AFNI program: afni
Output of -help
GPL AFNI: Analysis of Functional NeuroImages, by RW Cox (rwcox@nih.gov)
This is Version 2.56d of 06 Jul 2004
** This software was designed to be used only for research purposes. **
** Clinical uses are not recommended, and have never been evaluated. **
** This software comes with no warranties of any kind whatsoever, **
** and may not be useful for anything. Use it at your own risk! **
** If these terms are not acceptable, you aren't allowed to use AFNI.**
** See 'Define Datamode->Misc->License Info' for more details. **
Usage 1: read in sessions of 3D datasets (created by to3d)
afni [options] [session_directory ...]
-purge Conserve memory by purging data to disk.
[Use this if you run out of memory when running AFNI.]
[This will slow the code down, so use only if needed.]
-posfunc Set up the color 'pbar' to use only positive function values.
-R Recursively search each session_directory for more session
subdirectories.
WARNING: This will descend the entire filesystem hierarchy from
each session_directory given on the command line. On a
large disk, this may take a long time. To limit the
recursion to 5 levels (for example), use -R5.
-ignore N Tells the program to 'ignore' the first N points in
time series for graphs and FIM calculations.
-im1 N Tells the program to use image N as the first one for
graphs and FIM calculations (same as '-ignore N-1')
-tlrc_small These options set whether to use the 'small' or 'big'
-tlrc_big Talairach brick size. The compiled in default for
the program is now 'big', unlike AFNI 1.0x.
-no1D Tells AFNI not to read *.1D timeseries files from
the dataset directories. The *.1D files in the
directories listed in the AFNI_TSPATH environment
variable will still be read (if this variable is
not set, then './' will be scanned for *.1D files.)
-noqual Tells AFNI not to enforce the 'quality' checks when
making the transformations to +acpc and +tlrc.
-unique Tells the program to create a unique set of colors
for each AFNI controller window. This allows
different datasets to be viewed with different
grayscales or colorscales. Note that -unique
will only work on displays that support 12 bit
PseudoColor (e.g., SGI workstations) or TrueColor.
-orient code Tells afni the orientation in which to display
x-y-z coordinates (upper left of control window).
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
The default code is RAI ==> DICOM order. This can
be set with the environment variable AFNI_ORIENT.
As a special case, using the code 'flipped' is
equivalent to 'LPI' (this is for Steve Rao).
-noplugins Tells the program not to load plugins.
(Plugins can also be disabled by setting the
environment variable AFNI_NOPLUGINS.)
-yesplugouts Tells the program to listen for plugouts.
(Plugouts can also be enabled by setting the
environment variable AFNI_YESPLUGOUTS.)
-YESplugouts Makes the plugout code print out lots of messages
(useful for debugging a new plugout).
-noplugouts Tells the program NOT to listen for plugouts.
(This option is available to override
the AFNI_YESPLUGOUTS environment variable.)
-skip_afnirc Tells the program NOT to read the file .afnirc
in the home directory. See README.setup for
details on the use of .afnirc for initialization.
-layout fn Tells AFNI to read the initial windows layout from
file 'fn'. If this option is not given, then
environment variable AFNI_LAYOUT_FILE is used.
If neither is present, then AFNI will do whatever
it feels like.
-niml If present, turns on listening for NIML-formatted
data from SUMA. Can also be turned on by setting
environment variable AFNI_NIML_START to YES.
-np port If present, sets the NIML socket port number to 'port'.
This must be an integer between 1024 and 65535,
and must be the same as the '-np port' number given
to SUMA. [default = 53211]
If no session_directories are given, then the program will use
the current working directory (i.e., './').
The maximum number of sessions is now set to 80.
The maximum number of datasets per session is 1024.
Usage 2: read in images for 'quick and dirty' viewing
(Most advanced features of AFNI will be disabled.)
afni -im [options] im1 im2 im3 ...
-im Flag to read in images instead of 3D datasets
(Talaraich and functional stuff won't work)
-dy yratio Tells afni the downscreen pixel size is 'yratio' times
the across-screen (x) pixel dimension (default=1.0)
-dz zratio Tells afni the slice thickness is 'zratio' times
the x pixel dimension (default=1.0)
-orient code Tells afni the orientation of the input images.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
(the default code is ASL ==> sagittal images).
Note that this use of '-orient' is different from
the use when viewing datasets.
-resize Tells afni that all images should be resized to fit
the size of the first one, if they don't already fit
(by default, images must all 'fit' or afni will stop)
-datum type Tells afni to convert input images into the type given:
byte, short, float, complex are the legal types.
The image files (im1 ...) are the same formats as accepted by to3d.
New image display options (alternatives to -im) [19 Oct 1999]:
-tim These options tell AFNI to arrange the input images
-tim: into a internal time-dependent dataset. Suppose that
-zim: there are N input 2D slices on the command line.
* -tim alone means these are N points in time (1 slice).
* -tim: means there are nt points in time (nt is
an integer > 1), so there are N/nt slices in space,
and the images on the command line are input in
time order first (like -time:tz in to3d).
* -zim: means there are nz slices in space (nz is
an integer > 1), so there are N/nz points in time,
and the images on the command line are input in
slice order first (like -time:zt in to3d).
N.B.: You may wish to use the -ignore option to set the number of
initial points to ignore in the time series graph if you use
-tim or -zim, since there is no way to change this from
within an AFNI run (the FIM menus are disabled).
Usage 3: read in datasets specified on the command line
afni -dset [options] dname1 dname2 ...
where 'dname1' is the name of a dataset, etc. With this option, only
the chosen datasets are read in, and they are all put in the same
'session'. Follower datasets are not created.
INPUT DATASET NAMES
-------------------
An input dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
read in (by default, all of a dataset's sub-bricks are input).
A sub-brick selection list looks like one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
N.B.: The sub-bricks are read in the order specified, which may
not be the order in the original dataset. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be input into memory
in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks.
N.B.: You may also use the syntax after the name of an input
dataset to restrict the range of values read in to the numerical
values in a..b, inclusive. For example,
fred+orig[5..7]<100..200>
creates a 3 sub-brick dataset with values less than 100 or
greater than 200 from the original set to zero.
If you use the <> sub-range selection without the [] sub-brick
selection, it is the same as if you had put [1..$] in front of
the sub-range selection.
N.B.: Datasets using sub-brick/sub-range selectors are treated as:
- 3D+time if the dataset is 3D+time and more than 1 brick is chosen
- otherwise, as bucket datasets (-abuc or -fbuc)
(in particular, fico, fitt, etc datasets are converted to fbuc!)
N.B.: The characters '$ ( ) [ ] < >' are special to the shell,
so you will have to escape them. This is most easily done by
putting the entire dataset plus selection list inside forward
single quotes, as in 'fred+orig[5..7,9]', or double quotes "x".
CALCULATED DATASETS
-------------------
Datasets may also be specified as runtime-generated results from
program 3dcalc. This type of dataset specifier is enclosed in
quotes, and starts with the string '3dcalc(':
'3dcalc( opt opt ... opt )'
where each 'opt' is an option to program 3dcalc; this program
is run to generate a dataset in the directory given by environment
variable TMPDIR (default=/tmp). This dataset is then read into
memory, locked in place, and deleted from disk. For example
afni -dset '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )'
will let you look at the average of datasets r1+orig and r2+orig.
N.B.: using this dataset input method will use lots of memory!
General options (for any Usage):
-q Tells afni to be 'quiet' on startup
-gamma gg Tells afni that the gamma correction factor for the
monitor is 'gg' (default gg is 1.0; greater than
1.0 makes the image contrast larger -- this may
also be adjusted interactively)
-install Tells afni to install a new X11 Colormap. This only
means something for PseudoColor displays. Also, it
usually cause the notorious 'technicolor' effect.
-ncolors nn Tells afni to use 'nn' gray levels for the image
displays (default is 80)
-xtwarns Tells afni to show any Xt warning messages that may
occur; the default is to suppress these messages.
-tbar name Uses 'name' instead of 'AFNI' in window titlebars.
-flipim and The '-flipim' option tells afni to display images in the
-noflipim 'flipped' radiology convention (left on the right).
The '-noflipim' option tells afni to display left on
the left, as neuroscientists generally prefer. This
latter mode can also be set by the Unix environment
variable 'AFNI_LEFT_IS_LEFT'. The '-flipim' mode is
the default.
-trace Turns routine call tracing on, for debugging purposes.
-TRACE Turns even more verbose tracing on, for more debugging.
-nomall Disables use of the mcw_malloc() library routines.
N.B.: Many of these options, as well as the initial color set up,
can be controlled by appropriate X11 resources. See the
file AFNI.Xdefaults for instructions and examples.
REFERENCES
----------
The following papers describe some of the components of the AFNI package.
RW Cox. AFNI: Software for analysis and visualization of functional
magnetic resonance neuroimages. Computers and Biomedical Research,
29: 162-173, 1996.
* The first AFNI paper, and the one I prefer you cite if you want to
refer to the AFNI package as a whole.
RW Cox, A Jesmanowicz, and JS Hyde. Real-time functional magnetic
resonance imaging. Magnetic Resonance in Medicine, 33: 230-236, 1995.
* The first paper on realtime FMRI; describes the algorithm used in
3dfim+, the interactive FIM calculations, and in the realtime plugin.
RW Cox and JS Hyde. Software tools for analysis and visualization of
FMRI Data. NMR in Biomedicine, 10: 171-178, 1997.
* A second paper about AFNI and design issues for FMRI software tools.
RW Cox and A Jesmanowicz. Real-time 3D image registration for
functional MRI. Magnetic Resonance in Medicine, 42: 1014-1018, 1999.
* Describes the algorithm used for image registration in 3dvolreg
and in the realtime plugin.
ZS Saad, KM Ropella, RW Cox, and EA DeYoe. Analysis and use of FMRI
response delays. Human Brain Mapping, 13: 74-93, 2001.
* Describes the algorithm used in 3ddelay (cf. '3ddelay -help').
This page generated on
Tue Aug 3 16:42:45 EDT 2004