/guttenstein".
++ You can also use "SWITCH_SESSION" or "SWITCH_DIRECTORY" for the command.
SET_VIEW [c.]view
Switches controller 'c' to the named "view", which can be one of
'orig', 'acpc' or 'tlrc'. The underlay dataset must have an
appropriate transformation, or appropriate version.
SET_ANATOMY [c.]prefix [i]
Switches controller 'c' to be looking at the anatomical dataset with
the given prefix. The prefix must be a perfect match - this is NOT
a sub-string match.
++ If an optional integer is given (separated by a space) after the
prefix, this is the sub-brick index to view.
++ You can also use "SWITCH_ANATOMY" or "SWITCH_UNDERLAY" for the command.
++ The 'prefix' can also be the dataset IDcode string, if you insist.
++ The 'prefix' does NOT include the directory name; if you try to do
that, the driving operation will fail.
SET_FUNCTION [c.]prefix [j [k]]
Same, but for the functional dataset in controller 'c'.
++ If an optional integer is given (separated by a space) after the
prefix, this is the sub-brick index to view as the 'OLay'; if a second
integer is given, this is the sub-brick index to use as the 'Thr'.
++ You can also use "SWITCH_FUNCTION" or "SWITCH_OVERLAY" for the command.
SET_SUBBRICKS [c] i j k
Without switching underlay or overlay datasets, change the sub-bricks
being viewed in the viewer specified by the initial letter.
Index i = underlay sub-brick (grayscale)
Index j = overlay sub-brick for 'Olay' (color)
Index k = overlay sub-brick for 'Thr' (threshold)
For example, "SET_SUBBRICKS B 33 -1 44" will set the underlay sub-brick
to 33, the threshold sub-brick to 44, and will not change the color
sub-brick (since -1 is not a legal value).
++ You can also use "SET_SUB_BRICKS" for the command name.
OPEN_WINDOW [c.]windowname [options]
Opens a window from controller 'c'. The window name can be one of
axialimage sagittalimage coronalimage
axialgraph sagittalgraph coronalgraph
A very special case is to give the command 'OPEN_WINDOW allimage'.
This will open all 3 image viewer windows (axial, sagittal, coronal),
and then return immediately. None of the other options described
below will be carried out on those 3 viewers. If you wish to place
those windows in particular screen location with option 'geom=',
you'll have to use separate OPEN_WINDOW commands for each viewer.
If the specified AFNI controller ('A', 'B', ...) is not yet
opened, it will be opened first (like pressing the 'New' button).
If the command is of the form "OPEN_WINDOW c", then only the controller
itself will be opened.
When opening an individual window of either type (graph and image),
one allowed option is:
geom=PxQ+R+S or geom=PxQ or geom=+R+S
to make the window be PxQ pixels in size and located at screen
coordinates (R,S).
Another option for both graph and image windows is
keypress=c -> where 'c' is a single character to send as if
the user pressed that key in the specified window
++ multiple keypress= options can be used, but
each one can only send one keystroke;
example: "keypress=Z keypress=Z"
to zoom in twice in an image viewer.
For image windows, other options available are:
ifrac=number -> set image fraction in window to number (<= 1.0);
setting this to exactly 1 will turn off the
image viewer 'widgets' in the same way that
the 'Image display' GUI menu item does
mont=PxQ:R -> montage P across, Q down, every R'th slice;
* optionally, after the 'R' you can add
:G:C where G=gap between sub-images in pixels,
and C=color name to fill the gaps;
Example: mont=5x3:7:2:hotpink
opacity=X -> where X is from 0..9 (larger makes overlay more opaque)
crop=x1:x2,y1:y2 -> crop images from voxels x1 to x2, and y1 to y2
(inclusive) -- mostly for use in .afni.startup_script;
use x1=x2=0 and y1=y2=0 to turn cropping off.
zoom=Z -> set the zoom factor for this image window to Z,
which must be an integer from 1-4 (inclusive);
note that zooming and montaging do NOT work together!
overlay_label="some string"
-> This option sets the "Label Append String";
you can use 'single' or "double" quotes.
This string will be shown only if the overlay
label is turned on, which is done from the
image window intensity bar popup, or via
the AFNI_IMAGE_LABEL_MODE environment variable.
* If you wish to include a newline character,
encode it as '\newline' -- this is one of
TeX-like escapes described in README.texlike.
For example:
ALTER_WINDOW A.axialimage overlay_label="\newline\small Bob^{\red 3}"
* You can also set this string via environment
variable AFNI_IMAGE_LABEL_STRING.
butpress=name -> This option lets you simulate a button press
for one of the following buttons in an image
viewer window: Colr Swap Norm
Button presses (and key presses) are executed
in the order given on the command line; for
example,
butpress=Colr butpress=Swap
and
butpress=Swap butpress=Colr
will have different results.
For graph windows, other options available are:
matrix=number -> use 'number' sub-graphs (<= 21)
pinnum=number -> pin the graph length to 'number' time points
pinbot=a pintop=b -> pin the graph time window to run from 'a..b'
You can also open plugin windows with a windowname like so:
A.plugin.buttonlabel
where buttonlabel is the plugin's button label with blanks replaced
by underscores or hyphens (e.g., Render_Dataset). You can also use
the geom=+R+S option with this type of window opening, to position
the plugin interface window. There is no way to control any other
settings in the plugin interface (e.g., pre-set some fields).
If the specified image or graph window is already open, you can still
use this command to alter some of its properties.
++ You can also use "ALTER_WINDOW" for the command name, which makes
more sense if you are using this to apply some change to an already
open viewer window.
SET_ULAY_RANGE [c.]windowname bot top
This command sets the grayscale range for the given image viewer window
to be from 'bot' to 'top'. Examples:
SET_ULAY_RANGE A.axialimage 0 200
SET_ULAY_RANGE A.all 20 150
The second example shows that you can use 'all' to change all the open
image viewers (for a given controller) in one operation.
NOTE: Since the grayscale range for the underlay images is set separately
in each image viewer (unlike the overlay color range SET_FUNC_RANGE),
this command only applies to windows that are already open. If you
give SET_ULAY_RANGE and then OPEN_WINDOW in that order, the newly
opened window won't know anything about the underlay range you
set previously. If this is confusing -- I'm sorry.
CLOSE_WINDOW [c.]windowname
Closes a window from controller 'c'. You can only close graph and image
viewer windows this way, not plugin windows.
DATASET#N dataset ...
Drives the Dataset#N plugin for graph viewer windows. Each 'dataset'
is a dataset prefix name (without directory!). You can also add a
color name label (taken from the color menus) separated by '::'.
For example, to put 2 extra graphs on top of the underlay graph:
DATASET#N Fred.nii::red Elvis::blue
This driver command was added at the request of AFNI bootcamp students
in Guangzhou (Dec 2017).
++ See the note about resizing the window with 'geom=PxQ' in the SAVE_JPEG
command, described below. It seems to be necessary to save the image
of a graph viewer separately from the resizing command, probably because
the timing of these two operations can end of happening out of order.
++ Also, note that driving the plugin will NOT change the visible controls
if you open the plugin controller. The chosen datasets (and colors) are
saved, but these choices will not show up in the graphical interface for
this plugin.
++ At this time [Dec 2017], this command is the only one that can drive the
internal operation of an AFNI plugin.
SAVE_JPEG [c.]windowname filename
Save a JPEG dump of the given window to 'filename' (using the cjpeg filter,
which must be in the path). The windowname can be one of 'axialimage',
'sagittalimage', 'coronalimage', 'axialgraph', 'sagittalgraph', or
'coronalgraph'. If the filename does not end in the string ".jpg" or
".JPG", then ".jpg" will be appended.
++ Saving is done via the cjpeg program, which must be in the path,
and is included in the standard AFNI source and binary collections.
++ If the dataset has non-square voxels, then the default method of
saving images will produce non-square pixels (as extracted from
the dataset) -- this will make the images look peculiar when
you open them later. To avoid this peculiarity, set environment
variable AFNI_IMAGE_SAVESQUARE to YES (cf. SETENV below).
This comment applies to all image SAVE_* commands below, except
for SAVE_RAW* (where AFNI_IMAGE_SAVESQUARE has no effect).
++ For reasons I do not understand, if you OPEN (or ALTER) a window's
size with 'geom=PxQ', then do SAVE_JPEG on the window, using the
'-com' option on the AFNI command line, the image will still be
saved at the window's original size. The workaround for this
is to force the save with plugout_drive instead, after AFNI starts.
A sample script is below:
afni -com 'SWITCH_UNDERLAY run1_time' \
-com 'DATASET#N run2_time::blue run3_time::red' \
-com 'OPEN_WINDOW axialgraph keypress=I geom=900x600' \
-yesplugouts
sleep 1
plugout_drive -quit -com 'SAVE_JPEG axialgraph ag.jpg' -com 'QUITT'
SAVE_PNG [c.]windowname filename
Like SAVE_JPEG, but saves to the lossless PNG format.
++ Saving is done via the pnmtopng filter, which must be in the path.
Unlike cjpeg, this program is NOT part of the AFNI collection, but
must be installed separately (usually by getting the NETPBM package).
SAVE_FILTERED [c.]windowname filtercommand
Like SAVE_JPEG or SAVE_PNG, but instead of a filename, you
give a Unix filter that processes a PPM file. For example
SAVE_FILTERED axialimage 'pnmcut 10 20 120 240 | pnmtopng > zork.png'
will crop the image and save it into a PNG file. You'll need to become
familiar with the NETPBM package if you want to use this command.
++ As indicated in the example, you'll need to put filtercommand
in quotes if it contains blanks, which it almost surely will.
Other filter examples:
Save to a PPM file: 'cat > zork.ppm'
Save to a TIFF file: 'ppm2tiff -c none > zork.tif'
SAVE_ALLJPEG [c].imagewindowname filename
SAVE_ALLPNG [c].imagewindowname filename
SAVE_MPEG [c].imagewindowname filename
SAVE_AGIF [c].imagewindowname filename
Save ALL the images in the given image sequence viewer (either as a
series of JPEG/PNG files, or as one animation file). The windowname can
be one of 'axialimage', 'sagittalimage', or 'coronalimage'. Do NOT
put a suffix like '.jpg' or '.mpg' on the filename -- it will be added.
++ Unlike 'SAVE_JPEG', these commands do not work with graph windows.
*** The above SAVE_xxx commands also take an optional string of ***
*** the form 'blowup=4', indicating that the image(s) should be ***
*** blown up by the given factor before being saved. The legal ***
*** values of this factor = 1..8 (integral,inclusive). Example: ***
*** SAVE_JPEG axialimage FredAxial blowup=4 ***
*** Exceptions to the use of 'blowup=': ***
*** Image view montages are not blown up ***
*** Graph windows are not blown up ***
*** RAW images (cf. below) are not blown up ***
SAVE_RAW [c.]imagewindowname filename
Saves the raw data from the given image viewer to a file. This data
is the slice data extracted from the dataset, not further processed
in any way (unlike the other SAVE_* image options, which convert the
slice data to grayscale or colors). This output file contains only
the data, with no header of any sort indicating the dimensions of the
image or the actual type of data stored therein.
SAVE_RAWMONT [c.]imagewindowname filename
Saves the raw data from the given image viewer to a file, AS MONTAGED.
(The montage gap is ignored.) Same as 'SAVE_RAW' if the montage
isn't on.
SAVE_UNDERLAY [c] prefix
WRITE_UNDERLAY [c] prefix
These synonymous commands write a copy of the current underlay dataset for
the given image viewer to disk, using the given prefix.
SAVE_OVERLAY [c] prefix
WRITE_OVERLAY [c] prefix
These synonymous commands write a copy of the current overlay dataset for
the given image viewer to disk, using the given prefix.
** Note that these WRITE_ commands will over-write existing **
** datasets with the same name, so you must use care here! **
SNAP_CONT image.jpg
Take a snapshot of the main AFNI controller and save it into image.jpg.
SNAP_VIEWER [c].windowname imagename
Take a snapshot of a graph or image viewer, including the buttons (etc.)
and save it into an image file. For example:
SNAP_VIEWER axialimage Frodo.png
SNAP_VIEWER B.axialgraph Samwise.jpg
The snapshot does not include any windowing system additions, such as
the titlebar, resizing controls, etc. The main purpose of this command
is to help make documentation.
NOTE: This command requires the NETPBM package be installed, otherwise
the image saving won't work (except for .jpg files).
SET_DICOM_XYZ [c] x y z
SET_SPM_XYZ [c] x y z
SET_IJK [c] i j k
SET_INDEX [c] ijk
Set the controller coordinates to the given triple, or singleton for SET_INDEX;
DICOM_XYZ has the coordinates in DICOM (RAI) order, SPM_XYZ has the coordinates
in SPM (LPI) order, and IJK has voxel indexes instead of spatial coordinates.
ijk is the array index corresponding to a triplet of voxel indices. It is the
same as 'index' displayed in the top left corner of AFNI's controller when
Datamode-->Misc-->Voxel Coords is turned on.
Get different kinds of information from the AFNI GUI
GET_DICOM_XYZ [c]
GET_IJK [c]
Have AFNI print the controller current coordinates (to stdout by default -
see SET_OUTPLUG).
GET_OLAY_VAL [c]
GET_THR_VAL [c]
GET_ULAY_VAL [c]
Have AFNI print the controller value for underlay, overlay or threshold sub-bricks
at current coordinates (to stdout by default - see SET_OUTPLUG).
GET_ULAY_NAME [c]
GET_OLAY_NAME [c]
Have AFNI print the prefix of the dataset name for underlay or overlay
(to stdout by default - see SET_OUTPLUG).
SET_OUTPLUG fname
Set plugout drive commands like GET_DICOM_XYZ,GET_IJK,GETENV to append output
to a selected text file. The default output is to stdout of the afni GUI rather
than the plugout_drive's program. The string 'stdout' resets the output to
stdout. The default output file can also be set by the AFNI environment variable,
AFNI_OUTPLUG.Note the output is always appended, so if you need this to be a
new file, you will have to delete or rename the old copy first.
SET_XHAIRS [c.]code
Set the crosshairs ('Xhairs') control to the specified value, where
'code' is one of the following strings:
OFF SINGLE MULTI LR_AP LR_IS AP_IS LR AP IS
which correspond to the menu items on the Xhairs button.
SET_XHAIR_GAP [c.]val
Set the crosshairs ('Xhairs') gap to the specified number of pixels
between -1 and 19
READ_NIML_FILE fname
Reads the NIML-formatted file 'fname' from disk and processes it as if
the data in the file had been sent to AFNI through a TCP/IP socket.
INSTACORR [c] order
This command is to drive the InstaCorr functionality in AFNI. As in other
commands, the optional '[c]' is a single letter specifying to which AFNI
controller the 'order' that follows applies. If this single letter code
is NOT present, the default controller is 'A'.
The first INSTACORR 'order' that is implemented [20 Oct 2010] is
SET
which sets the InstaCorr seed (in controller 'c', default A) to the current
crosshair location and recomputes the correlation map, or
SET x y z
which sets the InstaCorr seed to the given DICOM coordinates. For this
second form, with 'x y z', if you place the character J after the z value,
the crosshairs will also Jump to that new seed location. Note that SET
can be used with individual or group InstaCorr.
You can use the WRITE_OVERLAY command to save the computed correlation
dataset to disk.
The second INSTACORR 'order' that is implemented [Apr 2013] pertains to
the new 3dGroupInCorr '-Apair' option. This order sets the 'Apair' seed:
APSET x y z
By itself, this order does nothing until the next 'SET' order happens.
At present, there is no order to turn on automatic Apair mirroring.
Instead, you'll have to send two (2) orders to have the same effect:
APSET -x y z
SET x y z
Since 3dGroupInCorr can only be attached to the A controller, APSET can
only apply to this controller. APSET will be ignored for other controllers
or if single-subject InstaCorr is being run instead of 3dGroupInCorr.
The third INSTACORR 'order' that is implemented [22 Jun 2011] is
INIT name=value name=value ...
which will initialize the individual InstaCorr setup for controller 'c'.
The 'name=value' pairs that follow take the following forms:
DSET=prefix ==> specifies the time series dataset
IGNORE=number ==> how many time points to ignore [default=0]
STARTEND=num,num ==> start and stop indexes for analysis [default=all]
STARTEND=num+num ==> start index, number of time points
(note that IGNORE=x is the same as STARTEND=x)
STARTEND=start@len,num,step ==> setup multiple section analyses
BLUR=number ==> blurring radius for data [default=0]
AUTOMASK=yes/no ==> whether to use Automask [yes]
DESPIKE=yes/no ==> whether to use Despike [no]
BANDPASS=fbot,ftop ==> bottom,top frequencies (comma separated) [0.01,0.10]
SEEDRAD=number ==> extra blurring seed radius [0]
POLORT=number ==> polort order, from -1..2 [2]
METHOD=code ==> codes: S=Spearman, P=Pearson, etc. [P]
COUNT=number ==> Iteration Count (from 1..6 inclusive) [1]
THRESH=number ==> Iteration Thresh (non-negative) [0.01]
The 'name' string can be upper or lower case. The '=' sign must immediately
follow the 'name' with no spaces, and then the 'value' must come right after
the '=', again with no spaces. The 'value' is interpreted as described
in the table above. At a minimum, the 'DSET' must be specified -- or what
would be computed? The rest of the specifications are optional and have
default values [shown above]. Once you set a value, then another INIT order
(to the same controller) will default to leaving that value the same;
for a silly example,
SET_THRESHNEW 0
INSTACORR INIT DSET=fred ignore=3 blur=4 method=P
INSTACORR SET 20 30 40 J
INSTACORR INIT method=S
INSTACORR SET
The second INIT order leaves the dataset, ignore, and blur values at 'fred',
'3', and '4' (respectively), and only changes the correlation method for
the second SET order.
At this time, none of the other InstaCorr options (e.g., a separate mask
dataset, or a global orts 1D file) can be controlled in this way. Also,
note that setting things up this way will NOT set up the interface control
widgets in the AFNI GUI, so that if you try to control InstaCorr at the same
time via the GUI interface and a plugout, very confusing things will probably
happen. And then a jumbo-sized elephant will sit on your computer.
PURGE_MEMORY [dataset_prefix]
If no prefix is given, the sub-bricks of all datasets will be purged from
memory, and when reused, AFNI will re-read them from disk. If a prefix
is given, only that dataset (in all coordinate views) will be purged.
++ "Locked" datasets will not be purged -- a dataset will be locked
into memory if it can't easily be re-read from disk (e.g., is from SUMA;
is being drawn upon, nudged, or acquired in realtime; is loaded from
a '3dcalc()' command line call; or is fetched across the Web).
QUIT
AFNI will exit immediately. Communication with the dead being difficult
(with existing technology), this action forestalls all further attempts
to send commands to AFNI.
QUITT
AFNI will exit even more immediately! That is, none of the usual
things at the end (e.g., 'goodbye' messages) will be done, and the
program just stops.
SETENV name value
Set the environment variable "name" to "value" in AFNI; for example
SETENV AFNI_CROSSHAIR_LINES YES
SETENV AFNI_IMAGE_SAVESQUARE YES
Most of the time, when you set an environment variable inside AFNI,
just changing the variable won't have any immediate visible effect.
Only when you instigate something that this variable controls will
anything change in AFNI. Thus, you may want to 'REDISPLAY' afterwards.
GETENV name
Get the value of environment variable "name", and print to the terminal.
For example:
GETENV AFNI_PLUGINPATH
would show the directory that plugins were loaded from, if set:
AFNI_PLUGINPATH = /home/elvis/abin
If a variable is not set, the output says as much:
AFNI_PLUGINPATH = <UNSET>
REDISPLAY
Forces all images and graphs to be redrawn.
SLEEP ms
Causes AFNI to sleep for "ms" milliseconds. The main use would be in
a script file to provide a pause between some effects.
QUIET_PLUGOUTS
Turns off normal plugout communications messages
NOISY_PLUGOUTS
Turns on normal plugout communication messages
TRACE {YES | NO}
Turns debug tracing on or off. Mostly for AFNI developers.
WRITE_CONT_SPX_HELP filename
Write the help for the main controller GUI in SPHINX form to filename
==============================================================================
Sample Script Using Xvfb
------------------------
This script uses the output files in a set of directories created by
afni_proc.py. It overlays the registered EPI with the structural image,
and saves an image snapshot from each directory. The goal is to give
the user a quick way of looking for grossly bad registrations.
You probably cannot use the script exactly as it is shown here. You will have
to modify the filenames to meet your needs, at least. This script relies on
the NetPBM package being installed on your system.
#!/bin/tcsh
#
# start the X Virtual Frame Buffer program (on screen 9)
#
Xvfb :9 -screen 0 1024x768x24 &
#
# set some environment variables
#
setenv AFNI_NOSPLASH YES
setenv AFNI_SPLASH_MELT NO
setenv DISPLAY :9
#
# make directory for output images
#
mkdir -p snapshots
#
# loop over the afni_proc.py results directories
#
foreach ddd ( *.results )
set sub = `basename $ddd .results`
set epi = pb02.${sub}.r01.volreg+tlrc
set anat = anat_final.${sub}+tlrc
# max value in EPI brick
set mval = `3dBrickStat -max $ddd/$epi'[0]'`
# clip level for EPI brick
set cval = `3dClipLevel $ddd/$epi'[0]'`
# threshold value to use for EPI brick overlay
set tval = `ccalc "min($cval,$mval/4)"`
# upper limit for EPI brick overlay
set uval = `ccalc "max(3*$cval,0.666*$mval)"`
# name for output image file
set jnam = $sub
# drive AFNI to get the images we want
afni -noplugins -no_detach \
-com "OPEN_WINDOW sagittalimage opacity=6" \
-com "OPEN_WINDOW axialimage opacity=6" \
-com "OPEN_WINDOW coronalimage opacity=6" \
-com "SET_PBAR_ALL +99 1 gray_scale" \
-com "SET_FUNC_RANGE $uval" \
-com "SET_THRESHNEW $tval *" \
-com "SWITCH_OVERLAY $epi \
-com "SEE_OVERLAY +" \
-com "SAVE_JPEG sagittalimage sag.jpg blowup=2" \
-com "SAVE_JPEG coronalimage cor.jpg blowup=2" \
-com "SAVE_JPEG axialimage axi.jpg blowup=2" \
-com "QUITT" \
$ddd/$anat $ddd/$epi'[0]'
#
# convert the JPEG outputs to PNM for NetPBM manipulations
#
djpeg sag.jpg > sag.pnm
djpeg cor.jpg > cor.pnm
djpeg axi.jpg > axi.pnm
#
# the commands below make a labeled composite image, and require NetPBM
#
# glue the images together
pnmcat -lr -jcenter -black sag.pnm axi.pnm cor.pnm > qqq.pnm
# make a text overlay
pbmtext $jnam > qqq.pbm
# overlay the text image on the composite, convert to JPEG
pamcomp -xoff=1 -yoff=1 qqq.pbm qqq.pnm | cjpeg -quality 95 > snapshots/$jnam.jpg
# throw away the trash
\rm sag.* axi.* cor.* qqq.*
end
#
# done: kill the Xvfb process, then vamoose
#
killall Xvfb
exit 0
==============================================================================
** GRAPHS **
============
The following commands are used to open graph windows and manipulate them.
These commands don't actually interact with the rest of AFNI - they are
really just using AFNI as a graph display server. [This functionality
was added per the request of Jerzy Bodurka, formerly at the NIH, to provide
a way to graph physiological signals monitored while the subject is in the
scanner, at the same time the EPI images are being sent to the AFNI
realtime plugin.]
At present there are two similar kinds of graphs:
XY = connected (x,y) pairs - you must supply (x,y) for each new point
1D = x increments by 1 each time, so you only give y for each new point;
when x overflows past the right boundary, it wraps back to x=0.
Each graph can have multiple sub-graphs, which are stacked up vertically
with separate y axes and a common x axis (sub-graph #1 at the bottom, etc.).
Label strings in the graphs are interpreted in a TeX-like fashion. In
particular, an underscore means to start a subscript and a circumflex means
to start a superscript. Subscript or superscripts that are more than one
character long can be grouped using curly {braces}.
Greek letters and other special characters can be included using TeX-like
escapes. For example, "time (\Delta t=0.1)" might be a good label for the
x-axis of a 1D graph. The full list of such escapes is
\Plus \Cross \Diamond \Box
\FDiamond \FBox \FPlus \FCross \Burst \Octagon
\alpha \beta \gamma \delta \epsilon \zeta
\eta \theta \iota \kappa \lambda \mu
\nu \xi \omicron \pi \rho \sigma
\tau \upsilon \phi \chi \psi \omega
\Alpha \Beta \Gamma \Delta \Epsilon \Zeta
\Eta \Theta \Iota \Kappa \Lambda \Mu
\Nu \Xi \Omicron \Pi \Rho \Sigma
\Tau \Upsilon \Phi \Chi \Psi \Omega
\propto \int \times \div \approx \partial
\cap \langle \rangle \ddagger \pm
\leq \S \hbar \lambar
\cup \degree \nabla \downarrow
\leftarrow \rightarrow \leftrightarrow \oint
\in \notin \surd \cents
\bar \exists \geq \forall
\subset \oplus \otimes \dagger
\neq \supset \infty \uparrow
\{ \} \\ \_ \?
All characters are drawn with line strokes from an internal font; standard
fonts (e.g., Helvetica) are not available. If you want classier looking
graphs, stop whining and find another program.
--------------------------
OPEN_GRAPH_XY gname toplab xbot xtop xlab ny ybot ytop ylab nam_1 .. nam_ny
This opens a graph window for graphing non-MRI data. Each graph window
has a gname string; this lets you graph into more than one window.
Other arguments are
toplab = string to graph at top of graph [empty]
xbot = numerical minimum of x-axis in graph [0]
xtop = numerical maximum of x-axis in graph [1]
xlab = string to graph below x-axis [empty]
ny = number of sub-graphs (all share same x-axis) [1]
ybot = numerical minimum of y-axis in graph [0]
ytop = numerical maximum of y-axis in graph [1]
ylab = string to graph to left of y-axis [empty]
nam_1 = name to plot at right of sub-graph 1, etc. [not plotted]
Arguments are separated by spaces. If a label has a space in it, you can
put the label inside "double" or 'single' quote characters. If you don't
want a particular label plotted, make it the empty string "" or ''. If you
don't want names plotted at the right of sub-graphs, stop the arguments at
ylab. Only the gname argument is strictly required - the other arguments
have default values, which are given in [brackets] above.
CLOSE_GRAPH_XY gname
Closes the graph window with the given name.
CLEAR_GRAPH_XY gname
Clears the graph out of the given window (leaves the axes and labels).
ADDTO_GRAPH_XY gname x y_1 y_2 .. y_ny [repeat]
Actually plots data into the given window. In the i-th sub-graph, a line
will be drawn connecting to (x,y_i), for i=1..ny. You can put many sets
of points on the line, subject to the limitation that a plugout command
line cannot contain more than 64 Kbytes.
--------------------------
OPEN_GRAPH_1D gname toplab nx dx xlab ny ybot ytop ylab nam_1 .. nam_ny
Opens a graph window that is set up to plot nx points across with spacing dx,
in ny separate sub-graphs. When the graph is full, the graph recycles back
to the beginning. The meaning and [default] values of parameters are:
toplab = string to graph at top of graph [empty]
nx = number of points along the x-axis [500]
dx = spacing between x-axis points [1]
xlab = string to graph below x-axis [empty]
ny = number of sub-graphs (all share same x-axis) [1]
ybot = numerical minimum of y-axis in graph [0]
ytop = numerical maximum of y-axis in graph [1]
ylab = string to graph to left of y-axis [empty]
nam_1 = name to plot at right of sub-graph 1, etc. [not plotted]
CLOSE_GRAPH_1D gname
Closes the graph window with the given name.
CLEAR_GRAPH_1D gname
Clears the graph out of the given window (leaves the axes and labels).
ADDTO_GRAPH_1D gname y_1 y_2 .. y_ny [repeat]
Actually plots data into the given window. You can put many sets of ny
values at a time on the command line, subject to the limitation that a
plugout command line cannot contain more than 64 Kbytes. Also, if you
put more than nx sets of values, only the first nx will be plotted, since
that will fill up the graph through one full cycle.
--------------------------
SET_GRAPH_GEOM gname geom=X-geometry-string
This lets you move/resize a graph (1D or XY). X-geometry-string is one
of the forms:
300x100 = set window size to 300 pixels wide, 100 high
+50+90 = set window location to 50 pixels across, 90 down
300x100+50+90 = set window size and location at the same time
--------------------------
This page auto-generated on
Thu Apr 18 14:47:21 EDT 2024