AFNI program: afni

Output of `-help`

**** At the bottom of this Web page are some slide images to outline the usage of the AFNI Graphical User Interface (GUI). ---------------------------------------------------------------- USAGE 1: read in sessions of 3D datasets (created by to3d, etc.) ---------------------------------------------------------------- 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_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 machine. 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: Simliar 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 port conflicts. 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 then quit. -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 & etc. 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. -list_ports List all port assignments and quit -port_number PORT_NAME: Give port number for PORT_NAME and quit -port_number_quiet PORT_NAME: Same as -port_number but writes out number only -available_npb: Find the first available block of port numbers, print it to stdout and quit The value can be used to set the -npb option for a new set of chatty AFNI/SUMA/etc group. -available_npb_quiet: Just print the block number to stdout and quit. -com ccc This option lets you specify 'command strings' to drive AFNI after the program startup is completed. Legal command strings are described in the file README.driver. More than one '-com' option can be used, and the commands will be executed in the order they are given on the command line. N.B.: Most commands to AFNI contain spaces, so the 'ccc' command strings will need to be enclosed in quotes. -comsep 'c' Use character 'c' as a separator for commands. In this way, you can put multiple commands in a single '-com' option. Default separator is ';'. N.B.: The command separator CANNOT be alphabetic or numeric (a..z, A..Z, 0..9) or whitespace or a quote! N.B.: -comsep should come BEFORE any -com option that uses a non-semicolon separator! Example: -com 'OPEN_WINDOW axialimage; SAVE_JPEG axialimage zork; QUIT' N.B.: You can also put startup commands (one per line) in the file '~/.afni.startup_script'. For example, OPEN_WINDOW axialimage to always open the axial image window on startup. * 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 4096. * To change these maximums, you must edit file '3ddata.h' and then recompile this program. Global Options (available to all AFNI/SUMA programs) -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 programs. For example: -VAFNI_1D_ZERO_TEXT= -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. -h_find WORD: Look for lines in this programs's -help output that match (approximately) WORD. -h_view: Open help in text editor. AFNI will try to find a GUI editor 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 on your machine. You can control which it should use by setting environment variable AFNI_GUI_EDITOR. -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 ----------------------------------------------------- USAGE 2: read in images for 'quick and dirty' viewing ----------------------------------------------------- (Most advanced features of AFNI will be disabled.) (The aiv program can be used now instead of AFNI.) 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:nt into a internal time-dependent dataset. Suppose that -zim:nz there are N input 2D slices on the command line. * -tim alone means these are N points in time (1 slice). * -tim:nt 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:nz 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). N.B.: The program 'aiv' (AFNI image viewer) can also be used to get a quick look at images (but not time series graphs). ------------------------------------------------------- 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 #17 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[$..0] will reverse the order of the sub-bricks. N.B.: You may also use the syntax <a..b> after the name of an input dataset to restrict the range of values read in to the numerical values in a..b, inclusive. For example, fred+orig[5..7]<100..200> creates a 3 sub-brick dataset with values less than 100 or greater than 200 from the original set to zero. If you use the <> sub-range selection without the [] sub-brick selection, it is the same as if you had put [0..$] 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 -Dname=val Sets environment variable 'name' to 'val' inside AFNI; will supersede any value set in .afnirc. -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. -XTWARNS Trigger a debug trace when an Xt warning happens. -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. -motif_ver Show the applied motif version string. -goodbye Print a 'goodbye' message and exit (just for fun). -ver Print the current AFNI version and exit. N.B.: Many of these options, as well as the initial color set up, can be controlled by appropriate X11 resources. See the files AFNI.Xdefaults and README.environment for instructions and examples. -------------------------------------- Educational and Informational Material -------------------------------------- * The presentations used in our AFNI teaching classes at the NIH can all be found at http://afni.nimh.nih.gov/pub/dist/edu/latest/ (PowerPoint directories) http://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/ (PDF directory) * And for the interactive AFNI program in particular, see http://afni.nimh.nih.gov/pub/dist/edu/latest/afni01_intro/afni01_intro.pdf http://afni.nimh.nih.gov/pub/dist/edu/latest/afni03_interactive/afni03_interactive.pdf * For the -help on all AFNI programs, plus the README files, and more, please see http://afni.nimh.nih.gov/afni/doc/program_help/index.html * For indvidualized help with AFNI problems, and to keep up with AFNI news, please use the AFNI Message Board: http://afni.nimh.nih.gov/afni/community/board/ * If an AFNI program crashes, please include the EXACT error messages it outputs in your message board posting, as well as any other information needed to reproduce the problem. Just saying 'program X crashed, what's the issue?' is not helpful at all! In all message board postings, detail is relevant. * Also, be sure your AFNI distribution is up-to-date. You can check the date on your copy with the command 'afni -ver'. If it is more than a few months old, you should update your AFNI binaries and try the problematic command again -- it is quite possible the problem you encountered was already fixed! ----------------------------------------------------------------- REFERENCES and some light bedtime reading (if you have insomnia) ----------------------------------------------------------------- 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. ** http://afni.nimh.nih.gov/sscc/rwcox/papers/CBM_1996.pdf 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. * http://afni.nimh.nih.gov/sscc/rwcox/papers/Realtime_FMRI.pdf 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. * I think the first paper to demonstrate realtime MRI volume image registration running on a standard workstation (not a supercomputer). * http://afni.nimh.nih.gov/sscc/rwcox/papers/RealtimeRegistration.pdf 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'). * http://afni.nimh.nih.gov/sscc/rwcox/papers/Delays2001.pdf ZS Saad, G Chen, RC Reynolds, PP Christidis, KR Hammett, PSF Bellgowan, and RW Cox. FIAC Analysis According to AFNI and SUMA. Human Brain Mapping, 27: 417-424, 2006. * Describes how we used AFNI to analyze the FIAC contest data. * http://dx.doi.org/10.1002/hbm.20247 * http://afni.nimh.nih.gov/sscc/rwcox/papers/FIAC_AFNI_2006.pdf ZS Saad, DR Glen, G Chen, MS Beauchamp, R Desai, RW Cox. A new method for improving functional-to-structural MRI alignment using local Pearson correlation. NeuroImage 44: 839-848, 2009. * Describes the algorithm used in 3dAllineate (and thence in align_epi_anat.py) for EPI-to-structural volume image registration. * http://dx.doi.org/10.1016/j.neuroimage.2008.09.037 * http://afni.nimh.nih.gov/sscc/rwcox/papers/LocalPearson2009.pdf ZS Saad, RC Reynolds, BD Argall, S Japee, RW Cox. SUMA: An interface for surface-based intra- and inter-subject analysis within AFNI. 2004 IEEE International Symposium on Biomedical Imaging: from Nano to Macro. IEEE, Arlington VA, pp. 1510-1513. * A brief description of SUMA. * http://dx.doi.org/10.1109/ISBI.2004.1398837 * http://afni.nimh.nih.gov/sscc/rwcox/papers/SUMA2004paper.pdf BD Argall, ZS Saad, MS Beauchamp. Simplified intersubject averaging on the cortical surface using SUMA. Human Brain Mapping 27: 14-27, 2006. * Describes the 'standard mesh' surface approach used in SUMA. * http://dx.doi.org/10.1002/hbm.20158 * http://afni.nimh.nih.gov/sscc/rwcox/papers/SUMA2006paper.pdf POSTERS on varied subjects from the AFNI development group can be found at * http://afni.nimh.nih.gov/sscc/posters ------------------------------------------------------------------------------------ SLIDE IMAGES to help with learning the AFNI GUI http://afni.nimh.nih.gov/pub/dist/doc/program_help/images/afni03/ ------------------------------------------------------------------------------------ http://afni.nimh.nih.gov/pub/dist/doc/program_help/images/afni03/Slide01.png ------------------------------------------------------------------------------------ http://afni.nimh.nih.gov/pub/dist/doc/program_help/images/afni03/Slide02.png ------------------------------------------------------------------------------------ http://afni.nimh.nih.gov/pub/dist/doc/program_help/images/afni03/Slide03.png 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AFNI program: afni

Output of -help

Output of `-help`