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Old Release Notes
From old website
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- 04 Dec 2003 [version 2.55j]
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- You can now animate AFNI image displays without holding down
any keys or mouse buttons.
- To animate an image window through the slice direction, put the
cursor over the image itself, then press the 'v' (for 'video')
key. 'V' will animate in reverse slice order. Press the space
bar (or any other key) to stop the animation.
- To animate in the time direction, you use the 'v' (or 'V') key
in the graph window.
- By default, the animation is done as rapidly as possible. To slow
it down, you can set the environment variable AFNI_VIDEO_DELAY
to a time delay in milliseconds; 50..100 is a good range of values.
- This variable can be set in your .afnirc file
or interactively in the Edit Environment controller
(available on the Datamode->Misc menu or the Button-3 popup
menu in the AFNI image windows).
- Both types of animation will loop around to the other side (of the
slice stack or time grid) when they get to the end.
- AFNI programs can now read images from MPEG-1/2 files.
- You can use program aiv (AFNI Image Viewer) to
look at such files.
- You can read them into to3d.
- AFNI itself will treat an MPEG file as an axial dataset
(e.g., the MPEG time-axis is treated as the I-S axis).
You can thus read MPEGs directly into AFNI (no sound, though).
- This is done via the
libmpeg2 library.
- If you use Mac OS X 10.3 (Panther), AFNI will now speak to
you when it starts up! If you don't like this, set environment
variable AFNI_SPEECH to NO.
- You can now Undo the Linear Fillin in the Draw Dataset plugin.
- Rick Reynolds has added the SurfMeasures program to
the surface packages within the AFNI+SUMA dominion.
- This program will output measures over one or two surfaces.
- Get node-based thickness, areas, volume, normals, etc.
- Get aggregate surface areas, volume, etc.
- Ziad Saad has added the SurfSmooth program to
the surface packages within the AFNI+SUMA dominion.
- This program will smooth surface geometry or surface data.
- For algorithm references see SurfSmooth -help.
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- 20 Nov 2003 [version 2.55i]
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- The "Draw Dataset" plugin now has multiple levels of Undo and Redo.
- This is to make it more compatible with SUMA's ROI drawing.
- SUMA now has a "pen" drawing mode similar to AFNI's.
- This is to make it compatible with drawing tablets such as the
Cintiq
display from Wacom.
- If you are interested in how to setup a Cintiq display
for use with AFNI and SUMA, post a message
on the
Message Board.
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- 05 Nov 2003 [version 2.55h]
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Since the last message in August, in chronological order:
- Environment variable AFNI_MAX_OPTMENU sets the upper limit
on the number of elements in a "option menu" (e.g., the "Anat"
button on the "Define Function" control panel). On some systems,
more than 255 elements causes the program to crash, so 255 is now
the default upper limit. To change this (e.g., so you can access later
bricks in a lengthy bucket dataset), set this environment variable to
a larger number (e.g., 666).
- If you type the name of a dataset file on the afni command line, the
program will now read it correctly, rather than try to assume it is a directory
of dataset files. That is, in "afni x y", x and y
can be dataset filenames or directories. Datasets loaded from the command
line directory are in a manufactured session called CLI in the "Switch Session"
chooser.
- In the "Draw Dataset" plugin, you can now attach a string label to each value. These
labels will be stored in the dataset .HEAD file. The intention is to make it easier
to recall which drawn ROI value corresponds to the hippocampus (for example).
- Clicking Button-1 in the intensity grayscale bar (right of the image) will cause
the image window to re-aspect itself. This is because the AFNI_ENFORCE_ASPECT
environment variable doesn't always work on some Linux and Mac systems; this new
feature makes it easy to manually correct the problem.
- Too-short input stimulus time series input to 3dDeconvolve will now be extended
with zero values, rather than cause a fatal error.
- Clicking Button-1 down in an image and then dragging the cursor (with the button still
down) lets you adjust the data-grayscale mapping curve interactively.
- For details, see the AFNI_STROKE_* environment variables in
README.environment.
- You can make AFNI plot the data-grayscale mapping function
using the "Display Graymap Plot" item on the intensity bar Button-3 popup menu.
- You can force the grayscale map to run from the 3D dataset minimum
to maximum (rather than the slice-by-slice mapping that is the default).
This is done with environment variable AFNI_IMAGE_GLOBALRANGE.
When you do this, the data-grayscale mapping curve does not change when
you change slices.
- You can popup the "Edit Environment" controls from the Button-3 popup menu attached
to the image window.
- Mac OS X 10.3 is now supported. You'll need the new source code if you want to
compile (the 10.2 binaries seem to work on 10.3), since Apple made a couple incompatible
changes to the C compiler in the upgrade.
- The realtime plugin now computes the FIM based on the registered dataset rather than
the original dataset, if realtime registration is turned on
(Rick Reynolds).
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- 08 Aug 2003 [version 2.55d]
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- Since 08 Apr 2003, you've been able to input .1D files to most 3dSomething
command line programs. The "spatial" direction is down the columns (vertical).
The default is that across the rows (horizontal) is a "bucket" dimension.
The new environment variable AFNI_1D_TIME, if set to YES, will cause the
horizontal direction to be the time axis (with TR=1). This makes it possible to input
.1D files to programs that process 3D+time datasets; however, the files will probably
need to be transposed first -- so that the time axis is horizontal rather than
vertical. For example,
1dtranspose fred.1D - > fred_q.1D
3dFourier -prefix fred_filt_q -highpass 0.1 -retrend fred_q.1D
1dtranspose fred_filt_q.1D - > fred_filt.1D
rm -f fred_q.1D fred_file_q.1D
- Most of the 1dSomething programs that required an output filename (like 1dtranspose)
now let you use a "-" as the output filename to indicate that the output will be
written to stdout.
- A bug was fixed in AFNI's Read Session function -- it should be working again.
- 3dWarp now has a -fsl_matvec option, which lets you input matrices
whose coordinates are in the LPI order used by FSL and SPM. For example, you
can resample an FSL functional dataset to be on the highres grid by doing
3dWarp -matvec_in2out example_func2highres.mat -fsl_matvec \
-gridset highres.hdr -prefix zstat_h zstat.hdr
The output dataset will of course be in the AFNI format. You can
convert it back to ANALYZE-7.5 format using program 3dAFNItoANALYZE.
- 3dWarp also now has a -quintic option, which selects
5th order Lagrange polynomial interpolation. (The default is still linear
interpolation.)
- Fixed a bug that occured only when the anatomical and functional (underlay and overlay)
datasets are the same. This situation couldn't arise prior to 01 Aug 2003,
and I failed to anticipate it.
- Fixed a typo that made the Cygwin version of AFNI
fail to compile.
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- 01 Aug 2003 [version 2.55a]
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- The interactive AFNI program no longer makes a distinction between "functional"
and "anatomical" datasets for display. For example, you can display a statistical dataset
from 3dDeconvolve as the underlay and an echo-planar dataset as the color overlay. The
choice is now yours.
- This seemingly simple change required editing more than 20 source code files in
more than 400 places. (The dichotomy between "function" and "anatomy" goes back
to the very first days of AFNI.) There may be some glitches -- please let
me know.
- This is the first step in a plan to revamp the capabilities of datasets and AFNI.
Other steps in the plan include:
- Non-rectangular regions.
- More complicated data types stored at each node (AKA voxel) location;
for example, vector and matrix types.
- More complicated color generation and overlay schemes; for example, overlaying
from more than one dataset.
Don't ask when!
- The next major release of SUMA is out! For complete details, downloads, etc.,
check here.
The vast changes include:
- Much better documentation.
- Multiple linked surface viewers.
- Simultaneous left and right hemisphere display.
- Talairach surfaces.
- ROI drawing on the surface.
- Node color data import.
- Control of color plane order and opacity.
- Video (continuous) and single frame recording.
- Volume-to-surface and surface-to-volume mapping programs.
- Coming soon will be the documentation of the tools for cross-subject
surface-based analysis using standardized meshes.
Kudos for Ziad Saad, who has worked ferociously (in a benign sense) on this for months.
The source code for SUMA is included with the AFNI source
distribution. SUMA binaries are also included with the Mac OS X AFNI
binaries, but not in other AFNI binary packages.
Minor changes made recently are:
- Rich Hammett has fixed yet another problem with the Siemens' DICOM mosaic format.
- 3dcalc news:
- The parser now takes much longer expressions.
- The program now saves the history of each input dataset into the output dataset's history.
- When saving results into a short- or byte-valued dataset, the program now checks
for non-integral values in the output -- if it finds any, it automatically provides a
scaling factor (like the "-fscale" option).
- New options to 1dplot let you control the x- and y-axes more completely.
- 3dinfo will now print ALL the history from a dataset, not just the first 8000 characters.
- 3dmerge now has a "-verb" option, so you can get some progress reports while it works.
- The "Nudge Dataset" plugin now lets you interpolate with the NN (nearest neighbor) option.
- Conversion to z-scores, etc., which rely on the statistical parameters set in the
dataset header, now should properly work again only when the statistical parameters
are correctly set. (Doug Ward has been complaining about this on the message board.)
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- 21 Jul 2003 [version 2.52i]
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In chronological order of implementation:
- New keyboard presses you can use in the image viewing window:
- PageUp and PageDown to change slices.
- Arrow keys to move 1 pixel at a time (like the arrowpad buttons).
- Delete key as the equivalent of "Draw Dataset" Undo button.
- Arrowpad buttons in the image viewer windows now wrap back to the other edge
when the crosshairs get to the edge of the image.
- Image viewer windows now won't get bigger than the display screen when
you switch datasets (oops).
- -median option in 3dmaskave.
- Fixed bug in Double Plot colors from Dataset#N plugin.
- New "pen" toggle in image viewer window lets you draw using mouse Button 1
(e.g., when using the "Draw Dataset" plugin to draw an ROI).
- Fixed Solaris 2.8 bug, where Button 3 popup menus wouldn't appear.
- Numerous changes to SUMA and corresponding changes to AFNI,
but we're not quite ready to finalize and document these.
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- 12 May 2003 [version 2.52h]
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You might (or might not) wonder how new AFNI version numbers are decided upon,
and when I decide to change the numbers and make a new release. The answer to both
questions is, "Randomly."
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- 01 May 2003 [version 2.52g]
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- Input of 1D time series files to AFNI command line programs
can now sub-sample along the time (row) axis as well as along the column
axis. This is done with braces, as in
'fred.1D{0..$(2)}'
which means to read only rows #0, #2, #4, ...,
until the end (signified by the '$'). To read only from columns
#3 and #5, and to read the rows backwards, you could use
'elvis.1D[3,5]{$..0}'
See the output of
'1dcat -help'
for a complete discussion of the 1D selectivity options.
- 3dcalc has the new '-taxis' option, which is useful for specifying the creation
of a 3D+time dataset when only 3D datasets are input.
See the output of
'3dcalc -help'
for the details.
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- 24 Apr 2003 [version 2.52f]
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- Bug Fix: Kate Fissell (Carnegie-Mellon) has convinced me
that program 3dTshift was incorrect; in fact, that it was shifting things
exactly the wrong way. This problem has been fixed (and the analogous one in
3dvolreg). I apologize for this error.
- New program 3dWarp lets you apply an arbitrary affine coordinate
transformation to a dataset (rotations and shears and scalings, oh my).
- 3dTagalign has been modified to allow tag-based registration to include
coordinate scalings and shears, if the user so specifies. Previously, it only
would rotation and shifts.
- You can now choose the colors used in 1dplot (and other similar graphs)
using environment variables.
- 3dUniformize has been added back into the default compilation ("make totality") and
also modified to handle byte-valued datasets.
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- 08 Apr 2003 [version 2.52e]
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- The AFNI distribution now includes a set of small images of
AFNI users. One such image will be randomly selected to
be shown in the splash screen when AFNI starts up. If
you want to contribute your image, create a .jpg image no larger
than 128x128, and e-mail it to me rwcox@nih.gov
as a MIME attachment.
- Save the JPEG file at quality factor about 90 - higher just wastes disk space.
The file should be between about 4K and 8K in size.
- If you want your name on the image, you'll have to include that
in a text overlay. AFNI won't draw your name under the image.
- Image files are stored in the plugin directory. If you want to
put some local images there but not contribute them to be seen
by the whole world, then any image fitting the name pattern
"face_*.jpg" will be included in the splash screen list.
- Such images larger than the 128x128 limit will be scaled
down when being displayed. The image scaling function
isn't particularly efficient, so this will slow down the
splash screen display.
- New faces will be added to the source distribution about weekly.
Binary distributions, on the other hand, are usually only re-made at
longer intervals.
- You can now process .1D files through most 3dSomething programs. (3dcalc
is the main exception, but 1deval can be used as a calculator on .1D files.)
- The main application is to use the statistical program 3dANOVA, etc.,
on collections of numbers not necessarily associated with a 3D grid.
This is how surface-based inter-subject statistics will be
performed (after surface nodes are brought into anatomical alignment).
- However, the surface-based statistics package, including display
of the results within SUMA, isn't ready yet.
- Each row of a .1D file corresponds to a "voxel"; each column is a
"sub-brick".
- Program 3dAFNItoANALYZE has a new option "-orient", which lets you
specify the orientation of the output volume(s). If necessary, the program will
flip the data around from the AFNI orientation to the desired orientation.
This can be useful for viewing ANALYZE files in SPM, for example.
- Fixed a bug in 3drotate that gave bad results when applying rotations
from a text file (e.g., "-dfile") that were very small, but not zero.
- Fixed a problem with reading MINC files that have incomplete slice scaling factors,
or have slice scaling factors that make the data values overflow the range of
the byte or short data types.
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French is Just Another Word for Nothing Left to Lose
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- 13 Mar 2003 [version 2.52d]
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- 1dplot has some new features:
- It now accepts multiple 1D files (e.g., 1dplot a.1D 'b.1D[3..5]').
- New option -xzero specifies the x-axis coordinate at the left.
(Default is zero.)
- New option -nopush skips the "pushing" out of the x- and y-axes
to round values.
- The algorithm used 3dAutomask with the -dilate option is altered
slightly, to eliminate voids inside the mask created by the dilation.
- New program 3dAnhist makes an attempt to analyze the histogram of a high-res
T1-weighted anatomical dataset for peaks.
- Its primary motivation is to let you find
out if the histogram has 2 well-defined peaks, presumably corresponding to gray- and
white-matter.
- New option -ort in 3dTcorrelate lets you specifiy extra timeseries
for detrending (in addition to the polynomials).
- Number of tags allowed in the tags plugin is increased to 666. This should be enough
for all but the most indefatigable user.
- 3dNotes has been modified to behave as its -help option claims
with respect to dealing with the "\n" (etc.) escapes in input Note strings.
- Some users are soooo picky, aren't they, Adam?
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- 03 Mar 2003 [version 2.52c]
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- Per Lukas Pezawas of CBDB/NIMH, modified 1dgrayplot to have -ps option,
like 1dplot.
- Modified mritopgm to have a clipping option.
- New-ish program 3dDeconvolve_f is the same as 3dDeconvolve, but does
all calculations in single precision instead of double precision.
Runs about 40% faster (e.g., 85 vs. 140 CPU seconds on a sample run
with 595 time points, 15 regressors, and 21000 voxels).
- In cases where the matrix is very nearly collinear, the
calculations in single precision may lose accuracy.
- [See 27 Nov 2002]
Modified mri_read_dicom.c to allow user to skip slice gap/thickness
fixup entirely (cf. README.environment, as usual).
Fixed a bug in AFNI itself that could cause a crash when switching
from viewing a functional bucket overlay to a non-bucket overlay.
- Yesterday's fix caused AFNI to crash when started without a
functional dataset in the current session. That's been fixed.
- Rich Hammett of the SSCC/NIMH/NIH/PHS/HHS/USA has modified the
DICOM reading function to deal with yet another variant of the
Siemens mosaic format.
- Will no one rid me of this troublesome format!?
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- 24 Feb 2003 [version 2.52b]
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- Some people (e.g., Hauke and Mike)
complained about the change in the Rescan operations
(see 15 Jan 2003). You can now set environment variable
AFNI_RESCAN_METHOD to select the older Rescan method.
- The Button-3 (right-click) popup for a colorscale now has a
label that shows the color value at the level where you clicked
the button and also the corresponding functional overlay value.
- SUMA related changes to AFNI:
- You can now control the node boxsize and surface linewidth
from the "Control Surface" popup.
- If node boxes are being drawn, the node closest to the
crosshair point with have a * drawn inside its box.
- Fixed a bug so that colormaps drawn from AFNI to SUMA
are only sent once (they were sent twice before; we noticed this
problem when drawing ROIs in AFNI and displaying them interactively
in SUMA).
- N.B.: You must recompile SUMA to use it with this new
version of AFNI, since the interprocess communication
protocol used to exchange data between the two programs
has been changed.
- Windows BMP output from the image viewer now uses the "-bpp 24" flag
to program ppmtobmp to save the result as a 24 bit image, rather
than as a color-quantized 8 bit image.
- 3dcalc now allows RGB-valued dataset input. Since only one
number per voxel is actually used in the calculation, the default
is to compute with the grayscale intensity corresponding to the
RGB value in each voxel. However, the new option "-rgbfac"
lets you change what combination of R, G, and B values is used.
- When using the "Draw Dataset" plugin, the keypad "Delete" key pressed in
an image window now functions like the plugin "Undo" button.
- The DICOM reading function now can handle missing coordinate information
found in some editions of the Siemens Numaris Mosaic format. (Thanks to
Rich Hammett of the SSCC for this fix.)
- A time index change in the main AFNI controller will now be reflected
in the new volume renderer. This lets you scroll through 3D+time functional
datasets in the 2D slice, 3D renderer, and SUMA views all at once.
(Only for the truly heroic FMRI data analyst.)
- 3dhistog now writes it header lines as a comment field, so that
the output can be read directly by 1dplot, etc.
- Fixed a bug in the AFNI grapher Double Plot code with the Plus/Minus
option; this bug was introduced with the Dataset#N plugin.
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- 04 Feb 2003 [version 2.52a]
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- AFNI, at long last, now supports "continuous" colorscale
functional overlays. Details on how to setup your own colorscales
and so forth, can be
found here.
- Rich Hammett of the SSCC has modified 3dTsmooth to allow the user
to input his/her own filter coefficients from a file. For details,
see the output of
3dTsmooth -help.
- .afni.startup_script can now be used to set the colorscale,
and to restore the setting of the Function Range controls.
For more details, see
README.driver.
- Program 3dcopy will now read non-AFNI datasets
(i.e., MINC, SPM, CTF) as input, and then write them out as
AFNI-formatted datasets with new names.
- When you are viewing a functional "fim" dataset that has no threshold statistic
attached, the "Thresh" slider scale is now de-sensitized. The old behavior
was to hide this slider.
- The new Imon tool (by Rick Reynolds of the SSCC and Rasmus Birn of the
FMRIF) is for users of GE "realtime" EPI. This program
can monitor the I.* image files created in realtime to see if
any are missing (a problem we get here from time to time).
Optionally, it can feed the images, as they appear on disk, to the AFNI
realtime acquisition plugin. If you are interested in this software, post your questions
on the AFNI message board.
- You can now input double (8 byte float) values into to3d using the
new "3Dd:" input specifier. However, since AFNI doesn't
support double-valued datasets, these values will be converted to 4 byte
floats.
- I've modified (again) the behavior of the threshold slider when no statistic
is attached. Now, it is always active, unless the functional dataset is in
RGB format - in that case, no threshold is applied. If no statistic is
attached (i.e., a "fim" dataset), then the threshold applies directly
to the functional data itself. In this way, you can threshold the functional
values themselves, before colorizing them.
- I added a few more default colorscales, including a couple with gaps in the
middle.
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New AFNI Interactive Features
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- 22 Jan 2003 [version 2.51n]
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- In an image viewer, the keyboard arrow keys now scroll the crosshairs
1 pixel at a time (like the 4-way arrowpad in the lower right corner).
- In zoom+pan mode, these keys will pan the image instead of
moving the crosshairs.
- The Page Up and Page Down keys will move the image slider one slice
up or down (like the '<' and '>' keys).
- New environment variables:
- AFNI_DEFAULT_OPACITY lets you set the default level for
the color overlay opacity in the image viewers.
- AFNI_DEFAULT_IMSAVE lets you set the default image save
method (.jpg, .gif, etc.) in the image viewers.
- AFNI_VALUE_LABEL now defaults to YES rather than NO.
- AFNI_AGIF_DELAY lets you set the inter-image delay when
creating animated GIFs.
- The beginnings of AFNI scriptability are presented for your consideration.
Scripting is the ability to control/execute some AFNI functions from
a text file.
- The "Datamode->Misc->Save Layout" menu item will save a script
that will restore some features of your AFNI window setup,
if you just press "Set" with a blank filename. The script file
is saved into file ".afni.startup_script", in the current directory
(not necessarily the current session).
When you start AFNI in the same directory, the script will
be executed. Features currently saved include:
- Controllers, image viewers, and graph viewers open (but not plugins).
- Threshold slider and color pbar settings (from "Define Function".
- Func and Thr resample modes (from "Define Datamode").
- The "See Function" state.
- The "Datamode->Misc->Run Script" menu item will let you read in
a script and have its commands executed in the middle of an AFNI
run.
- See README.driver for details
about what can be done in a script.
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- 15 Jan 2003 [version 2.51m]
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- The C code behind the dataset Rescan buttons now works slightly differently.
If you were doing bizarre things like replacing the contents of datasets then
pressing Rescan, you may see some different results now.
- A bug in 3dresample was fixed; this bug made it impossible to Talairach-ize
(via the markers) a +orig dataset that was the output of 3dresample.
- A bug in 3dmerge was fixed; this bug could produce negative values when
doing a -1blur on a non-negative dataset. (Can you say "Gibbs phenomenon"?)
- If you are using surfaces (e.g., SUMA), you can now change the line thickness
of the surface intersection overlays in AFNI by altering the
AFNI_SUMA_LINESIZE environment variable in the
Datamode->Misc->Edit Environment control panel.
- All instances of C++ reserved words (such as class) have hopefully been replaced
in the AFNI source code.
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- 27 Dec 2002 [version 2.51k]
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The -unpooled option to 3dttest lets you use a t-test
that does not assume equal variances in the two populations. This
option is very old (late 1994); however, the number of degrees-of-freedom
(DOF) varies between voxels in this formulation. At present, there
is no support in AFNI for statistical distributions whose
parameters vary spatially.
As a palliative, I have added the
ability to 3dttest to output an auxiliary dataset with the
DOF stored in each voxel. The t-statistic and DOF parameter can
then be converted to a z-score (for example) using the fitt_t2z
function in 3dcalc. Details are given in the
-help output of 3dttest.
- I'm working on a new dataset format that will allow the storage
of more complicated information, including spatially varying
statistical parameters.
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Christmas Stocking Stuffers
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- 24 Dec 2002 [version 2.51j]
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- Some changes to the
realtime plugin
(which, as far as I know, is only in
use at NIH, MCW, UCSD, and Simon Frasier).
- Fix to DICOM reading software to get the through-slice orientation
correct in to3d when reading multiple single-slice files. (Oops.)
- Also added support for DICOM "Rescale" and "Window" tags. To enable
these, you must set the environment variables
AFNI_DICOM_RESCALE and AFNI_DICOM_WINDOW
to YES, respectively.
- I'm not sure it makes sense to use the Window tags in FMRI
data analysis, but you'll have to be the judge. The DICOM
manuals are laconic, terse, obscure, and pleonastically redundant.
- If a DICOM file has such tags, but the environment variables
aren't set, then a warning message will be printed.
- New program aiv (AFNI Image Viewer) is a simple program
for displaying a bunch of images. For example:
aiv *.jpg
This will open a window that looks suspiciously like an AFNI
image viewer.
- The motivation that led to aiv
was to make it easy to scroll through the Webcam images from
our 3 T scanner.
- aiv can read the same formats as to3d,
but is not limited to having all the 2D images have the
same size or data type.
- aiv isn't intended to replace
xv or other
X11 image viewers - it is just an alternative that you
might find handy for some purposes.
- Matthew Belmonte has fixed an obscure bug in his
permutation test plugin.
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- 11 Dec 2002 [version 2.51i]
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- AFNI can now read CTF MEG SAM and MRI files, so we
can display results from our MEG system.
- 3dIntracranial was modified to work with byte-valued
datasets.
- Image viewer windows now scroll through their slices if you
press the '<' or '>' keys while the mouse cursor is
in the image sub-window (i.e., like the graph viewer
time point moves with the same keystrokes).
- Some changes to the realtime plugin to make things more
flexible for NIH and UCSD users.
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- 02 Dec 2002 [version 2.51h]
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- Another variation on the Siemens DICOM Mosaic format surfaced
last week, from an Allegra scanner at NYU [via George Tourtellot].
The image reading
functions have been modified to deal with this case correctly.
- Also see 13 Nov 2002's entry.
- The opacity and brightness graphs in the new volume rendering
plugin have been modified to let you display the coordinates
of the graph 'handles' as you move them. You must drag these
handles with mouse Button 3 depressed to get the label to
appear - if you use Button 1, the handles move as before,
but the (x,y) coordinate label doesn't appear.
- This feature lets you set the break points for opacity
and/or brightness at precise numerical values. [It was
suggested by Ziad Saad, who was using the renderer to
look at MRA data.]
- If you Button 3 click in the histogram graph, you'll
also get an (x,y) coordinate label.
- This feature does not work in the older
"Render Dataset" plugin, which is no longer being upgraded.
- On my older X11 server at home, this feature sometimes
causes the server to crash. This doesn't happen on my
Linux box at the NIH, so I suppose whatever bug in the
server that caused the crash was fixed some time ago.
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- 27 Nov 2002 [version 2.51g]
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Some disturbing DICOM files were given to me this morning. In them, the
"Spacing Between Slices" attribute was set to 1.0 mm, and the "Slice Thickness"
attribute to 4.0 mm. The acquisition was done with a 4.0 mm thickness and
a 1.0 mm gap between slices. However, the DICOM standard clearly states
that "Spacing Between Slices" is the center-to-center slice distance. This
is what to3d uses for the "z voxel size". In this morning's data, the
result is a falsely thin set of slices.
The fix just implemented is twofold:
- Check if "Spacing Between Slices" is less than "Slice Thickness".
If so, then print a warning and add the two to get "z voxel size".
- This means that DICOM files with overlapping slices will be
misinterpreted. But I've never seen a MRI experiment like this,
so I'm not worrying too much.
- And/or, if the new environment variable AFNI_SLICE_SPACING_IS_GAP
is set to YES, then "z voxel size" will always be set to the sum
of "Spacing Between Slices" and "Slice Thickness". This will allow for the
(rare) case when the interslice gap is larger than the slice thickness.
By the way, these files came from a scanner manufacturer whose name comprises 2 letters
from the first third of the alphabet.
I have modified program 1dplot to accept a new option " -ps".
With this option, the program writes the plot in PostScript format to
stdout, instead of to an X11 window on the screen. For example:
1dplot -ps gort.1D > gort.ps
This feature (requested by Lukas Pezawas) makes it possible to make such
plots as a part of a script file (e.g., from the " -dfile" output
of 3dvolreg).
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- 22 Nov 2002 [version 2.51f]
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- AFNI (and to3d) can now read JPEG image files.
To view a series of identically-sized JPEG files, you can use
a command like
afni -im *.jpg
Input of JPEG files is done using the external program djpeg
as a filter; this program is now built by the make totality
command, and is in all the binary distributions as well.
- If you also install the netpbm software (not included
with AFNI), GIF, BMP, TIFF, and PNG image files can be
read using filter programs from that package.
- AFNI and to3d are designed to deal with arrays of images
of exactly the same dimensions, so aren't particularly useful for
looking at mounds of images of different sizes.
- The mpeg_encode and whirlgif programs are now also built
with AFNI, meaning that saving image sequences to MPEG-1 and
animated GIFs should be easier now.
- To use whirlgif from within AFNI, you still have to
have netpbm installed.
- Cf. 14 Aug 2001 for more details on output image format converters.
- When the interactive program starts,
AFNI now checks its version number with the master copy on this
server. If they don't match, a message is printed to the terminal.
- If you input something like "zork+orig" to a "-prefix" option
of a 3d* program, you would get a dataset with a name like
"zork+orig+orig.HEAD". This is annoying (to me, anyhoo). The software
now checks for this, and cuts off the extra "+view" suffix.
Aside
Today is the 39th anniversary of the murder of President Kennedy.
I was 9 then, and I remember our neighbor coming over to tell us what
happened. I was eating lunch at home. School that afternoon was very subdued.
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Jaguars, Mosaics, yada yada yada
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- 13 Nov 2002 [version 2.51e]
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- My copy of Mac OS X 10.2 (Jaguar) finally arrived. From now on, the
binary and source distribution of the AFNI package will be
for this version, stored under the name macosx_10.2. The
macosx_10.1 version is being defenestrated.
- The image input functions used in
to3d
will now read the
Siemens DICOM Mosaic format that is produced by EPI sequences
on the Allegra 3 T scanner with the Numaris 4 software.
- This stuff hasn't been extensively tested yet!
In particular, computing the slice locations from the
Siemens-mangled values in the DICOM header is a little iffy.
- to3d has long been able to read the Siemens-proprietary
256x256 mosaic format.
- Rasmus Birn
added a delay option to
waver
for the gamma variate hemodynamic response function.
- New program
rotcom
will print out the transformation matrix+vector
that results from the "-rotate ... -ashift ..."
options that would be input to 3drotate.
- You can now open up to 10 AFNI controller windows (with the
"New" button); the previous limit was 5.
- This change is in honor of
Mike Beauchamp;
I hope he has enough screen space to handle this many images at once.
- 3dAFNItoANALYZE has been modified to allow the output of 4D
ANALYZE format files from AFNI 3D+time or bucket datasets.
- You can now use Shift+Button1 to draw in the "Draw Dataset" plugin.
(Button2 is hard to use if it is on a wheel mouse.)
- I modified the "Draw Dataset" plugin to have 2D and 3D neighborhood
drawing modes, which effectively let you draw with thicker lines.
- 2D neighborhoods are in the drawing slice only.
- 3D neighborhoods extend out to neighboring slices, and so
it is best to be displaying a 3x3 image montage when using
these (so you can see what the out-of-slice results are).
- The largest 2D neighborhood is the 5x5 square of voxels
about the drawn point. The largest 3D neighborhood
is the 5x5x5 cube of voxels about the drawn point.
If you want to draw larger blobs, see the Addendum, infra.
- Doug Ward fixed a bug in the deconvolution plugin that would
cause it to crash if the baseline was turned off.
Plus, I returned from a trip to
Machu Picchu.
Visiting the
Intihuatana at the
vernal equinox was quite interesting, at least from a sociological/anthropological
point of view.
I've added "2D Circle" and "3D Sphere" modes to the drawing plugin,
which let you choose the radius (in mm) of the ball that will be filled in
by the drawing value. [Per the request of Brian Knutson of Stanford.]
-
A bug in the DICOM file input function has been fixed. This bug only
showed up when reading a large number of files on the to3d command
line. It could cause the latter files to fail to be opened, or could cause
the X11 server connection to fail.
- A bug in a dataset creation macro was fixed. This probably doesn't
affect any existing program, but did affect something under development.
- AFNI has been modified to read ANALYZE-75 .hdr/.img file pairs
directly as AFNI datasets.
- Since there is no easy way to determine the orientation of
an ANALYZE-75 image from the .hdr file, AFNI assumes
that these files are oriented with x=Left-to-Right, y=Posterior-to-Anterior,
and z=Inferior-to-Superior (i.e., LPI axial slices). This assumption
can be modified by setting environment variable AFNI_ANALYZE_ORIENT.
- ANALYZE files that have 4 dimensions will be loaded as 3D+time datasets.
- ANALYZE files that have the string "stat" in their name will
be loaded as functional (fim) type datasets; all others will be loaded
as anatomical type datasets.
- In particular, AFNI will now load the output files of a
FSL FEAT
directory (normally named something.feat; cf.
this).
It will try to read the *2*.mat files to allow you to
overlay the stat functionals on the highres and
standard anatomicals.
- This stuff is still very alpha, and likely has rough spots. In particular,
I'm sure the FSL FEAT stuff will have trouble with data that isn't
stored in the LPI axial orientation.
- AFNI now prints (to stderr)
a warning message when it loads a "large" .BRIK
from disk. The default threshold of "large" is 100,000,00 bytes, but
this can be altered by the environment variable AFNI_LOAD_PRINTSIZE.
The only function of this message is to let you know what is happening
when disk I/O may take a long time.
- A modification to the use of malloc() on Linux seems to make it
work better when allocating large numbers of large blocks of data
(as happens with large multi-volume datasets).
I have added program 3dDespike, which is intended to remove large spikes
in 3D+time datasets. Usage and methods documentation can be found at
this page.
- The following bugs have been squashed (or at least stunned a little):
- On some systems, closing an image viewer that had a dialog ("Disp" or "Mont")
window open would cause AFNI to crash.
- On some systems, when a graph viewer opened, it would display garbage
until the user did something to force a redraw (e.g., resize).
- When an image viewer window was first opened, it would actually sometimes
repaint the image 2 or 3 times. This was due to a timing issue between
AFNI and the X11 server.
- 3dToutcount now writes the output of the -save option as a
(time-dependent) FIM
functional dataset, rather than an anatomical type. This makes more sense, so
you can show the "outlier-ness" of a point as a color overlay on the image time
series, and then jump to that point in a graph viewer to see what's screwy about it.
- The angle and shift ranges on the Nudge Dataset plugin have been enlarged.
The problem with Cygwin has been fixed. You should be able to compile
and run AFNI on this platform now. We are not supplying
binaries for Cygwin.
The new "Control Surface" button lets you control the color of surfaces
that have been transmitted to AFNI from SUMA.
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Miscellaneous Micro Modifications
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- 07 Aug 2002
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- 3dToutcount has a new option "-polort", which lets
you detrend each voxel time series with a polynomial, prior to
looking for outliers. Detrending is done with robust L1 regression
(described below).
- Sympathetically,
new plugin L1_fit lets you do L1 fitting to time series
graphs, much as plugin
LSQfit does with L2 (least squares) fitting.
The new plugin controls the "Tran 1D" function of the same
name, which determines the model that will be fit.
- Starting AFNI in a directory with no anatomicals but
with functionals used to fail. Now the first functional will
be copied as a warp-on-demand anatomical dataset to let you view
something.
- The realtime plugin, and rtfeedme, have been modified to
allow multiple image channels to flow into AFNI.
See
README.realtime for the details
(look for the NUM_CHAN control parameter).
- A bug was fixed that caused the graphing windows to crash on
occasion on some computers.
-
I've also added "Load" and "Save" buttons to the Talairach Atlas Colors
control panel. "Save" lets you save the current color selections to
a file; "Load" lets you read them in.
- Also, if you set the environment
variable AFNI_TTRR_SETUP to the name of a saved
color file, this will be loaded when you open the Atlas Colors
panel.
- Even with this autoload option, you still have to open
the Atlas Colors panel before
"See TT Atlas Regions" has any effect.
- As usual, you can put the definition of
AFNI_TTRR_SETUP into your .afnirc
file. However, be sure to use an absolute path
(e.g., /home/rwcox/.afni_ttcolors), since
otherwise the file will be read relative to the directory
in which you start AFNI.
- The format of the saved color file is a simple set of equations,
such as
Hippocampus = red
(one equation per line).
You could manually edit this file. Note that the color names
must be drawn from the labels on the palette defined on the
standard AFNI color menus. Region label names that
contain blanks have the blanks replaced by underscores, as in
Middle_Occipital_Gyrus = blue
Not all regions need be present in the file; regions that
are absent will not have their color setting changed when
the file is loaded.
Program to3d can now read DICOM files. Since we don't use DICOM here
(as far as I know), this facility has not been extensively tested.
- The input function should read both the
DICOM Part 10 format and the earlier ACR/NEMA format.
- The code can only deal with 1 sample per pixel monochrome uncompressed
images.
- Tags that are required, or images won't be read:
- 0028 0010 "Rows"
- 0028 0011 "Columns"
- 0028 0100 "Bits allocated" (must be 8 or 16)
- The code can set the voxel dimensions, slice location, and orientation,
if the appropriate tags are present in the file.
- The DICOM input function does not use the Rescale or
Window tags to modify the data.
- I'm not sure if it handles multislice or time-dependent
data files correctly, since I didn't have many samples of these.
Nor do I have samples from many scanner vendors.
- This code is derived from the RSNA/Mallinckrodt Institute sample
program dcm_dump_file.c. I am grateful to them for
making their code freely available, and to Jack
Lancaster of UTHSCSA for pointing this software repository out to me.
I am having network troubles for various silly reasons, and so some
binaries will be slow in coming.
Binaries News:
- The following binaries are being retired (i.e., removed forever)
since I no longer have easy access to such systems:
- hpux_10.20 -- HP-UX 10.20 systems
- linux_rh60 -- Linux Red Hat 6.0 systems
- linux_mdk72 -- Linux Mandrake 7.2 systems
- solaris26_gcc -- Solaris 2.6 systems
- sgi4k_6.5 -- SGI IRIX 6.5 systems with R4000 CPUs
- cygwin.tgz -- MS-Windows using Cygwin
- The following binaries are still present and accounted for:
- linux_glibc22 -- Linux with glibc 2.2
- linux_glibc21 -- Linux with glibc 2.1
- To check your version of the C library, type
ls -l /lib/libc*.so
The numbers present after the "libc" string will tell you
the version.
- macosx_10.1 -- Mac OS X 10.1 (soon to be 10.2?)
- solaris28_gcc -- Solaris 2.8 compiled with gcc
- sgi10k_6.5 -- SGI IRIX 6.5 compiled with SGI's cc
- solaris28_suncc -- Solaris 2.8 compiled with Sun's cc
This has been removed, since it has so many problems. -- 21 Nov 2002
New program SUMA is released today. SUMA is the
AFNI surface mapper. Details about downloads, installations, and
usage can be found at the SUMA link at the top of this page.
Some propaganda/information:
-
SUMA is a standalone cortical
surface viewing program that also has the ability to "talk live" to AFNI.
- Using AFNI and SUMA together, you can simultaneously display functional
activation maps overlaid on 2D image slices, on 3D volume rendered datasets,
and on the folded or unfolded cortical surface.
- You can also be linked to the
underlying data time series graphs at the same time -- if you have enough
screen space to show so many windows.
- You will need to download the latest AFNI version (2.50, also released
today, or later)
for it to interoperate with SUMA.
-
SUMA does not generate surfaces from MRI volumetric data. SUMA can read
surfaces created by the FreeSurfer (Harvard/MGH) and SureFit/Caret (Washington
University) software packages.
-
SUMA is distributed in C source code form with the rest of the AFNI package.
- Some pre-compiled binaries are also available at the SUMA download link.
- However, SUMA depends critically on the OpenGL libraries installed
on your system. If you use a binary linked here against a different version of
OpenGL than is on your system, things are not likely to work well. For this
reason, compilation at your site may be the best solution. YMMV.
-
SUMA uses OpenGL to draw the surfaces.
- It is best if you have an accelerated
graphics card, since OpenGL software-only rendering is slow.
- We have had
impressive results with the GeForce 3 and 4 cards with Linux; these cards
require installation of the most up-to-date
nVidia device drivers.
- One advantage of the GeForce 4 card is that it also supports dual-monitor
display, which is very useful when you want to display surfaces, volumes,
slices, and time series all at once.
- SGI systems with fast graphics subsystems also work well.
- We have not had a chance to check SUMA on any accelerated
graphics cards in other systems.
- We do know that SUMA works (slowly) with unaccelerated graphics cards on Solaris 2.8 and
Mac OS X 10.1.5.
-
Questions about SUMA installation and usage should be posted to the AFNI message
board, and not sent via e-mail.
- The word "suma" means "good" in the language Aymara, which is spoken in the
vicinity of Lake Titicaca in South America.
- Today is the true Independence Day for the United States of America:
- On July 1, 1776, Congress debated the motion regarding separation from Britain
(which had been moved and temporarily tabled back in May).
- On July 2, Congress voted for the motion and independence.
- On July 4, Congress adopted Jefferson's (et al.) Declaration as the instrument of secession.
- I strongly recommend the book "Novus Ordo Seclorum" by Forrest McDonald, a superb
discussion of the intellectual origins of Independence and the Constitution.
Credit:
SUMA was developed by Ziad Saad, who has been working furiously for the last 6
months on this project. With the right (and not very expensive) graphics hardware, SUMA is a visually
stunning program - and a very useful one. I want to thank and congratulate
Ziad for his efforts and accomplishments.
SUMA and AFNI talk to each other using an in-development protocol
named NIML. For more information on this topic
click here.
- New program 3dANALYZEtoAFNI lets you produce a .HEAD-only
AFNI dataset from 1 or more 3D ANALYZE *.hdr/*.img file pairs.
This new type of dataset will not have a .BRIK file. Instead, the
*.img files will collectively be used as the source of image volumes
when the dataset is read in by an AFNI program (which means
you can't delete the *.img files!).
- The input files for 3dANALYZEtoAFNI should not be
4D (or higher dimensionality) files. Each input file stores
exactly 1 sub-brick (3D volume) in the AFNI dataset that
is created.
- If some of the sub-bricks are statistical parameters (e.g., t-statistics),
then you can attach auxiliary parameters (e.g., degrees-of-freedom) to the
resulting dataset .HEAD file using program 3drefit.
- Note that AFNI programs do not write datasets
in this format. They always write datasets in the .BRIK file
format.
- However, you can use 3dAFNItoANALYZE [cf. 29 Nov 2001], to convert
a .BRIK formatted dataset to a sequence of ANALYZE format 3D files.
- The output of 3dinfo applied to a dataset created with
3dANALYZEtoAFNI will include a line like so:
Storage Mode: Volume file(s)
which indicates that the dataset is stored in a list of separate
volume files (stored in the .HEAD file attribute named
VOLUME_FILENAMES).
- After you create the dataset
3dANALYZEtoAFNI, you could compress the *.img files
with gzip, as in
gzip -9v *.img
AFNI will be able to read these in when it opens these
files as a dataset; however, other (lesser) software packages
probably will not
be able to use them in this format.
Recent efforts have been largely devoted to making changes to
prepare for the release of SUMA, the AFNI surface mapper program
(to be released by the end of June, we fervently hope).
Other changes since the last installment include,
in more-or-less chronological order:
- You can now create RGB-valued datasets using PPM input 2D files to
to3d (these could be converted from other image formats using
various image conversion programs, such as are found in the netpbm
package). In particular, this allows you to compute (outside of AFNI itself)
the exact colors you want at each voxel of an overlay.
- Note that
the color pure black (R=G=B=0) will not be overlaid when the
dataset is a "fim".
- You can also input 2D or 3D RGB files to to3d using the 3Dr:
input format, similar to 3Df: etc., as described in
FAQ #12.
- New program 3dThreetoRGB lets you create an RGB dataset
from 3 input bricks. In this way, you could use 3dcalc
to compute the R, G, and B components separately, then combine
them to make a funky overlay.
- At this time, you cannot volume render an RGB dataset, or do much of
anything else with it, for that matter. Except display it as an overlay
(Function dataset) in a 2D slice viewer window.
- Program 3dAutomask has been modified somewhat to produce
what I think is a better mask.
- The rendering plugins now have a new toggle button "I" to the left of the
view-angle choosers. When "I" is selected, then changes in the angles
made by pressing an arrow key are "incremental" in the direction chosen,
as opposed to absolute changes in the angles.
- This lets you spin the
brain volume about a chosen anatomical axis (assuming the dataset was
correctly oriented in to3d).
- When you change an angle with
"I" selected, the incremental viewpoint is computed and the new
absolute angles are recorded in the angle text fields.
- The "Where Am I?" Talairach Atlas popup now includes a display of the
coordinates in MNI template coordinates as well as in Talairach-Tournoux Atlas
coordinates. The transformation is the one described at
this page.
- Correspondingly, there is a "Jump to (MNI)" button available
on the Button-3 popup menu in the slice viewer windows,
when you are in the +tlrc view.
- If you use 3dclust on a +tlrc view dataset, you can add
the command line option -mni to have the coordinates
reported in MNI template coordinates instead of Talairach coordinates.
- 3dclust has also been modified to let you specify the "rmm" parameter
as 0 to mean 6 nearest-neighbor clustering, "vmul" as zero to specify no
volume editing, and "vmul" as negative to specify minimum volume = abs(vmul)*voxel volume.
- Program Ifile (by Ziad Saad) is for assembling the files output
by the GE RT-EPI pulse sequence into AFNI datasets.
- Also, Ziad generated a new Saad, little Samia!
- Changes from Doug Ward:
- Option -stim_base was added to 3dDeconvolve
(and the Deconvolution plugin). This
allows the user to specify which input stimulus functions are
to be included as part of the baseline model.
- Option -one_col has been added to program RSFgen.
With this option, the input stimulus functions are written as
a single column of decimal integers
(rather than multiple columns of binary numbers).
- Program 3dZeropad has a new option, -master, which
lets you specify that a dataset should be padded/cut down to match
the size of another dataset.
- Several changes to the AFNI image viewer module:
- The default font size for control buttons in the image viewers
has been reduced, and the buttons have been squished slightly closer together.
- Certain keystrokes, pressed when the mouse cursor is over
the image sub-window, can be used to control actions:
- Q or q: close the window (like pressing "Done")
- Z or z: change zoom factor (Z increases, z decreases)
- P or p: turn panning mode on or off
- C or c: turn cropping mode on or off (see below)
- I or i: change image fraction (I increases, i decreases)
- The new environment variable AFNI_CROP_ZOOMSAVE tells
the program to cut zoomed images down to the viewing size.
The default when saving a zoomed image is to save the entire
magnified image, including the parts not visible.
- This variable can be set in your .afnirc file,
or interactively in the
Datamode->Misc->Edit Environment pseudo-plugin.
- This variable has nothing directly to do with the new crop feature,
described next.
- The new "crop" button at the right lets you choose a sub-region
of the image to display:
- Press "crop" (the button will now invert colors);
- Click and hold down the mouse at the upper left corner
of the sub-region which you want to crop to;
- The cursor will change to a yellow and red diamond;
- Drag the mouse (holding the button down still)
to select a cropping rectangle;
- Release the mouse button to finalize the crop rectangle
(the "crop" button will now revert to normal colors).
To uncrop (return to the full image), press the "crop" button
to invert its colors, then press it again to change it back,
without doing the crop region selection. Other points:
- You can directly select the crop region, without using
the "crop" button, using Shift+Button-2. To turn
cropping off, just click and release Shift+Button-2,
without any dragging.
- Keystroke "C" or "c" is like pressing the "crop" button.
- The smallest crop rectangle allowed is 9x9 image voxels.
- You can select a crop region while showing an image Montage,
but if the rectangle you drag crosses sub-image boundaries,
the program will insult you.
- A Montage of cropped images usually is confusing unless
you put a colored border between them (using the Mont
control panel).
- Cropping while zoomed will actually crop a larger region
than you drag, so that the zoomed sub-region displayed
will correspond to the dataset voxels crop region that
you selected. The program tries to center the zoomed
sub-region on the crop region, but this is not always possible
if you selected a crop region that is right up against the
edge of the dataset volume.
- Turning "crop" on will turn the zoom "pan" off, and vice-versa.
- Switching to a dataset that has a different image size
should turn cropping off immediately. However, this may
not be immediately apparent if the window is also zoomed,
since zooming is not turned off when the image size changes.
- You can also crop in the volume rendering windows, since
these are just further instantiations of the same image
viewing module that is used for displaying 2D slices.
- Saving images from an image viewing window that is cropped will
save only the cropped region.
- The array of numbers that makes up an image
is cropped immediately as it is presented
for display to the viewing module.
- This fact means that the
auto-contrast computations work only on the cropped image array.
- This in turn means that the mapping from image numbers to
grayscale values is likely to alter when you crop an image,
since the min-to-max or 2%-to-98% range of values in the
cropped region may not be the same as in the whole image.
- You can set the numerical-to-grayscale mapping range to a fixed
value (thereby disabling auto-contrast) by
using the "Choose Display Range" item on the intensity
bar Button-3 popup menu. This is discussed more fully in
FAQ #8.
- New program 3dAutobox tells you how many planes on each
face of a dataset are all zeros in the mask that would be produced by
3dAutomask - these planes could be cut off
the dataset (with 3dZeropad) with little loss of information.
- New program 3dLRflip flips a dataset left-to-right. This
was written because some impaired person gave me datasets to register
(via 3dvolreg) that were mirror images of each other.
- 3dvolreg has a new option -wtrim which can be used
to save memory and time when registering large (anatomical) volumes.
- This option will probably become a default in the future.
- Also, the -clipit option is now the default
in both 3dvolreg and 3drotate; if you don't want this,
then you now have to use -noclipit on the command line.
- The default termination threshold for 3dvolreg has been
reduced, meaning that the program will probably iterate a little
longer trying to find a better fit.
- AFNI now includes the RGB cyclic spectrum colors from Ziad Saad. These
20 colors cycle around the spectrum at even increments, and were
formerly only available in AFNI
if you defined them in your .afnirc file
(e.g., copying from the sample AFNI.afnirc file).
- These colors are now loaded into the functional color overlay "pbar"
when the number of color panes is set to 20.
- One use is for mapping phase delays in retinotopic mapping.
- New program 3dresample (by Rick Reynolds) lets you re-sample
and re-orient a dataset to a new grid. This can be useful when you
want to compare dataset gathered at different voxels sizes and/or
slice orientations.
- In particular, it will be used in the scripts needed to
use SUMA, when you want to use an Axial SPGR
with a surface derived from a Coronal MPRAGE (just to name
one possibility).
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More Minor Mutations: MINC, Masks, Mac, ...
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- 11 Apr 2002
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- New program 3dAFNItoMINC will write an AFNI dataset
out in MINC format.
- This program requires that the MINCtools
program rawtominc be in your path.
- If you need the MINCtools package, look at
ftp://ftp.bic.mni.mcgill.ca/pub/minc/.
I use version 1.0 of the minc package and version 3.5.0 of the netcdf library.
- New program 3dAutomask will generate a binary mask file from
a 3D+time EPI dataset, which is supposed to only include the brain
voxels. The output of this program can be used as the -mask
input to 3dDeconvolve, for example.
- Some minor changes to get AFNI working on Mac OS X 10.1.3.
(The Web page for AFNI+OS X is not yet updated to
reflect these changes.)
- You can now zoom in/out with the 'Z'/'z' keys in an image window,
and toggle panning mode withe the 'p' key.
- You can now save zoomed images (but the entire image is saved in
its magnified state, not just the visible part).
- New plugin Dataset#N lets you plot multiple extra time
series in a graph window (like Dataset#2, but more so).
- Talairach Atlas "Where Am I" window now shows the (x,y,z) coordinates
of the focus point.
- Zooming has been speeded up (quite a lot), by rewriting the
image resampling code to use fixed point operations instead of
floating point.
- Save One of a zoomed image now will save the entire image as zoomed
(not just the part you see). It will also draw any
geometric overlays into the saved image file (e.g., crosshair lines, slice label overlay,
and the as-yet undocumented surface-slice intersection overlay).
- To get good resolution on the geometric overlays, you
may need to save them when zoomed.
- Geometric overlays can be turned on/off from the Button-3
popup menu attached to the intensity bar to the right of the image.
- You can now have the crosshairs drawn with a geometric overlay
instead of a voxel overlay. The advantage is that such crosshairs
are always only 1 screen pixel wide, no matter how much you expand
the image window or zoom level. This feature is activated
by setting environment variable "AFNI_CROSSHAIR_LINES" to "YES".
-
This variable can be set at runtime in the Datamode->Misc->Edit Environment
pseudo-plugin, or in your .afnirc file.
- In the future, this may become the default way of drawing the
crosshairs.
|
The Ides of March (Almost)
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- 13 Mar 2002
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A number of small to medium sized changes since FDR was introduced
in February. In temporal order of the changes to the source code
(ignoring small bug fixes):
- The Histogram plugin now lets you write results to a file
(changes courtesy of V Roopchansingh of MCW).
-
Doug Ward has added some new wrinkles to 3dDeconvolve:
- The "-tout" option was extended in order to write
a t-statistic sub-brick for each of the GLT linear combinations.
That is, if the -tout option is used along with the -glt option,
then the output bucket dataset will contain one t-statistic
sub-brick for each row of each GLT matrix.
- The "-nocout" option can be used to suppress outputs for the
individual coefficients in a model. In this case, you will
want to use "-glt" to specify the statistics you want to save.
- Option "-polort -1" can be used to specify that no baseline
parameters be used in a model. This would be appropriate for
cases where the baseline was removed previously by some other program.
- Option "-nobout" can be used to suppress saving into the bucket
dataset the baseline parameters and statistics thereof.
- to3d was modified so that if the "-2swap" option is present
on the command line, but the image reading routines auto-swap
the image data, then the images won't be byte-swapped again.
(Such auto-swapping only occurs with GEMS I.*, Siemens *.ima,
and ANALYZE *.img files.)
- Pressing the 'q' key while the cursor focus is in an image
will cause the image viewer window to close. This makes the
image viewers be a little bit more like the graph viewers.
- If you start AFNI with a list of directories that
don't actually have datasets, the old behavior was to ignore
that list entirely and create a "Dummy" dataset and session in
the current working directory ("./"). The new behavior is
to make the dummy session be the first directory on the
command line. [Only of real interest to users of the realtime plugin.]
- The image viewer windows have a new "Zoom" feature, controlled by
the new "Z" button on the right edge. You can zoom in by a factor
of 2, 3, or 4. The "pan" button underneath the Z button lets you
move the zoomed image around in its window. Use the BHelp feature
on these buttons to see the details on how to pan.
- You can combine this feature with
the Draw Dataset plugin when drawing ROIs to make precise selection
of the regions a little easier.
- This feature was
implemented very quickly, and as a result isn't that fast or slick.
(My actual motivation was to provide functionality for viewing
the details of the intersection of cortical surface models with
a slice plane; see the Preview below.)
- Zooming is implemented by rendering the entire magnified image
into an X11 Pixmap -- an off-screen window stored by the X11 server.
Then, as needed, pieces
of this are copied into the visible image window. This copying
operation is very fast -- since it is done entirely by the X11 server --
so after the zoom level is established (the slow part),
panning around is quite quick. However, this approach means that if
you have several zoomed image windows open at once, you can consume a
lot of memory in the X11 server. On some systems, this will cause
unpleasant problems, such as crashing AFNI (benign) or
crashing the X11 server (bad). If this problem arises, you should
avoid zooming more than a factor of 2 or 3.
- Consider a 1000x1000 image window, zoomed up by 4. The Pixmap
would be 4000x4000, or 16 million pixels. If each pixel is 3
bytes (a 24 bit visual), this would occupy 48 megabytes of
memory. Do this too much, and the X11 server will likely
be very unhappy with you (e.g., crash).
- At this time, "Save", "Mont", and "Rec" do not interoperate
with zooming.
- Rick Reynolds has put out a new version of the volume
renderer. It is still being worked on, and has some rough
edges. However, it is not based on Volpack, and so should
be more extendable than the old one. We plan to integrate
volume rendering more closely into the AFNI experience,
allowing
display of non-cubical non-axial datasets, adding rendering
projections such as MIP, etc. Stay tuned to this spot for
the latest news.
- New environment variables by the millions! As usual,
see README.environment
for the details.
- "AFNI_GRAPH_TEXTLIMIT" can be used
to make the Button-3 popup window in the graph viewers be
a scrollable text window instead of a spring-loaded menu pane.
This is useful if you use the Deconvolution plugin, and get so
many lines of text output that they don't fit on the screen anymore.
- "AFNI_GRAPH_BASELINE" and "AFNI_GRAPH_GLOBALBASE"
let you change the default mode of the graphing baseline. This is useful
for users (such as Mike Beauchamp) who want to start AFNI already
set up for global baselines with a base of 0, for example.
- "AFNI_VALUE_LABEL" lets you specify that the
dataset value label at the bottom of the Define Function control panel
will be turned on even if only 1 or 2 image viewers are open. (The
default is that all 3 image viewers must be open.)
- "AFNI_FIM_IDEAL" lets you specify the name
of the initial FIM ideal timeseries file.
[Only of real interest to users of the realtime plugin.]
- "AFNI_KEEP_PANNING" keeps the zoom panning mode turned on
until you explicitly turn it off -- the default is to
turn panning mode off after you release mouse Button #1.
At this moment, the only binaries available are linux_mdk72,
solaris26_gcc, and solaris28_gcc. The other platforms
for which I have customarily compiled AFNI (IRIX and HP-UX) are
at my former employer (MCW), and I no longer have access to those
systems. On the brighter side, I'm close to getting my own SGI and
Macintosh, so I'll be able to support those systems better than in the
past.
Preview of Coming Attraction:
We (Ziad Saad and I) are working hard on incorporating the display
of surface models into AFNI. The models will be imported from
other software (e.g., SureFit,
FreeSurfer).
You will be able to view functional overlays on the surface dynamically
linked to the AFNI functional overlays.
This is where the bulk of our efforts is going now. We hope that
the alpha-test version of this will be available sometime in
April.
(But in software, the best laid plans gang aft agley, even more than
in other human or rodent endeavors.)
- Doug Ward has contributed a new program 3dFDR, which
implements the False Discovery Rate (FDR) algorithm for
thresholding of voxelwise statistics. Instead of controlling for alpha (the
probability of a false positive anywhere in the volume), the FDR algorithm
controls for the proportion of false positives relative to the number of
detections. The documentation is available in the new file 3dFDR.ps.
- Doug has also made a few changes to 3dDeconvolve (instigated by the
notorious Luiz Pessoa).
- The -nlast input option has been modified so that it
always has the same meaning (i.e., whether or not the -nodata option is
in effect). Thus, for concatenated runs, -nlast
indicates the last data point
that will be used from each individual run within the concatenated dataset.
- The screen output from 3dDeconvolve (and the Deconvolution plugin) has
been extended to include the p-values for the individual IRF coefficients
(previously, p-values were reported only for each stim function). Also,
when the -glt option is used, the t-statistics and p-values are reported
for each row of the GLT matrix (previously, F-stats and p-values were
reported only for the entire GLT matrix).
- A bug was fixed in AFNI that could result in the Define Function control
widgets not being set up correctly when viewing the same functional bucket
dataset in 2 separate AFNI control windows.
- New program 3dAutoTcorrelate takes as input a 3D+time dataset and produces
as output an anatomical bucket dataset where sub-brick #n is the correlation of
voxel #n with all other voxels. This can produce gigantic datasets, so should
only be used on 1- or 2-slice datasets (which you can cut out of larger datasets using
the 3dZeropad program). This program was produced at the instigation of the
notorious Peter Bandettini (dude, where's my bagel?).
- Slice image viewers in AFNI now can display interslice projections.
These are controlled from the Disp control panel, as usual, with the
new Project menu. You can choose the projection slab width (e.g., plus/minus
3 slices), and the projection function (e.g., Minimum, Maximum, Mean, Median).
This function may be useful for viewing MRA datasets.
- Since the Disp control panel is getting so big, some people have complained it
overflows the screen height. You can force it to be enclosed with scrollbars by setting
the environment variable AFNI_DISP_SCROLLBARS to YES.
- This version is labeled "2.40d" and is dated "01 Feb 2002".
I have ported most of AFNI to run under the Cygwin Unix
emulator on Microsoft Windows. The link that describes
what you must do to install/run AFNI on Windows
is at the top of this page. Please let me know (via the Message Board)
what your experiences are with this port, and if you wish it to be
maintained in the future.
The distribution tar+gzip archives for AFNI have been renamed
to afni_src.tgz (unpacks into afni_src/)
and afni_doc.tgz (unpacks into afni_doc/).
This is partly because the year 1998 is fairly long gone by now (and
thus the old afni98.tgz and AFNI98/ are anachronistic),
and partly because I've been reorganizing the way I keep files stored
here (e.g., I now use CVS instead of RCS).
The files in afni_src/ are somewhat rearranged from those in
the older AFNI98/ directory.
- The GE I.* image file reader in to3d now properly reads and sets the
x-axis and y-axis offsets, which are useful when using non-centered 2D images
acquired by surface coils.
- The other image input methods (ANALYZE *.hdr and Siemens *.ima) do
not set x- and y-offsets in to3d. I don't think that
information is present in the ANALYZE format, and don't know where
it is in the Siemens format. (If someone would enlighten me and give
me some sample off-center images, that would be useful.)
- Also in to3d, the default anatomical type for a 3D+time dataset
has been changed from SPGR to Echo Planar. This has no impact on
anything, since the anatomical type of a dataset is not used anywhere,
but makes more sense to me (and I am the arbiter of sense).
- If you set the environment variable AFNI_GLOBAL_SESSION to the
name of a directory with datasets, then copies of these datasets will appear
in each AFNI Switch Session chooser. Since the
datasets in each session are presumed to be aligned in space, the only useful
function that I can think of for this capability is to put some common
Talairach (+tlrc) datasets in this global directory. You could then use such
a dataset as a universal anatomical underlay, for example.
[Suggested by Sally Durgerian of MCW.]
It is possible (even easy) to create huge functional bucket datasets using
3dDeconvolve (for example). It can get to the point where the option
menu for sub-brick selection in Define Function is too wide to fit
on the screen. I've added two ways to get around this problem:
- If you set environment variable AFNI_MENU_COLSIZE to a
number like 40, then the maximum number of entries in
a option menu column will be raised from the default 20. This will make the
menus be taller and narrower.
- If you make the menus too tall, then they
won't fit on the screen vertically, of course. On my 1280x1024 screen,
40 is a good number. YMMV.
- You can also now right-click (Button 3) on the label to the left of
a option menu. This action will popup a scrollable chooser that lets you pick an
item from the menu (then press Apply or Set to have
it take effect).
-
The maximum number of entries visible at once in a scrollable chooser is set
by environment variable AFNI_chooser_listmax (if defined)
or by AFNI_MENU_COLSIZE.
- The scrollable chooser menu-substitute is also a handy way to switch
between sub-bricks progressively.
- Note that only one scrollable string chooser can be open at once in
AFNI. Thus, if you press something like Switch Session
that pops up a chooser window, then the menu-substitute chooser will
disappear. This "feature" is a deliberate design decision, made to simplify
the program's structure.
- These changes are documented (a little) in
README.environment (as is customary).
The reason these shenanigans are needed is that Motif 1.2 does not provide a
"combobox" scrollable menu interface widget. Motif 2.1 does, but AFNI is
intended to run on some legacy systems that do not have the later version of Motif.
Motif 1.2 does have "tear-off" menus, but in my experience, they tend to crash
the program, which is not apparently desirable.
[13 Dec 2001]:
If you downloaded the change above before this date, you should re-upgrade.
I discovered that if you press Button 2 in an option menu that
is itself in a popup menu, then the application and X11 server hang up
forever, and you have to go to another terminal to kill AFNI.
This problem is independent of these changes (I just happened to
discover it now), and appears to be a bug in the Motif graphics library
which is used to build the AFNI user interface.
I have patched the ButtonPress handler for option menus in AFNI
to avoid this problem. (Technical detail: if Button 2 is detected
in the event handler for the option menu, then XUngrabPointer is called.
This action releases the popup menu, and everything seems to goes back to normal.)
[14 Dec 2001]:
Another Motif mouse-click bug: hold down the Ctrl key, and press Button 1
in a blank area of the AFNI controller. This is a very fast way to
exit the program. (I found out about this bug on the comp.windows.x.motif
newsgroup. It is only present on some systems.)
- Late last week, I posted a release of AFNI that would
crash in the rendering plugin and maybe a couple other places.
I hope that this is fixed now.
- 3dAxialize has been modified to allow flipping of the
input dataset to an arbitrary cardinal orientation (there are 48 of them).
This can be useful if you need to present your data to some
other program that needs it in LPI order, say
(x=Left-to-Right, y=Posterior-to-Anterior, z=Inferior-to-Superior).
- 3dIntracranial now has a -nosmooth option, to
turn off the smoothing of the mask surface. This has some application,
but I can't recall what at this moment.
- 3dTstat can now compute the standard deviation without
linear detrending of the voxel time series.
- The new environment variable AFNI_START_SMALL lets
you tell the program to set the initial dataset to be the
smallest one in the first session directory. If you use the
layout feature to open an image and/or graph window when AFNI
starts, then it must perforce load the initial dataset from disk.
The "normal" thing is for the initial dataset to be the first
in collation (alphabetical) order. If that dataset happens to
be huge and compressed, then it might take AFNI quite a while to open.
This setting may help you get around this problem.
- Programs ge_header, mayo_analyze, and siemens_vision
are now compiled in the binary packages and by
"make totality". They print out header information
from GE I.* files, ANALYZE *.hdr files, and Siemens *.ima files, respectively.
- I changed the cursor shape and color slightly in many places in AFNI.
The first person who figures out why (without any hints from Ziad or Rick!)
gets a free cup of coffee from me - but you have to be in Bethesda to collect.
With this release, to3d can now read GE Medical System
I.* image files (with the "IMGF" magic number at the start of the file).
The program
can extract the voxel grid sizes and orientations from the image header
(the first 7900 bytes or so of each I.* file),
as well as the image TR and the spatial offset. If you wish to use
the image header's TR, you can set TR to 0 in the
"-time:zt" or "-time:tz" command line option.
If you do supply your own TR, the program will print out
the image file's TR for comparison.
-
The slice thickness of an individual slice will be used as the
"z voxel size". If there are gaps between the slices, then
you will have to adjust this size to match the slice thickness plus gap,
in order to allow the slices to be spatially distributed correctly.
(Or you can use the ancient abut program to intercalate slices
of zeros.)
-
If you are creating a 3D+time dataset and are presenting the slices
in "-time:tz" order, then the z orientation may
not be calculated correctly, since it is computed from the slice
positions of the first 2 input images. (In particular, this orientation
may end up backwards.)
-
Since the combination of the GE header information plus
(and the "-time:*" information, if present) is
enough to specify a dataset, if you also use the "-prefix"
option on the to3d command line, the dataset will be saved
without the GUI opening. If you want to have the GUI open up
(if only to check that the header information was correct), then
you must either omit the "-prefix" option or
you must add the "-nosave" option.
-
The new software will automatically determine if the GE file needs to
be byte-swapped, as it does with the Siemens and ANALYZE formats.
This means that you do not want to put "-2swap" on
the to3d command line if you are reading one of these file formats.
This new feature may affect scripts that you are using to assemble
AFNI datasets automatically; for example, GE images need to be
byte-swapped on Intel/Linux platforms, so if you are using to3d on
such a system, you might already have "-2swap". This will
have to be removed from your script.
-
These changes have only been verified with some images from the 3 Tesla
GE scanner here at the NIH. Problems should be reported to me, along
with some sample images. Thanks go to David Clunie for his
authorship of the
Medical Image Format FAQ.
-
Image files reconstructed from GE P-files (k-space data) by home-brew software
will not have the proper header, and so will not be recognized as a GE I.* file,
even if it has the proper type of name. In that case, you will have to continue
using the older methods for getting arbitrary image files into to3d
(FAQ #12).
-
Only 16 bit uncompressed GE image files can be read with this software.
(These are the only types I have ever seen; the other types seem mostly
to be used with CT data.)
-
The new program ge_header will print out some of the information
from a GE image file header. This program is not compiled in the default
build for the AFNI package; you have to compile it yourself with
"make ge_header". Some sample output:
% ge_header I.67[89]
-----------------------------------
File I.678
nx=64 ny=64 skip=7904 swap=YES compressed=NO bits-per-pixel=16
dx=3.75 dy=3.75 dz=6 slice offset=46 orient=APSI TR=1.65(s) TE=30(ms)
-----------------------------------
File I.679
nx=64 ny=64 skip=7904 swap=YES compressed=NO bits-per-pixel=16
dx=3.75 dy=3.75 dz=6 slice offset=54.5 orient=APSI TR=1.65(s) TE=30(ms)
where the parameters reported mean
nx,ny = image matrix size
skip = byte offset of image data
swap = YES or NO (data needs to be byte-swapped?)
dx,dy,dz = voxel sizes in mm
slice offset = slice position in mm
orient = orientation of this 2D slice
AP -> Anterior to Posterior (in this example, x-axis)
SI -> Superior to Inferior (in this example, y-axis)
LR -> Left to Right, etc
TR = repetition time in seconds
TE = echo time in milliseconds
Two changes made by request from message board denizens:
- Program 3dclust now has an option "-prefix" which
will write out a cluster-edited version of the input dataset. That is, each sub-brick
in the output dataset is a copy of the corresponding input, but with all voxels not
in a cluster set to zero. This can be used to cluster-edit a bucket dataset from
3dDeconvolve, for example. In this application, you would want to use the
"-1thresh", "-1tindex", and "-1dindex"
options.
- New program 3dAFNItoANALYZE will write out the sub-bricks of an AFNI dataset
into a collection of ANALYZE .hdr/.img file pairs (one 3D pair for each sub-brick).
Coupled with the ability of to3d to read ANALYZE files, this conversion ability
should make it relatively
painless to interoperate with SPM (to choose a random software package).
As usual, the only real documentation for new features and codes is the output
of the " -help" option of the relevant programs.
It turns out that many programs
(e.g., SPM)
store a scale factor in the
"funused1" ANALYZE 7.5 .hdr location. The AFNI image input
functions have been modified to allow for this scale factor, if
it is positive and not equal to 1.0. This change makes it easier to import SPM-derived
images into to3d and thence into AFNI:
- If you do not want to use this scale factor, then you must set the Unix environment
variable AFNI_ANALYZE_SCALE to NO.
- Values are scaled and then stored back in-place; for example,
shorts are stored back into the range -32767..32767, so if the scale
factor causes the shorts to be scaled into the range -0.5..0.5, then
the result will be that the data is all set to zero.
- If you set the environment variable AFNI_ANALYZE_FLOATIZE
to YES, then ANALYZE .img files will be converted
to floats on input to to3d (regardless of the scaling factor).
- The ANALYZE input function also attempts to detect if the
.hdr file was written by SPM. (It does this by looking at the
"originator" field.) If it thinks that the file came from SPM,
it guesses that the volumes are oriented
in order x=L-R, y=P-A, z=I-S,
and transmits that information to to3d.
Otherwise, no orientation information is passed to to3d, and
you must supply the dataset orientation manually (as usual).
- If you want to see the contents of an ANALYZE .hdr file, then the
AFNI program mayo_analyze will print it out for you.
(However, this program is not compiled in the pre-packaged binaries;
you have to compile it yourself via "make mayo_analyze".)
You can now search the documents at this Web site, using the
Search link in the "Main AFNI Links" section
(e.g., at the top of this page).
- Last time [below] I said there was a problem in Linux malloc()
that would cause to3d to crash during outlier checking.
Well, that was wrong - it was my fault. The bug has been fixed;
the source and binary distributions are available from the
usual suspects.
- In the past, 3dmerge didn't complain if you tried to
average together datasets that didn't have .BRIK files - it just
silently ignored those datasets. Now it prints an error message
and exits.
- Please note that only the interactive AFNI
program can deal with
warp-on-demand datasets.
-
AFNI programs can now read
MINC format
image files directly as datasets -- you don't have to run through
to3d to convert them to AFNI format. When AFNI
starts, it now searches for filenames ending in ".mnc" as well as
".HEAD". You can also specify a .mnc file on a 3dSomething
command line as an input dataset.
- The goals of this effort were to
- Mollify (or molluskify?) Sean Marrett.
- Make AFNI easier to use alongside the MNI
and MGH toolsets.
- AFNI programs do not write MINC files.
- New program 3dMINCtoAFNI can be used to convert
a MINC file to an AFNI dataset.
- If present, the global MINC attribute ":history" is
preserved into the dataset's History Note.
- You can disable the reading of MINC datasets by
setting environment variable AFNI_MINC_DATASETS to NO.
- You can force the conversion of MINC datasets to
floats on input by setting environment variable
AFNI_MINC_FLOATIZE to YES.
- No doubt there are MINC files that AFNI won't
be able to handle. In particular, the image data
must be either 3 or 4 dimensions, and the 3 primary
dimensions must be named
"xspace", "yspace", and "zspace"
(in any order - AFNI determines the orientation
of the dataset from the MINC dimension order).
- If the image data has 4 dimensions, and there are 10
or more points along that axis, then the dataset is
taken to be 3D+time EPI; otherwise, it is treated
as an anat bucket (MINC datasets are not converted
into func datasets at this time).
- The TR stored in the header of the MINC files that
I've seen is not reliable.
- Slice-dependent time offsets are not set up for
MINC 3D+time datasets.
- To see how AFNI thinks of a particular .mnc file,
try running "3dinfo filename.mnc".
- You cannot use sub-brick selectors with .mnc files in command
line AFNI programs. You'll have to use 3dMINCtoAFNI
if you want this capability.
-
AFNI has a new command line option "-q" (for "quiet") that will
suppress most startup messages that are printed to the terminal.
-
You can download datasets (.HEAD or .mnc files) from Web/FTP servers directly
from within AFNI, using the Datamode->Read Web button;
.BRIK.gz and .mnc.gz files will be automatically un-gzip-ed when they are
read in this way. (Staging of temporary files for FTP and/or decompression
is done in the directory
defined by environment variable TMPDIR, or in /tmp if TMPDIR is undefined.)
-
One user (Jerzy Bodurka of NIMH) found a problem with to3d's
automatic outlier count on Linux. This occurs only when he has 8 slices
of 64x64 short images with 512 time points. The program crashes in malloc()
about halfway through the outlier check. This seems to be a bug in the
Linux C library's malloc(); I can't make this error occur with
other image configurations or on other systems, so there is no real way to fix the problem.
If this crash occurs with your data, turn off
the outlier check with the command line option "-skip_outliers"
or by setting the environment variable AFNI_TO3D_OUTLIERS to NO.
By mistake, the earliest release of this date had some debugging
messages left in a dataset timeseries extraction function. This
would result various junk strings starting with "ab" to be printed
to the screen (depending on which code was being run).
Sorry about that - the stuff at the Web/FTP site has now been
fixed.
- Mac OS X 10.0 binaries are now available at the usual download places,
under the name "macosx_10.0".
- Please also read http://afni.nimh.nih.gov/afni/afni_darwin.shtml
for details about other software you must install to get AFNI to run
on OS X.
- Please note that I don't have a machine with OS X 10.1, so
I don't know if (or how well) AFNI runs on that system.
- The old program FD2 has been modified to run under X11 TrueColor
visuals (at long last). This work was done by Andrzej Jesmanowicz of the
Medical College of Wisconsin.
- Plugin menu alphabetization is now the default. If you want the older
menu order back (which was loosely based on functionality),
you have to set the environment variable
AFNI_PLUGINS_ALPHABETIZE to NO
(e.g., in your .cshrc or .afnirc file;
cf. README.environment).
- Some changes were made to the interactive AFNI program to make
it less likely to crash when it runs out of memory. (Of course, these
changes may induce new ways of crashing, or may be totally ineffective ....)
- Doug Ward has updated 3dDeconvolve as described
here.
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Drawing Upon New Resources
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- 25 Sep 2001
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- The Draw Dataset plugin has been modified to have 3
new convenient features:
- You can now create a copy of a dataset on input, and
draw on that, rather than drawing on a pre-existing dataset.
This basically incorporates the functionality of the
Copy Dataset plugin.
- The new drawing mode Filled Curve lets you draw
a closed curve and have it filled with the current drawing
value.
- The new SaveAs button lets you save the current
drawing to a new dataset, which will become the current
dataset for further drawing.
I also fixed a bug in the Undo feature: if you used
Quit to cancel editing, then restarted the plugin,
Undo would no longer work. It does now (I think).
- New program 3dcopy does what it sounds like: it copies
datasets (.HEAD and .BRIK files, and changing
the ID code). In this regard, it can be considered a sibling of
3drename (as Unix utility cp is to mv).
- The 2D image viewer Labels can now be controlled to a limited extent
by setting some environment variables, either
from the Edit Environment
controls (on the Datamode->Misc menu), or in your
.afnirc file. Look for the AFNI_IMAGE_LABEL_*
variable names in Edit Environment (near the bottom).
- The HP-UX system on which I compile the hpux_10.20 binaries
is down (maybe permanently), so the precompiled binary package for
this system is not available.
[ 02 Oct 2001]:
The AFNI
educational materials page
now contains a description of how to use the drawing plugin to
create ROIs (item #11).
The HP-UX binaries are back.
- I have fixed a bug in the "Sav1.jpg" (and similar functions) in
the image viewers. When an image had no colored pixels, it
would be saved incorrectly, and garbage would result.
- There is a new and experimental feature in the image viewers
for 2D slices. You can now have each image get a text overlay
indicating its slice position (e.g., 20I, 40.7R). This is
controlled from the "Label" item on the
hidden Button-3 popup on the image intensity
bar (just to the right of the image).
- Caveat: these overlays are not saved
with any of the "Save" functions. Currently, the only way
to save these to an image file is to do a window snapshot
(e.g., with
program xv).
- Although you can enable Labels in other image viewing windows
(e.g., the volume renderer)
they won't display anything, since the driving modules for these
don't supply label strings to the images when requested.
- I have ported the AFNI package to Mac OS X (Darwin).
Information on how to compile on this platform can be
found here. No doubt there
will be problems, but give it a try.
- Experimental new program 3dAnatNudge will try to align
a "scalped" (3dIntracranial) high-resolution T1-weighted
volume (SPGR, MP-RAGE) to a lower resolution EPI volume.
This may or may not be useful; read 3dAnatNudge -help
carefully before using.
- The volume rendering plugin "Color Opacity" menu has
a new item "ST+Dcue". This is the same as the "ShowThru"
option, with depth cueing added: colored voxels in the back half of
the volume will be faded out, giving the impression that they are farther
away. Combined with a rotating brain animation, this makes it a little
easier to visualize the spatial layout of a complex set of blobs.
Fixed a bug in 3dTcorrelate that resulted in incorrect
Pearson correlations being computed on some types of computer systems
(primitive non-Linux systems, that is).
- I have fixed a bug in the outlier message handling in program
to3d. In batch mode, the program would try to popup a
message window anyway - this is illegal, and would cause a crash.
In the words of Maxwell Smart, "Sorry about that, Chief."
One user here has found to3d crashing with an "out of memory"
message during the outlier count. I think this is due
to the outdated Linux system he is using, since I can't reproduce
it on a more up-to-date system, but am not sure. If anyone else sees
this problem, let me know the details (exact error messages, and
system you are using -- from output of uname -a).
I have also added an option -save_outliers fname, which
will cause to3d to save the outlier count to a 1D file (named
fname), which can later be plotted using a command like
1dplot -one fname -- this is intended to let
you look at the outlier information after a non-GUI run, without
having to run 3dToutcount on the 3D+time dataset.
- New program 3dTcorrelate lets you compute the correlation
coefficient of 2 3D+time datasets, voxel-by-voxel. (Why you would
want to do this is good question.)
I have modified the "Draw Dataset" plugin to allow you to load regions
from the Talairach Atlas database into the drawing. For this feature
to be active, you must either be drawing in a +tlrc dataset, or in
a +orig dataset when the anatomical underlay dataset has a transformation
from +orig to +tlrc already defined. Please use this feature with caution;
blind adoption of the Talairach Atlas database as defining ROIs for
analysis is a very bad idea. You should use it instead as
a starting point for manually adapting the ROIs to each subject.
I have fixed a couple of problems with the Talairach Atlas database
that is used in the "See Atlas" and "Where Am I?"
features:
- Several errors in the database have been corrected:
those involving Brodmann areas 28, 29, 32, 37, and 42 (which I alluded
to in an earlier installment).
- The Nucleus Accumbens is now in the database, and its center of mass
in the "Talairach to" feature has been corrected. (I added
this myself manually by looking at the Atlas pages; it is a small
region, and may not be represented accurately herein.)
- To use these fixes, you need to not only re-download the AFNI
package binaries (or re-compile them from the new source), but also
re-download the dataset files
TTatlas+tlrc.HEAD and TTatlas+tlrc.BRIK.gz.
These files, as before, need to be stored in the same directory
with the AFNI plugins (replacing any existing copies of this
dataset). If you fetch binaries using wget, then the new
atlas dataset will be fetched at the same time. If you fetch binaries
or source in .tgz archive form, then you will need to fetch
the dataset manually. You can get the dataset files at these URLs:
Be sure to "Save Link As..." both files (.HEAD and .BRIK.gz);
loading them into your browser is not useful!
- The current systems for which I compile binaries are:
| Operating System |
Archive Name |
| Hewlett Packard HP-UX 10.20 | hpux_10.20.tgz |
| Linux Mandrake 7.2 (Intel CPU) | linux_mdk72.tgz |
| Linux Red Hat 6.0 (Intel CPU) | linux_rh60.tgz |
| SGI IRIX 6.5 (R10000 CPU) | sgi10k_6.5.tgz |
| SGI IRIX 6.5 (R4400 CPU) | sgi4k_6.5.tgz |
| Sun Solaris 2.6 | solaris26_gcc.tgz |
| Sun Solaris 8 | solaris28_gcc.tgz |
This list is subject to change at any point in the space-time
continuum (including the past).
- Many more programs now log their usage to the ${HOME}/.afni.log
file.
- When creating a 3D+time dataset, to3d now checks the
voxel time series for outliers, using the same method as
program 3dToutcount (described in 3dToutcount -help).
If any sub-brick has a "significant" number of outliers, then
this fact is reported. If to3d is being run with the
graphical user interface, then a graph of the outlier count vs.
sub-brick index is popped up. These default behaviours can be
turned off with use of the environment variable AFNI_TO3D_OUTLIERS;
see the output of to3d -help for details. A sample
display is shown in the image below:
In this particular example, the large number of outliers in the early
images is due to the initial
transient equilibration of longitudinal magnetization, the
spike at about sub-brick 33-34 is due to a sudden head movement,
and the general rise in outliers after #53 is due to my deliberate
replacement of slice #13 with slice #12 (mimicking an error in
the scanner's reconstruction software that sometimes occurs here;
which is why we prefer our own reconstruction software).
The horizontal red line near the bottom of the graph is the
threshold for reporting a sub-brick as having a "significant"
number of outliers. After the outlier counts are computed for
each sub-brick, their median and median absolute deviation (MAD)
are computed. The red line threshold is set at median+3.5*MAD.
- New programs 3dZcutup and 3dZcat let you cut datasets
up and reassemble them in the slice (z) direction. This could be
useful for analyzing very large time series: break them into 1 or
2 slice datasets, analyze them into functional buckets (say with
3dDeconvolve), then assemble the functional buckets back
into the full 3D dataset you want.
- AFNI and to3d can now work with and create single
slice datasets. I hope this works for you (i.e., doesn't crash).
- New programs 3dTqual and 3dToutcount produce "quality
indexes" of 3D+time datasets: they measure how "weird" each volume
is with respect to the median volume. Sub-bricks that are large
in "weirdness" should be examined visually to determine if there
is something wrong with them (e.g., large head motions).
- A number of AFNI programs now log their usage to a file
named .afni.log in the user's home directory. If you
wish to disable this feature, set the environment variable
AFNI_DONT_LOGFILE to Yes. The purpose of
this log file is to help you recall what you did in the past.
As time goes on, more programs will include this feature.
- The new "Save Anim MPG" toggle (on the image viewer Disp panel)
lets you save an image sequence to an MPEG-1 video file.
This uses the UC Berkely program mpeg_encode, which is not
made by the default AFNI "make totality"; however,
you can manually do "make mpeg_encode; mv mpeg_encode bindir/"
to compile your own copy. (Copies are in the wget
binary directories for all the systems I currently support.)
- You can now impose a global baseline for graphs, using the new
pullright "Opt->Baseline" menu in an AFNI dataset graphing window.
- You can also set the Double Plot timeseries to be treated as a
value to be added and subtracted to the data timeseries graph, rather
than as an overlay. This is controlled from the new "Opt->Double Plot"
pullright submenu in an AFNI graphing window. I use this
for plotting the 3dDeconvolve -iresp output with
-sresp generated error bands around it.
|
Talairach Atlas Stuff Fixes
|
|
- 01 Aug 2001
|
- I have fixed an error with the Talairach Daemon rendering that
prevented some people from seeing the Atlas regions overlays in
2D image or 3D rendering windows. Also fixed a bug in the
"Where Am I?" window that could cause AFNI to crash.
Sorry about any trouble, and hope these features work for you now.
- Added a new option to waver, so that you can specify
the hemodynamic response function with an arbitrary 3dcalc-like
command line expression.
- Added a popup hint to the intensity bar in a 2D image window, so
that it shows the voxel values that are mapped to the intensity
bar's gray/color scale.
|
More Talairach Atlas Stuff
|
|
- 27 Jul 2001
|
AFNI now has more features that use the Talairach
Daemon database from San Antonio. These are addition items
on the Button 3 popup menu in the 2D slice image viewer window:
- The "Where am I?" feature will show you
what anatomical structures in the database are within 7 mm
of the current focus (crosshairs) position. This feature
only works if you are currently in +tlrc coordinates, or
in +orig coordinates in a dataset that has a transformation
to +tlrc already defined.
- The "Atlas Colors" feature lets you overlay
the regions from the database onto 2D image viewers and
the volume rendering plugin. This feature requires that
you be viewing datasets in +tlrc coordinates at 1 mm resolution
(the default).
-
Note well
that these features are enabled only from the
2D slice image viewer windows; they cannot be enabled from
the volume rendering image viewer window.
To use these new features, you must have the dataset containing
the database information in your executable path. This dataset
is named TTatlas+tlrc. The simplest thing for you to
do is put it in the same place you store the AFNI binaries
and plugins. If you retrieve AFNI updates using the
wget program, then this dataset is already stored in the
binary directories, so you will get it next time you update.
If you compile AFNI from scratch, or you copy binary
distributions in .tgz archives, then you have to fetch
this dataset manually from
this directory.
You will need to get both the .HEAD and .BRIK.gz
files, and put them into the correct binaries directory (don't
put them into a normal dataset directory where you keep your
data -- AFNI looks for these files in the path).
Warning: You must not rely completely on the Atlas
database for identification of anatomical regions. Each brain
is different. Also, there is no guarantee that the database
is a perfect representation of the Talairach-Tournoux Atlas.
- In particular, I believe there are some problems with
a few of the Brodmann Areas (28, 29, 32, 37, and 42).
- The Nucleus Accumbens appears to be missing from this
database (but hey, it can't be
that
important, right?).
The 2D image viewers "Save" function has been altered
slightly:
- The "Save One" option is now in a separate control
box on the "Disp" control panel. This lets you
save an image montage (which can only be done with
"Save One" turned on) in any of the
newly supported image formats (e.g., .tif).
-
These formats require the presence on your system
of the netpbm programs, which are not supplied
with the AFNI package.
- The new "Save Anim GIF" button lets you save a
sequence of images to an Animated GIF file (which you can
put on a Web page for the edification/mystification
of the masses).
-
This option
requires that you have netpbm installed in your
path, plus one of the programs gifsicle (preferred) or
whirlgif. These two programs are actually shipped
with the AFNI source code, but are not made by
default; you can make gifsicle by issuing the
command "make gifsicle" once you have
selected your AFNI Makefile; then you have to
mv the gifsicle binary to the AFNI
binaries directory. Or you can download
the entire source for the gifsicle package
from here,
if you want to get the latest version straight from the
horse's mouth.
If both "Save One" and "Save Anim GIF" are
turned on, then "Save Anim GIF" takes precedence.
"Save Anim GIF" can also be selected from the
"Save" button's Button 3 popup menu (but
"Save One" can only be selected from the
"Disp" control panel).
The rendering plugin now selects the upper threshold for
underlay bricks more cleverly (at the 99.5% point on the
cumulative histogram, rather than always using the dataset
maximum). This makes the default rendering
more reasonable for T1-weighted underlay images, since a
few sporadic ultra-bright voxels won't determine the
rendering brightness any more. If you are rendering a dataset
where you only want to see the ultra-bright voxels
(e.g., MRAs), then you will need to manually adjust the
upper threshold ("Top") for your purposes;
note that the dataset value range is given at the left of
the row with the "Top" control.
- An example of the combination of all the above changes can
be seen here
(contains a 1.5 Mbyte animation).
AFNI now incorporates some of the data from the
U Texas San Antonio Research Imaging Center
Talairach Daemon database. The first manifestation of this is
the new "Talairach to" choice on the image window
Button-3 popup menu (available only when viewing a dataset in
Talairach coordinates, or one that has a transformation to Talairach
coordinates defined with it). Choosing this pops up a list of brain structures.
Choose one, and the crosshair focus position will jump to the
centroid of that structure, as defined by the Talairach-Tournoux Atlas.
Thanks go to Jack Lancaster and
Peter Fox of the RIC at UTHSCSA
for providing me with the Talairach Daemon database and with
instructions on how to read it.
Any problems with this feature of
AFNI are of course not their responsibility in any way.
Users must be
aware of the limitations of the Talairach system -- inter-subject
variability is about 7 mm (root-mean-square), and possibly higher
in some cortical regions far from the commissures (e.g., occipital
lobe). Thus, it is not wise to depend solely on this feature for
anatomical navigation through the human brain. It will get you close,
but the final identification is up to your visuo-cognitive system.
- Doug Ward has made a number of changes to the 3dDeconvolve
package. These are too numerous and involved to list here, but are documented at
this page.
- The Save button on the image viewing windows now lets
you save to a variety of other image formats, if your
system has the netpbm package of image conversion filters
installed (and if they are in your path). Choosing the image
save format is done from the Disp control pane, or from
a Button-3 popup that is now "attached" to the Save button.
- New program strblast lets you replace identifying strings
buried in binary files. This is useful if you plan to distribute
raw image files from MRI scanners, which often have the subject's
name inside them somewhere.
- Program 3drotate can now take its rotation+shift parameters
from a file, rather than from the command line (per the request
of David Glahn of UCLA).
- Program waver has a new option -tstim, which lets
you input only the stimulus times. This is supposed to be an aid
to making reference .1D files for use with 3dDeconvolve,
3dfim+, or other analysis programs.
- A new button is on the image viewer windows: "Rec"
(just to the right of the "Done" button). This
menu button lets you record a sequence of images and save
them for display in a new image viewer window. As each
new image is displayed in the master image viewer, a copy
is saved to the recording window. Once you are satisfied
with the sequence of recorded images, you can save them to
disk. In this way, you can save animations of images as
you change some viewing parameter (e.g., correlation
threshold, or overlay color rotation). At present, the
only detailed documentation is displayed when you use
"BHelp" on the "Rec" button.
- A potentially fatal bug in 3dAttribute was fixed.
- to3d now prints an error message if it can't find
an image file specified on the command line.
- Doug Ward has added the new program 3dExtrema, which
finds local maxima (or minima) in a functional volume.
The documentation is in file
3dExtrema.ps
or
3dExtrema.pdf.
- Doug also added some features to program RSFgen
(for generating random stimulus patterns).
It is documented in file
3dDeconvolve.ps
or
3dDeconvolve.pdf.
Source and binaries for these changes are available now.
New binary packages are available at this time:
linux_mdk72 = Linux Mandrake 7.2
solari26_gcc = Solaris 2.6 (SunOS 5.6)
The following binary packages are no longer being updated, since
I do not have access to machines of this type:
hpux_10.20 = HP-UX 10.20
linux_rh52 = Linux RedHat 5.2
- New program 3dRowFillin lets you fill in skipped slices
when doing ROI drawing - this capability is also in the
Draw Dataset plugin. You can now draw on every
third slice (say) and then have the gaps filled in by the
program or plugin. (You'll probably have to clean up the
results afterwards.)
- The "-@" switch has been added to a lot of programs,
which lets you extend the command line. See
FAQ 32
for more details.
- A problem with the Linux malloc() library function was
discovered and worked around. This affects programs that
allocate large numbers of large blocks of memory.
- New program 3dToutcount tries to estimate the number
of "outliers" in 3D+time datasets. [This program is based
on a brief discussion with Bill Eddy of CMU and is subject
to change!]
- The Define Function control panel has a new
item: the "Rota" buttons, which let you rotate the colors
on the color pbar. This is great for making dynamic
images. (Now just have to get a way to save them.)
Also, added "hints" (AKA "tooltips") to the color pbar
to show the range of values in each color pane.
[Per the suggestion of Ziad Saad of NIMH.]
- Fixed another potentially fatal (SEGV) error in 3dvolreg
[pointed out by Tom Ross of MCW].
- Added -sum and -sqr options to 3dMean,
to provide a faster-than-3dcalc way to sum dataset
values (and sum the squares).
|
Excitement Beyond Measure
|
|
- 15 Apr 2001
|
The new AFNI Web/FTP server is up!
- A bug in the new 3dvolreg could cause the program to crash with
a Segmentation Fault or Bus Error. This has been fixed (I hope).
- The volume rendering plugin now lets you render the crosshairs
in the color overlay, which means you can let them "Show Thru"
the brain. For details, read the "Help" text for the "See Xhairs"
control.
- to3d can now read Siemens Vision .ima image files. I only had
one example of this format, so am not sure it will work for
all such files. Program siemens_vision will print out information
from the header of a .ima file.
A set of small-ish additions to the last week's update:
- 3dTsmooth now has a new set of options, allowing you to use
Blackman or Hamming windows for lowpass filtering of 3D+time datasets.
- New environment variable AFNI_AUTOGZIP allows you turn
on write compression ("gzip -1") only for datasets that will
compress about 80% or more (e.g., mask datasets).
- You can use the special filename "ALLZERO" when inputing
via the 3D: mechanism to to3d -- this will let
you create a dataset of all zeros with a specified geometry very
easily. (If you want to create a dataset of all zeros that is
a geometrical copy of an existing dataset, you could use
something like
3dcalc -a dset+orig -prefix zero -expr "0"
This is a brute force approach, but works.)
- AFNI now lets you overlay the color function on grayscale
slices in a translucent fashion. The opacity of
the overlay is controlled in each image/slice viewing window
by a new control at the right edge of the window (just below
the "i" image fraction control). The default
is still opaque overlays (indicated by "9" on the
control), but smaller opacities will let some of the grayscale
anatomical underlay show through -- a setting of 4-6 seems
to produce nice combinations.
(This control is only available if you are using an X11 TrueColor visual.
Still using PseudoColor? Too bad.)
- In most programs, the -prefix option now lets you
redirect the output into another directory, as in
"-prefix ../fred" to put the new dataset into
the parent directory of the current location.
- 3dTstat now has -min and -max options.
|
|
- 28 Feb 2001 - AFNI 2.29a
|
Many new things, small and large, since the previous installment in our continuing story.
Many changes to 3dvolreg and 3drotate to make registering
data from the same subject on different days better and simpler.
Please read file README.registration carefully for important
details on how to combine these programs for this purpose.
New options include:
- -rotparent for specifying that rotation parameters
are to be copied from the header of a previously registered dataset
(usually an SPGR from the same day, that was registered to a
master SPGR)
- -gridparent for specifying that the output dataset should
be adjusted to fit the grid location of another dataset (usually an EPI
from the master session)
- -tshift for doing the equivalent of 3dTshift
prior to registration (mainly a convenience)
- -zpad for zeropadding the volumes on all 6 faces before rotation
and then stripping these buffer slices off after resampling to the
new grid; the intention
is to reduce edge-effect artifacts, especially in Fourier interpolation
Please note that these registration methods are works in progress, and may not
always succeed. It is important to visually examine the results to make sure
they are reasonable. [Thanks go to Ziad Saad and Sally Durgerian for testing
these additions and providing feedback.]
New program 3dZregrid will resample (interpolate) a dataset to a
new slice thickness in the z-direction. This is intended to make it
possible to register anatomical datasets between sessions when you
forgot to specify the same slice thickness (d'oh).
New program 3dMean makes it easy to take the voxel-wise
mean of a bunch of datasets (3D or 3D+time). This is faster
and simpler than using 3dcalc for this purpose. The principal
application seems to be averaging a collection of 3D+time datasets
prior to analysis.
New program 3dOverlap lets you compute the number of nonzero
voxels in common in a collection of dataset bricks. The output
is a single number. For example, if the input is a single brick, the
output is the number of nonzero voxels in that brick.
(You can optionally save the count of overlaps from each voxel into
a new 3D dataset. This could be useful as a mask in later applications.)
New program 3dAttribute will print out values of attributes
from dataset header files. The main application of this is for
use in scripts, and is intended to help people stop digging
through the .HEAD files. [This means you, Ziad.]
New program 3dClipLevel is a little toy that tries
to estimate the value at which you should clip an anatomical dataset
to exclude the background (air) region. This is intended to
work on EPI, SPGR, and similar images. You probably want to
check the value with some experiments (e.g., with the Histogram
plugin) in order to make sure they are reasonable for your datasets.
Matthew Belmonte's (belmonte@mit.edu)
thresholding and permutation test plugins
are now incorporated into this release. See file
README.permtest for details, and for the paper to
cite if you use these items.
Program to3d can now read Mayo ANALYZE 7.5 .hdr/.img files.
You specify the .hdr file on the command line.
[Why support this format? Because some people at NIH use it.]
Program to3d also has a new -zpad option, but it is
designed to add slices of zeros in the z-direction only.
The intention is to make it easier to pad a dataset at creation time,
which is useful when doing inter-session registration. This
operation can also be carried out later with the new -z
option to program 3dZeropad.
Program 3dclust now has the -dxyz=1 option, making it easier
to form clusters based on voxel criteria rather than geometrical ones.
[per the request of Petr Hlustik]
Program 3drefit can now zero out the slice-dependent time-offsets
using the new option -notoff. This is useful if you have
processed a 3D+time dataset in some way that destroys the integrity
of these shifts (e.g., done some interslice calculations, such as
blurring the dataset spatially).
Program 3dmerge now allows input datasets to use the
sub-brick selectors [..]. [per the request of MS Beauchamp]
Doug Ward has added some options to RSFgen for generating
random stimuli patterns using Markov chains.
Graphs of anat bucket datasets in AFNI now interact correctly
with the anat bucket chooser in Define Function.
[per the request of ZS Saad]
AFNI image viewing windows now have a minimum size. This
helps avoid problems with small datasets that produce tiny windows,
which are hard to manipulate. This size is controlled by the
environment variable AFNI_IMAGE_MINFRAC -- see file
README.environment for details. It can also be altered
interactively
from the Datamode->Misc->Edit Environment control.
You can now interactively add hosts to the AFNI "trusted" list, which
is used for accepting connections from realtime image sources
and from plugouts. This is done from the
Datamode->Misc->Edit Environment control (AFNI_TRUSTHOST item).
[Someday this may even be useful.]
You can now change the current working directory (CWD) during
an AFNI run. This is done from the
Datamode->Misc->Edit Environment control (AFNI_CWD item).
By default, the CWD is the directory in which you start AFNI.
If you want to write files (e.g., Save:One), they
go into the CWD. [per the request of ZS Saad]
The command line sub-brick selection apparatus [..] has been extended
to also allow
you to edit the dataset during input; that is, you can set all
voxels outside a certain range to be zero. For example:
'fred+orig[5]<100..200>'
will read in the #5 sub-brick of the dataset, and set all
values outside the range 100..200 (inclusive) to zero.
You can use <..> by itself, or with [..].
For more information on these matters,
read the output of afni -help.
The mcw_malloc() functions have been speeded up considerably.
This makes AFNI start up much faster when there are
many input files/directories. [Does this make you happy, Mike?]
Several scripts by Ziad Saad have been added to the distribution.
These files are useful for automating certain repetitive functions
in the AFNI package. Their names all start with the
character "@", and they all have -help options.
- Don't ask how I make up the version numbers -- I don't know
where they come from.
A few small changes to the AFNI package:
- Doug Ward has upgraded 3dDeconvolve to allow for stimulus times that
fall in-between TR times.
- A problem with the layout code has been fixed. If you use layouts and let
AFNI run for hours, you need to upgrade. Otherwise, you will find that
AFNI starts doing bizarre things. (This problem was discovered by Z Saad
of NIMH.)
My new e-mail address is rwcox@nih.gov .
The final release of AFNI from MCW takes place today.
The source code and binaries are now released under the GNU Public
License (GPL).
The documentation is released under the
Open Content License.
This version of AFNI is still copyrighted by
the Medical College of Wisconsin, but may be redistributed freely
under the terms of the licenses.
The AFNI package will continue to be extended and distributed
from the NIH, once I am established there. There will be a hiatus
until I can get a new server set up there.
The most visible change when you run AFNI itself is a
new logo. Other recent changes include
- You can now have the buttons on the Plugins menu be sorted
alphabetically, by setting the environment variable
AFNI_PLUGINS_ALPHABETIZE to YES.
- The Dataset Copy plugin now has the ability to
change the datum type when making a zero-filled copy of
a dataset. (This change courtesy of Vinai Roopchansingh of MCW).
- Program 3dNotes now has an option to replace the History
Note - this can be useful if you have some compromising
information in there.
- The -twopass option of 3dvolreg now is more
robust in finding displacements due to large-ish head motions
between scanning sessions.
- Fixed a bug in 3dTcat with the -rlt+ option.
The proper action of this option is to preserve the mean of
each input voxel time series. Due to an indexing error, the
mean of each time series would be slightly altered.
- Added option -points to program 3drotate.
This lets you compute the transformed (rotated+shifted) points
corresponding to a set of (x,y,z) input triples (e.g., cluster
centers).
- You can now make the plugin menu buttons be alphabetized, by doing
setenv AFNI_PLUGINS_ALPHABETIZE YES
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Once more into the breach
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- 03 Oct 2000
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- The ROI Average plugin now has a To Disk?
option to allow writing of a time series to disk directly.
- The Nudge Dataset plugin now lets you print out the
equivalent command line for 3drotate. Also, the help
message now warns of the problem that can occur when nudging
a plugin so that values are shifted outside of the 3D volume
over which the dataset is defined. (To avoid this problem, the
dataset should be 3dZeropad-ed before nudging.)
- The new -twopass option to 3dvolreg is designed
for registering high resolution volumes gathered on the same
subject in different scan sessions. It can find rotations up
to 10-15 degrees, unlike the standard algorithm.
- The new -rotcom option to 3dvolreg will print
out the equivalent 3drotate command options. You can
use this in conjunction with -twopass to register
anatomical datasets between sessions, and then apply the same
rotations/shifts to the functional datasets. This is intended
to make it easier to compare data from the same subject between
scanning sessions. (You will probably need to use the new
-duporigin option to 3drefit after these
operations, so that the adjusted datasets are defined over
the same 3D volume in (x,y,z) coordinates.)
- The AFNI Datamode->Lock menu now has the new
IJK lock toggle, which lets you lock together
controllers based on the voxel index (i,j,k) rather than the
voxel spatial coordinate (x,y,z).
- New option -dxyz=1 to 3dmerge lets you have
the clustering and filtering options behave as if the voxel
grid spacing were set to 1 mm, rather than the values in the
dataset header. This is useful if you want to define these
operations on a voxel-wise basis rather than a coordinate-wise
basis.
- AFNI Graph buttons now work for datasets
with no time-axis (but they still must have .BRIK files).
When there is only 1 sub-brick, the graphs are replaced with
a number in each sub-graph box showing the voxel value.
- You can now setup the AFNI window layout that is opened
at startup. This is done by giving a description in a "layout"
file. See README.environment
and the new Datamode->Misc->Save Layout button
for more details.
- AFNI now support the Xinerama extension to XFree86. This
is used to "glue" multiple video cards/monitors on one system
into a super-sized single logical display. (We now have a
Linux box with 4 18" 1280x1024 LCD panels at our scanner.
If you are interested in the details of getting AFNI to work
with such a beast, please contact me.)
- New program 3dUndump lets you create a dataset from an
ASCII list of voxel coordinates and values. This is sort of an
inverse to program 3dmaskdump.
- The binary distributions no longer support Red Hat Linux 5.x.
If you are using a Pentium II or above with Red Hat Linux 6.x
(or any glibc-based system, I think, including Mandrake 7.x),
then you might try the linux_rh61_pgcc distribution. This
is compiled with the Pentium GCC compiler, which produces
floating point code that is 10-15% faster than the "vanilla" gcc.
- Additional filtering options for 3dmerge allow you to
exclude some voxels from the filtering calculations (using a mask)
and to define your own linear filter weights.
- Edit Environment now allows you to set the
AFNI_ENFORCE_ASPECT flag (to overcome a problem with KDE).
- You can now specify your own image for display in the AFNI
splash window. See file README.environment for information.
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Do You Like This New Header?
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- 18 July 2000
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A few small additions/changes:
- New program 3dTagalign, in conjunction with the
Edit Tagset plugin, lets you align datasets
based on manually placed "tags".
- The order of display of sub-graphs in the coronal and axial
graphing windows has been altered when the user has
set the environment variable AFNI_LEFT_IS_LEFT.
This is to make the graph layout correspond to the pixel
order in the corresponding image windows. Before this release,
when AFNI_LEFT_IS_LEFT was set, the images were in
the coronal and axial windows were flipped but the graphs
were not.
- New program 3dZeropad lets you add planes of zeros
to the edges of a dataset. The primary motivation for this
is to let you pad older "small" Talairach box datasets to
the size of newer "large" Talairach box datasets (the
date of change was March 1996).
- Added the new 2D transformation function 2D Chain.
This function lets you chain together several 2D filtering
operations. It is controlled from the Datamode->Misc menu.
Ugh - 22 June 2000
- Doug Ward added a -mask option to program AlphaSim.
- New environment variable AFNI_BYTEORDER_INPUT lets you
specify the byte-ordering assumed for datasets that do not have
byte-order specified in their header files (pre May 1998).
This can be useful if you are transporting a lot of datasets
from Sun/Solaris (say) to Linux/Intel (say).
- The new Edit Environment item on the
Datamode->Misc menu lets you alter some AFNI_
environment variables interactively - which means you don't
have to exit and restart AFNI to change
AFNI_RENDER_SHOWTHRU_FAC, for example.
Yet More Increments - 16 June 2000
- The popup menu under the "Inten" label atop the color
pbar in an AFNI controller menu has had 3 menu
items added.
- "Save to PPM" will save a color representation of the
current pbar to a PPM formatted image file.
- "Tran 0D" and "Tran 2D" let you apply transformation
functions to the functional image slice prior to
colorization. You may need to change the "Range"
used for the pbar if you use a function such as "Log10".
In addition, the checked display used for the "none" color
has been fixed to work properly with TrueColor X11 visuals.
- 3dNLfim can now compute the R2
"coefficient of multiple determination" - a measure of
goodness of fit of the nonlinear model analogous to
the square of the correlation coefficient. This value
can be used in the experimental Betafit plugin.
- Some changes to the Hilbert Delay and Gyrus Finder plugins
were made to make them work with SCO Unix. If any problems
show up, please let us know!
- 3dcalc now has a "-nscale" option to turn off the
autoscaling that sometimes causes problems (e.g., when
computing a 0-1 valued image).
Solaris 2.8 - 26 May 2000
The Solaris machine to which I have access has been upgraded to
Solaris 2.8 (SunOS 5.8). Thus, from now on the Solaris binaries
which I distribute will be compiled on this system, and will
not work on earlier levels of Sun's operating systems. I
have modified the name of the binary file to solaris28_gcc.tgz
to mark this change. The wget directory name has also
been changed accordingly. Sorry about this, but this computer is
not under my control in any way (I've never even seen it).
Incremental Improvements - 19 May 2000
- Doug Ward has added the -mask option to 3dNLfim, which
should make it easier to eliminate unwanted extra-brain voxels
from the analysis.
- The new plugin Dataset#2 controls the new 1D transformation
function of the same name. This is designed to let you overlay
the graphs of a second dataset onto the usual timeseries graphs of the
current anatomical dataset. In particular, it can be used with the
output of 3dNLfim -snfit to graph the timeseries fit
on top of the original data
(using Dataset#2 and Double Plot).
- Command line program imcutup can be used to cut up image files
that are arranged in 2D layouts, so that they can be input into
to3d (which requires a 1D string of images). This program
was written since I've found that some sites get their 64x64 images
back as 4x4 montages in a 256x256 image file.
A New Way to Fetch AFNI - 09 May 2000
A new way to get AFNI (source, binaries, and documentation) is
documented on this page.
This new method allows you to fetch only files that have changed since
you last got them.
FIM+ing - 01 May 2000
A new command-line program, 3dfim+, is now available.
Written by Doug
Ward, it computes the same things as the FIM+ codes in the
interactive AFNI program. Doug has written a manual for the
program, which is available from the documentation directories.
Nudging - 19 Apr 2000
A new plugin, Nudge Dataset ( plug_nudge.c)
is now available. It lets you move a dataset around, via
small rotations and/or small translations. It is intended to let
you fine tune the placement of one dataset with respect to another.
Lots of Changes in the Last Few Months - 12 Apr 2000
- New program 3dWavelets by Doug Ward does some basic
wavelet time series decomposition on 3D+time datasets.
- 3dIntracranial now works a little better.
- You can now add your own function to the FIM+ menu.
Usage instructions and
sample codes are in the file afni_fimfunc.c.
- Added some random number generation functions to 3dcalc.
- Added 3A: input formats to allow to3d to read
image data that is formatted in ASCII.
- Added -median and -MAD options to 3dTstat.
- Added -sagittal and -coronal options to
3daxialize (thus rendering its name kind of pointless).
- Some new features of AFNI that you can control
using Unix environment variables
(cf. README.environment):
- You can force switching back to "view brick"
mode when switching datasets in AFNI.
- You can specify a system-wide
.afnirc-style startup file to be read when
AFNI initializes (in addition to the user-specific file).
- You can specify the darkest level in the grayscale image display.
- AFNI now allows direct input of datasets, using
the new -dset option. See the output of
afni -help for information.
- Some programs now support input of "on-the-fly" calculated
datasets. See the section CALCULATED DATASETS
in the output of afni -help for syntax details, and the
-help options for the various programs to see if
this input option is supported.
- The rendering plugin now allows you to change datasets in script
files. Details can be found in the FAQ list at
Q65.
- 3dvolreg (and the corresonding plugin) now has an option
-1Dfile to write out the estimated movement parameters
to a *.1D formatted file. This can be used as input to
FIM as an "ort", which will then cause any residual signal
components
correlated with the subject movements to be detrended out. This
can help correct for interpolation errors.
Bug Fix - 24 Jan 2000
- Sally Durgerian of MCW discovered a bug in the way that
3dROIstats handles the -mask option. When
the 6th character of the dataset name was a numeric digit,
the program thought this was a sub-brick selector - this is
because it should have been looking at the 6th character of
the "-mask###" string, but was using the wrong
pointer. This error has been fixed.
- Program to3d now displays a warning message when
short input images (16 bits - the usual kind you get from
scanners) contain negative numbers. This can be a sign
that the images need to be byte-swapped.
(See the
answer to Q18 in the FAQ list for more details on
byte-swapping.)
- Program 24swap now allows the specification of areas of
the input file that should not be swapped at all.
Are we having fun yet? - 18 Jan 2000
- Doug Ward has added a few features to programs
3dDeconvolve and RSFgen - the details
are posted here.
- Added a new item "ShowThru" to the volume rendering
Color Opacity menu (on the Overlay control
panel). This allows you to have the color overlay show through
otherwise opaque grayscale underlay voxels. This can be useful
or confusing, depending on your mental state.
- New command line
program afni_vcheck will print out the AFNI
version it was compiled with, and will also query the MCW
web server to see what the latest available version is. This
functionality is also available interactively
from the Misc menu
on the Define Datamode control panel in AFNI.
[The version at this moment is 2.25b.]
- A new plugin for scatter-plotting the voxel values from 1 sub-brick
vs. another has been created.
- Program from3d has a couple of new options to let you
dump 2D image data out of a dataset more usefully.
Welcome to the Twenty-First Century - 04 Jan 2000
- The maximum number of datasets per directory has been increased
from 192 to 512. The maximum number of directories has been
increased from 60 to 80. These changes apply to the interactive
AFNI program.
- The rendering plugin has a new menu item on the Button-3 popup
under the Color label in the Overlay control panel.
This item is labeled Mixing, and controls how overlay colors
are mixed after the ray-based compositing done by Volpack. See the
output of the rendering Help button for more information.
- 3dROIstats has a new option -summary, written by
Mike Beauchamp of the NIMH.
- The FIM+ computations in AFNI now have 3 more options.
See the
answer to Q41 in the FAQ list for more information.
- 3dcalc now has a Gaussian random number generation function
gran(m,s), which can be useful when making up sample datasets.
One More Thing - 20 Dec 1999
Doug Ward of MCW found that the sub-dataset feature
(06 Dec 1999, infra) wasn't properly set up
in 3dttest. This oversight has been corrected.
Yet More About Anatomy Parents - 15 Dec 1999
After I wrote the screed about the importance of
"anatomy parents",
Tom Ross (MCW Dept. of Psychiatry)
pointed out that it would be nice if AFNI programs
would preserve the anatomy parent relationship when they make
new datasets from old. So now they do. If necessary, you can
use 3drefit -apar to alter the anatomy parent of
a newly created dataset. Unfortunately, this is what you will
have to do for datasets created before you installed this update.
Four More Little Things - 13 Dec 1999
- A bug in the "convert to z-score" routine, as used in
3dmerge -1zscore, was fixed. Values of z
larger than 13.0 will no longer be generated. N.B.: The
p-value of z=13.0 is less than 10**(-38).
That should be unlikely enough for you.
[fix requested by Michael Beauchamp]
- Program adwarp has been modified so that it will not
overwrite existing datasets, unless the new -force
option is used.
[fix requested by Tom Ross]
- 3dcalc has 2 new functions: lmode() and
hmode(). They compute the mode (most common
value) of their arguments - they only differ in how they
break ties.
[change requested by Michael Beauchamp]
- The ROI Average plugin had a bug when it was being
applied to multiple sub-bricks at once. It did not properly
re-initialize itself with each separate sub-brick.
[fix requested by Rasmus Birn]
One More Little Thing - 08 Dec 1999
New program 3drename is for renaming datasets from the
command line - .HEAD and .BRIK files together.
See the output of 3drename -help for usage information
(it isn't very complicated).
Further Changes - 06 Dec 1999
Additions to 3dDeconvolve, et cetera - 24 Nov 1999
Doug Ward has added a number of capabilities to program
3dDeconvolve. He has described these fully on the
(OLD) AFNI Message Board.
Bug Fix, et cetera - 23 Nov 1999
- Programs AFNI and adwarp did not work correctly
when writing out a dataset that was supposed to be written out
in a byte-swapped order (relative to the CPU native order).
This can occur, for example, if the environment variable
AFNI_BYTEORDER is set. The data was actually written
to disk in the native order, but the .HEAD file was
set to the same as AFNI_BYTEORDER -- the result was
unpleasant, since the dataset was now marked as being in a
byte order different than it actually was. This error has
been fixed.
- 3dcalc now allows inter-voxel computations, using
the new "differential subscripting" option. See the output
of 3dcalc -help for the usage details.
Small Changes - 18 Nov 1999
- New program 3dDetrend is for removing linear trends from
voxel time series, using linear regression. The component time
series to be removed can be specified as *.1D files
and/or mathematical expressions a la program 3dcalc.
- Program 3dcalc now allows the use of sub-vector selection
with the *.1D input option. The list of pre-defined
variables has been extended to include 't' (= time coordinate)
and 'l' (letter 'ell' = time index).
- The interactive AFNI program now recognizes a new environment
variable AFNI_OPTIONS. If present, the string value of this variable
will be placed on the afni command line. This allows you to
set things up so that your desired command line options will always be
executed, even when you forget to type them. See file
README.environment for more details.
- The code that pops up control windows in AFNI has been modified
in an attempt to ensure that such windows are entirely on-screen when
they appear.
(When they appear partially off-screen, they are a pain to use;
eventually, I couldn't take it any more.)
- Matthew Belmonte of Cornell has contributed a new Makefile for OSF/1 and
patched a few programs to work better under this operating system.
Bug Fix - 02 Nov 1999
2 Changes and 2 Additions - 01 Nov 1999
- Program 3dclust is one of the oldest AFNI programs, and
has a somewhat clumsy command line usage, with the rmm and
vmul values appearing just before the dataset. This sometimes
causes problems, if the user inadvertently puts some command line
option (e.g., -1dindex) between vmul and
the dataset name. Some warning messages have been added to detect
this problem. In addition, a new command line option -verbose
will print out some progress information to let the user know what
the program is doing.
- New program 3dTshift allows you to time-shift the voxels in a 3D+time
dataset to have the same temporal origin. [Note that using Fourier
interpolation (the default method) will not introduce extra serial
correlation in the data time series, which is a worry that has
been expressed.]
- New program 1dtranspose is for transposing rows and columns of
an ASCII file of numbers like the AFNI *.1D files.
For example, you could take the row-wise output of 3dmaskdump
and turn it into column-wise output, if that is more convenient for
your purposes.
- You can now set the colors of the buttons on the Plugins menu,
using environment variables. Details are in file
README.environment, as usual.
The purpose
of this change is to let you highlight the plugins you use the most, since
the size of the Plugins menu is getting kind of long.
Yet More Additions - 18 Oct 1999
- Added program 3dmaskdump as a command line way to dump
out to ASCII values from datasets, using a mask file to select
which voxels.
- 3dfractionize can now preserve the values of the input
file in the output mask, rather than create a fractional count.
This is useful when dealing with multi-valued mask files, as
might be created using the -1clust_order option of
3dmerge.
- The interactive AFNI program can now read images and
display them as time-dependent data, so that you can use
the graph viewers. (Formerly it could just display image
files as spatially-dependent data - images only, no graphs.)
The new options are -tim and -zim - see
the output of afni -help for details on usage.
(The purpose of this change is to let AFNI function
something like FD2 as a way to take a quick look at
image time series data, without having to assemble it with to3d.)
Some Additions - 14 Oct 1999 = Version 2.24b
- Added program 3dStatClust by Doug Ward - this does
clustering on parameter vectors as output by (say) 3dNLfim.
The purpose is to find groups of "similar" voxels, as defined
by closeness in some parameter space.
For details on the method and usage, see the documentation
file 3dStatClust.ps (available in file afni_doc.tgz,
at the AFNI distribution site).
- Added the Histogram plugin, which lets you graph a
histogram of the data values stored in a dataset sub-brick.
- Added program 1deval, which evaluates an expression
at a sequence of evenly spaced points - the purpose is to
simplify the creation of .1D files.
- Added AFNI_ENFORCE_ASPECT environment variable,
to make AFNI to enforce the aspect ratio constraint
on image windows when the X11 window manager fails to do so
(this happens on some Linux window managers).
- Added program 3dTstat to compute the same stuff that
plug_stats.c does, but in a batch program. Statistics
of a 3D+time dataset that can be computed are the mean,
slope, and standard deviation (all for each voxel).
- Added option -apar to 3drefit, which allows
you to (re)set the "anatomy parent" of a dataset after creation.
See the answer to Q58
in the
FAQ list for a reason why you might want to do this.
- Added option -warp to 3dfractionize,
to allow inverse warping from +tlrc
coordinates back to +orig coords during the
fractionation process. This allows you to create a mask
in Talairach coordinates, and then create a version of it
back in the scanner coordinates, so you can use
it to extract voxel values from a +orig dataset.
Minor Changes - 25 Sep 1999
- The Write Center ('w') menu item in a graph window
writes out the center time series to a file. This filename is
formed from the index coordinates of the center voxel. It has now
been rearranged so that the order of these coordinates is the same
as is displayed using the Voxel Coords? mode, and
as output by the various voxel dumping programs and plugins.
- The Set 'w' Suffix menu item in a graph window had a
bug: when used twice in an AFNI run, it would overwrite
its allocated buffer by one byte, eliciting a complaint from
AFNI's internal memory checking functions. This error has been fixed.
Minor Changes - 20 Sep 1999
- Datasets that do not have a byte order flag
in their .HEAD files are assumed to be in the native
order of the machine currently being used. All AFNI
programs, since May 1998, create datasets with such a byte order
flag, but datasets created with more ancient versions will
not contain this type of information. Such datasets have caused
confusion, since they are processed incorrectly if moved from
an SGI system to an Intel system (say). AFNI programs
now print out a warning message when such an un-byte-ordered dataset
is opened.
- The History Note now has the username and hostname added to the
time stamp, so that you can know not only when a dataset was created,
but also where and by whom.
- to3d now cuts out all but a few of the input image filenames
from the History Note, since otherwise you might end up with a History
Note that was uselessly long.
- 3dclust now recognizes the -1dindex and -1tindex
options (from 3dmerge), which will let you pick the sub-bricks
on which you wish to get the clustering report.
- 3dTcat now has two new options for removing linear trends
from the datasets it catenates.
- 3dmaskave has a new option -slices to let you restrict
the operation to particular slices in the dataset.
- 3dpc now has a -mask option, to restrict the principal
components analysis to voxels of your choice.
- 3dcalc will interpret the x, y, and z
expression symbols as the voxel (x,y,z) coordinates, if
no dataset usurps these symbolic names. Similarly, the
i, j, and k symbols can be used in an
expression to indicate the voxel 3D index.
Changes - 11 Sep 1999 = Version 2.24
- The Notes facility in the AFNI package has been extended.
A new plugin was written to allow you to view and edit Notes
interactively (see 3dNotes from 26 Aug).
- Also, a special read-only History Note was added - each
AFNI program that creates a dataset puts a copy of the
command line used into the History Note -
plugins that create a dataset do something similar.
The hope is that datasets will be more self-documenting - it will be easier
to find out how a dataset was created from the dataset itself.
The History Note can be viewed from the Notes plugin, but cannot
be edited by the user.
- The Notes (user-generated and History) are also displayed by the
program 3dinfo and by the Info buttons on the
Define Datamode->Misc menu.
- Two new optional calculations were added to the FIM+ submenu in
AFNI graph windows. These are the % From Ave
and Average values - for details, see the
answer to Q41 in the FAQ list.
Minor Changes - 30 Aug 1999
- You can now set a limit on the % Change computed by the FIM or
FIM+ control - the motivation and method are described in
file README.environment.
- The venerable count program (one of the first I wrote here
at MCW, these many years gone by) has a new option to allow floating
point output.
New Members of the AFNI Family - 26 Aug 1999
- Tom Ross (tross@mcw.edu) and Katie Heimerl of MCW have contributed several
new programs to the distribution:
- 3dFourier allows for Fourier filtering (lowpass and
highpass) of 3D+time datasets. There is also a corresponding
plugin for interactive use.
- 3dNotes lets you add notes to a dataset header file,
and retrieve them for reading later. (When is the plugin
version coming for this, Tom?)
- 3dROIstats lets you get statistics about each of a
whole collection of ROIs defined by a mask dataset.
Each separate value stored in the mask dataset defines a
distinct ROI.
- In other news, the AFNI splash screen debuts officially with
this release. (See the FAQ list or README.environment
for information on how to control this feature, if you don't like it.)
- Program 3dmaskave has a new option -indump, which
will dump a list of voxel index coordinates. Correspondingly, the
AFNI image window popup now has a "Jump to (ijk)"
button, which lets you jump the crosshair focus position to any
given triple of array index coordinates.
- The plugins by Ziad Saad have been fixed - there was a problem with
their use of malloc and the new malloc management
routines implemented in version 2.22. These plugins are labeled
3D Dump98, 4D Dump, Hilbert Delay98, and 3D+t Extract
on the Plugins menu.
Collectively, this new distribution is called version 2.23. The source
code is available at this moment, and binary distributions will be
out shortly.
Reordering Plugin - 02 Aug 1999
The reordering plugin ( plug_reorder.c) by Jay Kummer of MCW
is now included in the AFNI source code and binary distributions.
I (Bob Cox) have not tested this plugin personally; any questions should
be directed to Jay (kummer@mcw.edu).
Float Scanning, and a Solaris Bug Fix - 31 Jul 1999
- Tanya Kisler of U Pittsburgh had a problem with a float-valued dataset that
could not be processed properly with 3dmerge. It turned out that
some illegal floating point bit patterns (i.e., NaN)
had crept into the .BRIK file. The new program float_scan
can scan for and fix such errors. Also, if you define the Unix environment
variable AFNI_FLOATSCAN, the AFNI brick input routine
will scan each floating point brick for errors when it is read in, and
will replace illegal values with zeros. Since all the programs use the
same I/O functions, enabling this feature will provide some protection
against bogus floating point datasets. (See file README.environment
for a complete list of Unix environment variables used by AFNI.)
There is no analogous protection possible for byte- or short-valued
bricks, since any bit pattern is a legal integer. Some bit patterns
are not legal floats, which is why this problem can arise in
the first place.
- Sandra Kinderman of UCSD found that some keypresses in the graph windows
didn't work in the Solaris version of AFNI. Now that I
have access to a Solaris 2.6 machine, I was able to fix this
problem (hint: it involves the use of XComposeStatus).
Bug Fix - 19 Jul 1999
David Dubowitz of Caltech discovered that 3dcalc didn't work properly
with 3D+time datasets stored as bytes. This bug has been fixed.
More Smallish Additions - 18 Jul 1999
- The volume rendering plugin now has the ability to recall its previous
settings. Settings can be saved to a file and restored later, and can
also be restored when you scroll back through the accumulated images.
The intention is to make it easy to render different datasets in the
same fashion. The Help button has more information, under
the heading Scripts.
- Doug Ward has modified 3dDeconvolve to have a -nodata
option, which lets the user evaluate the effectiveness of a particular
experimental design (i.e., stimulus pattern), without actually
analyzing any data.
3dDeconvolve also has a new -glt option
to allow the user to specify a
general linear test, (e.g., a matrix contrast in regression parameters).
This lets the user conduct a (within-run) test for differences in
response to different stimuli.
The documentation file 3dDeconvolve.ps has been updated accordingly.
- New program RSFgen can be used to generate random temporal stimulus
patterns. In conjunction with 3dDeconvolve -nodata, this
can be used to find good patterns for event-related FMRI experiments.
- Program 3dNLfim now has an option that will write out
the signal fit (or signal+baseline fit) to a 3d+time dataset.
- Yesterday marks the inauguration of the
(OLD) AFNI Message Board,
a place where AFNI users can exchange ideas, tips, etc.
One Small Addition, Etc. - 07 Jul 1999
- A new program 3dTsmooth, is available to do some simple time series
smoothing of 3D+time AFNI datasets. See the output of
3dTsmooth -help for more details.
N.B.: Smoothing does not increase the detectability
of a time series pattern (except visually). The decrease in noise variance is
compensated for by a decrease in the number of degrees of freedom in
the statistical estimate of the pattern's parameters. It is better to
perform regression (linear: 3dDeconvolve or FIM; nonlinear: 3dNLfim)
directly on the unsmoothed time series data. If you just want to look at
smoothed time series data, you can do this in an AFNI graphing
window by using the Median or OSFilt 1D transformations
selected from the Opt->Tran 1D menu.
- AFNI now checks plugins to see if they are compiled at a time
before the AFNI main program itself. If so, a warning message
is printed out. When AFNI is updated, user written plugins
should be recompiled, since some internal data structures may be different.
The warning is intended to remind you of this fact.
- The volume rendering plugin didn't work correctly when switching between
datasets, or when viewing a dataset that was being actively changed by
the drawing plugin. These bugs have been fixed.
Two Bug Fixes and Two Additions - 08 Jun 1999
- A bug was found (by Mike Beauchamp of the NIMH) in program 3dmerge.
The program would always do the -1zscore transformation
on any statistics sub-bricks that were output. This happened because the
if() statement that controlled the calculation was mysteriously
commented out by the Dark Side of the Force. This error has been repaired.
- Program 3drotate failed to create a new ID code for the rotated dataset.
This could produce confusing results, since when an AFNI run
has 2 datasets using the same ID code, then the parenting relationships in
coordinate transformations (e.g., to the +acpc and +tlrc
views) could be done mistakenly. This error has been repaired.
- Doug Ward of MCW has written the program 3dIntracranial, which
tries to segment a T1-weighted dataset and remove the non-brain tissue.
This has only been tried on images from our 1.5 Tesla scanner, using
our custom-built local gradient/RF coil combination. Documentation can be found in
the manual 3dIntracranial.ps, which is in the new doc.tgz file,
and can also be found on the AFNI main page.
- The .afnirc file has been extended to allow setting of the
AFNI-relevant Unix environment variables. This provides
a convenient place to keep such setup information. See the
new edition of the file README.environment, which can be found on the
AFNI main page or in the AFNI distribution files.
Bug Fix - 01 Jun 1999
- A bug was found in the
"% Change" calculation in the interactive FIM calculation.
The average baseline level did not take into account the last "ort"
function used. For the default calculation, the last ort is a
linear trend. For voxels that have a small baseline and a large
linear slope, the error in the % Change might be significant.
In datasets that I have examined, this only occurs just outside the
edge of the brain, where the effects of motion are large and the
signal intensity is small. For voxels inside the brain, the
typical % Change is altered by a factor of at most 0.05; for example,
a true 1% change might end up as 0.95% or 1.05%.
- In a related story, a new feature was added to the interactive FIM
calculation: the ability to select a polynomial detrending (or "ort")
function. The default is still a linear function (polynomial of
order 1), but the new polort control can now be set
from 0 (baseline=constant)
to 3 (baseline=cubic polynomial in time).
Small Changes - 27 Apr 1999
- New program 3daxialize can be used to re-write a dataset so
that its slices are stored in axial order within each sub-brick.
The main motivation for this program is to create datasets that
can be used with the rendering plugin.
- Program imupsam is available for upsampling 2D images to
a smaller voxel size, using high-order interpolation.
- A button Set All was added to the Lock
menu in AFNI, to make it easier to lock all
controller windows together.
- A bug in 3dinfo was fixed, where the dimensions of
the dataset along each axis might be misreported.
- A bug in the AFNI initialization from the .Xdefaults
file was fixed.
- The "3D:" image reading code was modified to allow for possible
footers at the end of each slice. See the
FAQ for more
information.
- AFNI was tested briefly with the latest version of
LessTif, and seems to work OK.
Small Changes - 01 Apr 1999 [not a joke]
- The rendering and drawing plugins have been modified so that they can
be used together; it is now possible to draw in a dataset (in a 2D
image window) and see the 3D rendering updated immediately.
- Some small-but-annoying bugs in the rendering plugin were fixed.
- 3dcalc has had an output scaling problem fixed, so that each
sub-brick will get its own scaling factor. See the output of
3dcalc -help.
- The new program adwarp (by Doug Ward) provides a batch
capability like the interactive AFNI Write
buttons: the ability to resample a dataset in Talairach coordinates
based on an "anatomical parent" transformation. See the output
of adwarp -help for details.
- The SOLARIS_DIRENT_PATCH, described in file
machdep.h, will hopefully let AFNI work on
Solaris 2.6 systems.
- Memory allocation is now handled by internal routines that provide
some increased ability for debugging. If these cause trouble, they
can be disabled -- see README.environment
for the details.
These changes, and those described below, collectively comprise what
is now known as version 2.21e.
Bug Fix - 02 Mar 1999
Tom Ross of MCW has discovered a problem with the 3D registration
software in AFNI. This affects the results of Fourier interpolation
(the default mode) in both 3dvolreg and the 3D registration plugin.
The effect is that the registered images are slightly blurred.
This bug does not affect the polynomial interpolation methods
( -heptic, etc.).
If you are using a version of AFNI downloaded before today,
you should re-acquire the software
if you are using, or plan to use, or think you might consider
planning to use, 3D registration.
Smaller news items:
- Some new functions were added to the repertoire of 3dcalc;
see the output of 3dcalc -help for information.
- 3dRegAna has a new feature that allows the input of
a very long command line. This is documented in the
FAQ list.
- Some changes and fixes were made to the volume rendering plugin.
New Modules - Lincoln's Birthday, 1999
- Program 3dfractionize can be used to resample a high-resolution
mask dataset to a low resolution grid.
- Program 1dplot can be used to graph (to the screen, and thence
to a PostScript file) AFNI/FIM format timeseries (*.1D) files.
One application is graphing the "-dfile" output from 3dvolreg.
- The first version of a 3D volume rendering plugin is available.
It's fun, but crude, and subject to change at any second.
Some sample images
are here
(over 3 MB).
In addition, 3dcalc has had a few small changes -- see the output
of "3dcalc -help" for details.
Bug Fix - 02 February 1999
Doug Ward of MCW found a problem with the " See Function"
button - if it is pressed in when there is no functional dataset
to see, then you switch to a view or session where there is a
functional dataset, it would not be seen. This could be fixed
by turning the button off then back on. The necessary line of
code in AFNI has been fixed.
Wiremesh surface graphs have been added to the image display
"Disp" control panel, just below the "RowGraphs" button.
This will plot the image intensity as the height of a 2D graph
(i.e., I(x,y) vs. x and y).
Bug Fix - 20 January 1999
Tom Ross of MCW pointed out that the program cdf did the " -p2t"
conversion incorrectly for the F statistic. This has been fixed
(a 1 line braino in the code). To check if your copy of cdf is
correct, try
cdf -p2t fift .1 8 8
The output should be about 2.59, but in the incorrect version it
is about 0.386.
Changes - 15 January 1999
- The program 3dpc is now available to compute principal components
from a number of input data bricks (thanks to some help from
MCW graduate student Vinai Roopchansingh).
- A new command-line method for specifying subsets of data bricks from
a dataset has been implemented. This allows some programs to
operate on user-selected inputs. The details can be found
in the output of "3dcalc -help". Programs that can
use this option are:
3dcalc, 3dpc, 3dinfo, 3drotate,
3dvolreg, and from3d.
Changes - 03 January 1999
- The "Disp" control panel on the image viewing window has a
new chooser button, labeled "RowGraphs". This is for plotting
rows from the underlay (grayscale) as x-y line graphs.
Use "BHelp" on the RowGraphs button for a little more information.
- The "Xhairs" chooser (in the main AFNI control panel)
now allows you to have crosshairs displayed only along
certain axes (for example, "LR+AP" means that crosshairs
parallel the the Left-Right and Anterior-Posterior axes
will be shown, but not those parallel to the Inferior-Superior axis).
- The new environment variable "AFNI_ALWAYS_LOCK" will set all
AFNI controller windows to be locked together at startup.
(See README.environment for
information about Unix environment variables that can affect
the way AFNI works.)
- The graph windows can now have a horizontal dashed gridline drawn
at the level y=0 (if the data spans a negative-to-positive range).
This is controlled by the "h" key, or from the
"Opt->Grid" submenu.
Changes - 22 December 1998
The 3D registration plugin and the command line program 3dvolreg did
not produce the same " dfile" for output -- the values were the same,
but the assignment of angles to axes was incorrect in the plugin.
This was brought to my attention by Eli Merriam of UPMC. The
plugin has been fixed, and should be re-compiled or re-downloaded.
Changes - 17 December 1998
- Doug Ward has speedup up the linear regression functions
in 3dDeconvolve and 3dRegAna.
- FFT based calculations are speeded up by about 20%
on some CPUs, thanks to using an unrolled N=32 FFT
function as the basic unit. This affects the 3D blurring
and 3D rotation operations in particular.
- Some scaling bugs were fixed in 3dmerge and elsewhere,
which arose when using datasets with internal scaling factors.
Additions to the AFNI package - 24 November 1998
- 3D (volumetric) registration is now available in program 3dvolreg.
This executes 2-6 times faster than AIR 3.08 and produces
nearly identical estimates of the movement parameters.
See file
README.registration
and the output of "3dvolreg -help" for more details.
- The new program 3drotate can be used to deal with datasets
that are acquired oblique to the anatomical scans. The preferred
modus operandi would be to rotate the anatomical scans to be
aligned with the functional scans.
- New program 3dTcat lets you catenate 3D+time datasets together
to make really big files. Burn up those 18 gig drives!
- Program 3dmerge has a new option "-1dindex" which lets you
specify which sub-brick of the input dataset(s)
is to be operated upon.
- Setting the Unix environment variable "AFNI_LEFT_IS_LEFT"
will make AFNI display
axial and coronal images with the subject's left on the
left of the screen.
- The dataset "Lock" feature now works on time indexes as
well as on spatial coordinates.
Additions to the AFNI package - 18 September 1998
- The new program cdf will compute the p-value given the
threshold, or the threshold given the p-value, for several
canonical probability distributions. This program is an
extension of the older program p2t.
- AFNI now accepts the command line option "-install",
which will make the program install its own colormap.
You can use this to get around the problem of not having
enough color cells available (on 8 bit displays) due to
colormap hogging by Netscape, CDE, etc.
- When you read in a new color palette file (*.pal), the last
palette table read in will become the active palette.
Previously, you had to then pick the new palette off the
palette chooser menu after reading it in, which confused
some people [no names will be mentioned, just initials: SMR].
- 3dmerge has a new option "-1zscore", which is designed to
convert a statistic sub-brick from an arbitrary distribution
(e.g., t-test, F-test) into an N(0,1) variable (also called
a z-score). This option is desiged to be used in conjunction
with the "-doall" option, so that it applies to all sub-bricks
of the input dataset. Sub-bricks that are not statistics
will not be affected by "-1zscore".
- 3dmaskave has new options that allow the specification of voxels
that are reported on to also include a range of allowable values,
and to restrict the output to a single sub-brick of the input.
At present, the only documentation for these changes is this Web page
and the output of the " -help" option for the affected programs.
Additions to the AFNI package - 14 September 1998
- A new batch program 3dDeconvolve is available to do multiple
linear regression and linear deconvolution of a 3D+time dataset.
- The Deconvolution plugin is an interactive version of this
that allows quick exploration of these linear time series
fitting techniques in an AFNI graph window.
- To3d now has a command line option "-2swap" and an interactive button
that let you byte-swap the image data.
The deconvolution/linear regression modules were written by Doug Ward (ward@mcw.edu),
and are documented in the PostScript file
3dDeconvolve.ps.
Small changes to AFNI - 22 August 1998
- The "Plot" button in the timeseries chooser (activated from the
"FIM" menu) has finally been implemented.
- AFNI now works with X11 TrueColor visuals (8-24 bit planes).
[However, the older program FD2 still requires PseudoColor.]
Small changes to AFNI - 12 August 1998
This non-release of AFNI adds the following:
- Ability to plot points+lines together in a graph window.
- Modified 3dmaskave and plug_maskave to allow the use of
a sub-brick from a bucket dataset as the mask.
- plug_maskave now allows the creation of an ROI averaged
time series, which can be used as the FIM reference
(for example).
- Added nonlinear fit model "model_convgamma", that models the data
time series as a gamma variate impulse response convolved with a
user-input reference time series. The nonlinear parameters of
the gamma variate are fit separately for each voxel.
- Nonlinear fit programs 3dNLfim and plug_nlfit have a new option to allow
the time step of the model function to be set to the time step of the
input dataset (the default is to set delta-t=1.0, regardless of true TR).
The source code is available in the usual places, for the usual suspects.
Release of AFNI 2.20b - 14 July 1998
This release of AFNI fixes some bugs that have been uncovered since
the last release (2.20a - 30 April 1998). A few new capabilities
have been added as well.
If you are outside of the MCW/MU community, you should download the
new files, even if you just got AFNI recently. The final bug fixes
below were only made late at night on July 14, 1998, and the files
set up for distribution on July 15, 1998.
Recent Bug Fixes
- Program 3dcalc now computes the logical functions "OR", "AND",
and "MOFN" correctly.
- The Palette selection popup menu under the "Define Function"
Inten label now works even if there is no .afnirc file.
- The Dataset Type menu on the "Dataset Copy" plugin now works
correctly for anatomical types as well as functional types.
- The "Dataset Rename" plugin now works correctly with compressed datasets.
Recent "Improvements" (since April 1998)
- Added erosion+dilation operations to the clustering options
of 3dmerge. In some cases, a cluster is generated that
comprises 2 or more large blobs connected by small "necks".
Erosion can cut the necks off, and re-dilation will preserve
the main blobs.
- The new "-1clust_order" option allows the values in a cluster
to be replaced by an index indicating which cluster the voxel
is in -- 1=largest, 2=next largest, etc. This is intended
to facilitate the creation of VOI masks from functional data.
- Program AFNI now allows the .afnirc file to be skipped.
- Program 3dnoise now allows the noise level to be set from the
command line, rather than computed from the data.
- Program 3dcalc had a number of changes, besides the bug fix
described above. They are (see "3dcalc -help" for details):
- Operations are now allowed on bucket and other multi-brick
datasets that are NOT 3D+time.
- Memory management was improved to allow operations on larger
collections of data. (Buying more memory is still a good plan.)
- A *.1D file can be input in place of a dataset. In this case,
the value at each spatial voxel at time index n will be the
same, and will be the n-th value from the time series file.
- The "-verbose" option will print out the progress of the
calculations. This can be informative when running 3dcalc
on large multi-brick datasets.
- Program 3drefit option "-nowarp" allows the removal of all
warping (coordinate transformation) information from a dataset.
If a dataset is created by transformation from another (as in
the +orig to +tlrc case), the coordinate warp is stored in the
transformed dataset header file. In some cases it is desirable
to remove this information -- for example, to prevent the use
of "Warp on Demand" within AFNI, which will re-transform the
data from the original source, even if the transformed data
were subsequently edited (thresholed and clustered, say).
Less Recent "Improvements" (since January 1998)
- Compressed dataset .BRIK files: see README.compression.
- Storing the byte order of datasets in the .HEAD file:
see README.environment.
- Volume of interest (VOI) selection and statistics: see README.roi.
- Minor tweaks to graphing:
- Autoscaling of graphs using the "a" key or from the
"Scale" submenu.
- Gaps between graph boxes from the "Colors, Etc" submenu.
- Choice of an arbitrary time series for the horizontal axis
from the "X-axis" submenu.
- Addition of the "Percent Change" calculation to the interactive
FIM menu.
- Added the "Purge Memory" and "Info" buttons to the "Misc" menu
in afni (under the "Define Datamode" control panel).
Created by
Alex Clark
Last modified
2005-03-24 16:28
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