AFNI HISTORY
all levels
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : afni_history -html -reverse -type NEW_ENV
---- log of AFNI updates (most recent first) ----
15 Dec 2021, RW Cox, 3dttest++ and 3dClustSim, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_CLUSTSIM_MEGA
If AFNI_CLUSTSIM_MEGA is set to 'YES', then 3dttest++ will run 3dClustSim
using the '-MEGA' option, which gives a finer grained output table of
cluster size thresholds. Also, a few changes to 3dttest++ help to clarify
that the 12 character limit for set labels is not the same as the 256
character limit for dataset labels.
27 Sep 2021, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_INSTACORR_JUMP
If YES (default), Shift+Ctrl+click sets the instacorr seed and jumps the
crosshairs to that location. If NO, sets the instacorr seed but there is
no crosshair jump. (For Phil Kohn)
10 Dec 2019, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV)
Add 'Zoom lock' to the locking capability
Also a new environment variable AFNI_ZOOM_LOCK to turn this on at
startup, vs interactively later.
24 Oct 2019, RW Cox, AFNI gui, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_IMAGE_COLORSCALE defines colorbar for image viewer window
Formerly fixed, now user can specify the color scale to use here from
one of these: magma viridis plasma googleturbo
Also, I restored the 'g' (gamma) button affect on this color scale.
11 Jul 2019, RW Cox, 3dDeconvolve 3dREMLfit, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_INDEX_PREFIX changes '#' in sub-brick labels
06 Jun 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_OPACITY_LOCK
YES = Locks the opacity (1-9) arrows between all image viewers.
This is set to YES by default, and can be set to NO to get the
old (unlocked) behavior.
11 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
Brainnetome atlas
This atlas is now included in the standard distribution
This also is in the default list of atlases
07 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
Eickhoff-Zilles 2.2 MPM atlas
This atlas is the newer 2.2 version of the MPM atlas
This atlas replaced the 1.8 version in the list, but both
are kept in the binary distribution
05 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
HCP Glasser atlas in AFNI atlases
Mike Beauchamp and Meghan Robinson contributed atlas
Now included and first in default list too
This atlas is in MNI space (not in its original Contee
grayordinate surface space.
Additionally, all the pmaps (probability maps) have been
removed from the standard distribution and default list
06 Nov 2018, RW Cox, AFNI GUI, level 1 (MICRO), type 3 (NEW_ENV)
new environment variable AFNI_FONTSIZE
Can be 'MINUS' for small, 'PLUS' for bigger, and 'BIG' for
super-embiggened.
12 Oct 2018, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
Longname support in AFNI atlases
Environment variable AFNI_ATLAS_NAME_TYPE to control
29 May 2018, RW Cox, AFNI GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_GRAPH_ALLOW_SHIFTN
Needs to be set to YES to enable the old FD-style N
method of changing the graph matrix. Some people just can't handle the
freedumb.
10 May 2018, RW Cox, AFNI GUI, level 1 (MICRO), type 3 (NEW_ENV)
remove AFNI_ENFORCE_ASPECT from having any effect
This never did very much good, so it is now OFF.
31 Oct 2017, DR Glen, SUMA popups disabled, level 1 (MICRO), type 3 (NEW_ENV)
SUMA popups are disabled by default, SUMA_SHOWPOPUPS
Popups in SUMA that required clicking are now off
by default. Bracket (hemisphere) hiding and small surface
warnings only go to terminal. Other messages can be shown
in popup messages with env. variable.
27 Mar 2017, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_LEFT_IS_POSTERIOR
To show posterior of brain on the left (instead of right) in sagittal
image and graph viewers. A complement to AFNI_LEFT_IS_LEFT.
27 Feb 2017, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IMAGE_LABEL_IJK
If this variable is set to YES, then the image label overlay (chosen
from the intensity bar popup menu) will show the slice index instead of
the slice coordinate. (for PT)
09 Feb 2017, RW Cox, thresholding, level 2 (MINOR), type 3 (NEW_ENV)
Fix inconsistency in thresholding with short-valued bricks
In the AFNI GUI, thresholding is done with floats.
But in 3dmerge and in Clusterize, if the thresh brick is a short,
thresholding was done with shorts. And the user-supplied threshold was
ROUNDED -- so that a threshold of 2.2 would become 2, which means that a
value of 2 was OK -- which it shouldn't be. Solution: change those
places to threshold with floats. However, if someone wants to keep the
old way for compatibility, then they can set AFNI_OLD_SHORT_THRESH to
YES.
18 Apr 2016, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
Open all 3 image viewers by default
New variables AFNI_OPEN_AXIAL (etc.) will turn off axialimage viwer (etc.)
if set to NO -- for LIBR and Tulsa.
07 Apr 2016, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_GIC_DEBUG=YES will cause lots of debugging printouts
For Sharyn and Cesar.
22 Sep 2015, RW Cox, 3dDeconvolve, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_USE_ERROR_FILE = NO turns off creation of 3dDeconvolve.err
02 Jun 2015, DR Glen, plugout_drive to stdout or file, level 1 (MICRO), type 3 (NEW_ENV)
Allow plugout_drive to get xyz,ijk,AFNI environment to file
plugout_drive for GET_DICOM_XYZ, GET_ENV was to stdout of afni
GUI. This was difficult to parse. Allow resetting output to file
using AFNI_OUTPLUG environment variable or SET_OUTPLUG command
03 Apr 2015, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_Classic_Label_Colors , see .sumarc after updating it for details
11 Mar 2015, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_CROSSHAIR_THICKNESS
Lets user set thickness of image crosshair lines. For someone named
Corianne, if that is a real name.
25 Feb 2015, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
Implemented dataset autoloading
See env SUMA_AutoLoad_Matching_Dset in ~/.sumarc
25 Feb 2015, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
Added env SUMA_AutoLoad_Matching_Dset to control transparency step
25 Feb 2015, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
Added env SUMA_Transparency_Step to control transparency step
23 Jan 2015, DR Glen, whereami GUI, level 2 (MINOR), type 3 (NEW_ENV)
Web-based links in Whereami GUI on by default
Links will be available by default now. Effectively
equivalent to setting these environment variables to YES:
AFNI_WEBBY_WAMI, AFNI_SUMSDB and AFNI_NEUROSYNTH.
20 Jan 2015, DR Glen, whereami GUI, level 2 (MINOR), type 3 (NEW_ENV)
SumsDB link
Link out from whereami GUI in afni to SumsDB database
with new environment variable AFNI_SUMSDB (YES/NO).
Must also set AFNI_WEBBY_WAMI to YES.
05 Nov 2014, P Taylor, 3dROIMaker, level 3 (MAJOR), type 3 (NEW_ENV)
Default neighborhoods now AFNI standard; labeltable functionality in.
Default 'hoods more standard, can still do other; labels by default.
04 Sep 2014, DR Glen, AFNI_ATLAS_PATH, level 2 (MINOR), type 3 (NEW_ENV)
Atlases and templates may be stored in location set by AFNI_ATLAS_PATH
Atlases and templates need not be in the default afni binary directory.
This variable may hold multiple directories that specify the possible
locations of atlases when the atlas definition does not include the
path in the filename. The atlases are typically defined in
AFNI_atlas_spaces.niml file or in a CustomAtlases.niml file
03 Jun 2014, RW Cox, afni GUI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_PBAR_FULLRANGE
If this variable is set to YES, then the color pbar in Define Overlay
will reflect the range set by the user for the colorization process. At
some point, this feature will become the default, and then you'll have
to set this variable to NO to get the old behavior -- where the range
set by the user is shown only at the bottom right of the Define Overlay
panel, and it then multiplies the independently set top value of the
pbar to get the colorization scale. In the new method, the top value of
the pbar cannot be set by the user independently of the range (or
autorange) parameter. The intention of this change is to make the
number -> colors process somewhat more blatant.
05 May 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_HomeAfterPrying to avoid a 'home' reset with prying
16 Apr 2014, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_SLAVE_THROLAY sets up Thr=OLay or Thr=OLay+1, for Paul Taylor
08 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_VO_InitSlices controls how volumes slices are shown at startup
See ~/.sumarc for details, run suma -update_env if variable is missing.
08 Apr 2014, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_ICORR_UBER_USER allows access to special InstaCorr distance measures
Set variable to YES to have access to special distance measures in
the plugin
04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_Dset_NodeConnections controls how connections to a node are displayed
See ~/.sumarc for details, run suma -update_env if variable is missing.
03 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_Dset_Font to initialize text in graph datasets
See ~/.sumarc for details, run suma -update_env if variable is missing.
31 Mar 2014, RW Cox, messages, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_MESSAGE_PREFIX will go before program messages to stderr
The purpose of this is to allow the user to distinguish between messages
from various instances of programs running in parallel, as in
foreach fred ( 1 2 3 )
setenv AFNI_MESSAGE_PREFIX case$fred
run_some_program -option $fred &
end
27 Mar 2014, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
Added SUMA_ObjectDisplayOrder to control object display sequence
This only affects the rendering in the few instances where alpha
blending is used. Run suma -update_env then search for env in
~/.sumarc for details.
12 Mar 2014, ZS Saad, afni-general, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IMAGE_VIEWER and AFNI_PDF_VIEWER for you know what.
26 Feb 2014, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
Remove AFNI_SLAVE_THRTIME and AFNI_SLAVE_BUCKETS_TOO variables
The functionality of AFNI_SLAVE_THRTIME is improved via the newer
'Thr=OLay?' controls.
The functionality of AFNI_SLAVE_BUCKETS_TOO is simply now subsumed by
AFNI_SLAVE_FUNCTIME.
31 Jan 2014, DR Glen, AFNI_IMAGE_GLOBALRANGE, level 2 (MINOR), type 3 (NEW_ENV)
New options for scaling display in afni GUI
AFNI_IMAGE_GLOBALRANGE can be set to SLICE (default), VOLUME (SUBBRICK),
or DSET. The GUI applies the lookup table to color the underlay with the
range determined from the slice, sub-brick or the whole multi-sub-brick
dataset. This environment variable may be set in a user's .afnirc file,
Additionally, the GUI allows changes from the environment plugin menu or
in two new places - the right-click menu on the image viewer colorbar.
Typing Control-m in an image viewer cycles among the global range types.
Previous YES/NO definitions for this variable correspond to VOLUME and
SLICE respectively and will continue to work as before. The lower right
corner of the image viewer shows the current range setting:
(2%-98%/Min2Max, Vol, Dset)
15 Jan 2014, RW Cox, afni image viewer, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_CROP_AUTOCENTER - automatically re-center crop sub-window
If set to YES, then the crop sub-window (if cropping is active) will
automatically re-center about the crosshair location -- as far as
possible. This feature can also be set for each image viewer window
separately from the intensity bar right-click popup menu. (NOW will
John Butman be happy?)
10 Jan 2014, ZS Saad, DriveSuma, level 1 (MICRO), type 3 (NEW_ENV)
Added SUMA_DriveSumaMaxCloseWait env
This controls how long DriveSuma waits before it considers
a currently open stream lost forever. Consider also
env SUMA_DriveSumaMaxWait.
21 Oct 2013, DR Glen, whereami GUI, level 2 (MINOR), type 3 (NEW_ENV)
NeuroSynth.org link
Link out from whereami GUI in afni to neurosynth.org
with new environment variable AFNI_NEUROSYNTH (YES/NO).
Must also set AFNI_WEBBY_WAMI to YES.
23 Jul 2013, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
Make AFNI_RECENTER_VIEWING an editable (in the GUI) variable
25 Jun 2013, RW Cox, AFNI_PBAR_TICK, level 1 (MICRO), type 3 (NEW_ENV)
Ability to disable new tick marks for colorscales and image bars.
Can set this to NO, or to the number of tick marks desired.
24 Jun 2013, RW Cox, AFNI_HISTORY_NAME, level 1 (MICRO), type 3 (NEW_ENV)
Lets user change username@machine in History notes
Because super-heroes need to have a secret identity, right?
29 Mar 2013, DR Glen, general compression, level 2 (MINOR), type 3 (NEW_ENV)
pigz for faster gzip-like compression
pigz is a gzip utility that makes use of multiple CPU's.
It produces and uses .gz files. To use, set AFNI_COMPRESSOR to PIGZ.
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LHunify to automatically merge LR hemispheres in all views
This is done by discarding the _lh _rh to state names that are
created by @SUMA_Make_Spec_FS
19 Feb 2013, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Histogram plugins can now do cumulative distributions
set AFNI_HISTOG_CUMULATIVE to YES
01 Feb 2013, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_ContourThickness to control the thickness of dset contour lines
Addition made in response to Valentinos' feedback.
Documentation is in .sumarc file.
01 Nov 2012, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
Abide by AFNI's AFNI_FLOATSCAN variable and look for bad values
SUMA will now scan for bad floats (NAN, and INF) and sets them
to 0, when the dataset is loaded. You can turn this feature off
with AFNI_FLOATSCAN set to NO.
18 Oct 2012, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_CREEPTO modifies 'jumpto xyz' behavior
06 Aug 2012, DR Glen, NIFTI reading, level 2 (MINOR), type 3 (NEW_ENV)
Handling view equivalents for NIFTI
AFNI_NIFTI_VIEW sets default view for AFNI datasets marked as
'aligned' (sform_code or qform_code = 2). This variable should
be set to 'TLRC', 'ORIG' or 'ACPC'.
23 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 3 (NEW_ENV)
Allow 7x7x7 interpolation in wsinc5 + spherical mask
via environment variables
19 Jul 2012, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
New variables to initialize range setting and symmetric range
See SUMA_Auto_I_Range, SUMA_Auto_B_Range, and SUMA_Sym_I_Range
in ~/.sumarc . If you don't see them, time to run: suma -update_env
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ArrowFieldSelectorTrigger set threshold for using ArrowFields
For datasets with sub-bricks >= SUMA_ArrowFieldSelectorTrigger
and arrow field is used to switch between sub-bricks
21 May 2012, RW Cox, FDR calculations, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_NON_INDEPENDENT_FDR == YES --> like '-cdep' in 3dFDR.
18 Jan 2012, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_Position_Original for controlling initial window position.
Use suma -update_env ; to update env file, then look for
env SUMA_Position_Original for help and default value.
22 Dec 2011, RW Cox, afni realtime plugin, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_REALTIME_External_Dataset environment variable
Lets the realtime user (let's call her/him 'CC') specify an external
dataset to be used as the registration base. CC doesn't have to use a
dataset that is in the cwd, unlike the plugin's GUI selector. Nor does
the setting of this environment variable affect the plugin's GUI.
09 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_DoNotSendStates restricts certain surfaces from getting sent to suma.
05 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_GUI_EDITOR controls user's preferred text editor.
See apsearch -afni_text_editor.
02 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_NodeCoordsUnits allows the specification of node coord. units
17 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV)
Added threshold locking capability under the 'Lock' menu
08 Nov 2011, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IMAGE_COLORANGLE
Set this to 360 to get the 'Colr' image to be a full circle colormap.
22 Jul 2011, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV)
Added AFNI_TIME_LOCK to turn on AFNI's Time Lock by default
11 Jul 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ATLAS_COLORS and default atlas in AFNI GUI
Set atlas to use for Atlas colors, Go to atlas location,
Draw Dataset and Renderer. Name of atlas can be set in
environment and modified in the AFNI GUI environmentalism menu.
Several other environmental variables regarding atlas usage
can also be modified there too.
28 Jun 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 3 (NEW_ENV)
Ability to skip the 'centering' done in AM2 regression
By setting environment variable AFNI_3dDeconvolve_rawAM2 to YES, as in
the command
3dDeconvolve -DAFNI_3dDeconvolve_rawAM2=YES ...
27 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WHEREAMI_DEC_PLACES
Set precision for whereami output
Higher field data and animal atlases require higher precision.
The default value used for focus point among template spaces is
still 0 decimal places (closest mm), but animal data requires three
decimal places. Value may range from 0 to 10.
23 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
Desai MPM atlases
New maximum probability map atlases derived from the Desai probability
maps just introduced in distribution.
19 Apr 2011, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_GRAPH_FONT lets user choose font for graph viewer text
9x15bold looks solid on a 100dpi screen, for example.
18 Apr 2011, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
Add AFNI_GRAPH_CX2R to allow for graphing complex time series
07 Apr 2011, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
Framework changes for generic atlases
Atlases now can have segmentation in a NIML structure attribute
in the atlas dataset header. The environment variable,
AFNI_CUSTOM_ATLAS, can contain a custom atlas prefix. Details on
NIML attributes will be forthcoming. In the meantime, existing
atlases should work as before with the minor exception of mask
datasets are now set to have voxel values of 1 rather than
the values from the atlas dataset.
22 Mar 2011, ZS Saad, afni-general, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_NIFTI_TYPE_WARN controls frequency of NIFTI type conversion warnings
Default is to warn once per session.
Search for AFNI_NIFTI_TYPE_WARN in README.environment for details.
08 Feb 2011, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 3 (NEW_ENV)
Add AFNI_INSTACORR_XYZ_LPI environment variable
21 Jan 2011, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_ENVIRON_RESET allows .afnirc to re-set existing variables
Per the suggestion of Alex Waite of MCW.
13 Dec 2010, RW Cox, many, level 1 (MICRO), type 3 (NEW_ENV)
Add AFNI_ECHO_COMMANDLINE environment variable
Runs inside afni_logger, for Daniel Handwerker
04 Nov 2010, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
Re-invoked AFNI_PBAR_AUTO / AFNI_CMAP_AUTO
Which Ziad had commented out for reasons he won't explain.
04 Nov 2010, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
Add AFNI_THRESH_TOP_EXPON to allow larger range of thresholds.
For Phil Kohn.
24 Sep 2010, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_SQRT_AUTORANGE is no more
Instead, AFNI_AUTORANGE_POWER is born.
23 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Allow users to specify colormaps for retinotopy results
See help section for variables:
SUMA_RetinoAngle_DsetColorMap and SUMA_VFR_DsetColorMap
in your ~/.sumarc, after running suma -update_env.
06 Jul 2010, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added SUMA_Cmaps_Dir to point to directory with colormaps
With this environment variable, users can point to a
directory containing SUMA colormaps (*.cmap) that should
be made available to SUMA. For help on colormap file formats,
open a surface controller ('View'-->'Surface Controller'),
click on BHelp (bottom left) and then click on 'New' button
which is to the right of the colormap selector.
18 May 2010, DR Glen, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
Allowed for flip angle variation through volume with scaling dataset
07 May 2010, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_FILE_COORDS_x
If this environment variable is set (for x=A,B,C,...), then AFNI
controller 'x' will write each viewpoint change xyz coordinates to the
file whose name is given by the variable value. For example
afni -DAFNI_FILE_COORDS_A=stdout
will write each new (x,y,z) triple to standard output. Coords are
written in DICOM order (natch). This feature is called the Jennifer
Evans special.
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_AlwaysAssignSurface (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LabelDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ConvexityDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ShowLabelDsetAtStartup (see suma -environment for details)
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Setup final color blurring level.
14 Jul 2009, DR Glen, afni, level 2 (MINOR), type 3 (NEW_ENV)
Added AFNI_ONE_OBLIQUE_WARNING
AFNI_ONE_OBLIQUE_WARNING = YES makes interactive spit out ONE warning
about obliquity per session then go quiet.
20 May 2009, RW Cox, realtime plugin, level 1 (MICRO), type 3 (NEW_ENV)
Also modify it to limit the number of open controllers.
cf. AFNI_REALTIME_MAX_CONTROLLERS
29 Apr 2009, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Make 'Where am I?' font size user controllable.
via AFNI_TTATLAS_FONTSIZE environment variable (editable).
08 Apr 2009, RW Cox, thd_filestuff.c, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ALLOW_ARBITRARY_FILENAMES
Set this environment variable to YES to allow 'strange' characters into
AFNI created filenames. You should know what you are doing if you use
this variable!
01 Apr 2009, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
Added SUMA_KeyNodeJump variable
This variable controls number of nodes to jump with arrow keys navigation.
See suma -environment for complete list and defaults.
09 Feb 2009, RW Cox, imseq.c, level 2 (MINOR), type 3 (NEW_ENV)
Add AFNI_ANIM_DUP environment variable.
Allows user to duplicate images when writing an animation (AGIF or
MPEG) file. A simple and stoopid way to slow down an MPEG.
03 Oct 2008, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_StartUpLocation to control initial window placement
See output for suma -environment for details.
15 May 2008, RW Cox, thd_initdblk.c, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IGNORE_BRICK_FLTFAC = YES means ignore brick factors on input
This is a quick hack for Ziad, and must be used with care! Example:
3dBrickStat -DAFNI_IGNORE_BRICK_FLTFAC=YES -max -slow fred+orig
30 Apr 2008, RW Cox, mcw_glob.c, level 2 (MINOR), type 3 (NEW_ENV)
setenv AFNI_SHELL_GLOB YES == wildcard expansion via the shell
For Graham Wideman and Mac OS X Server 10.5 problems.
08 Apr 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
allow residual Ct values via AFNI_MODEL_D3_RESID_CT_DSET dataset
e.g. setenv AFNI_MODEL_D3_RESID_CT_DSET residual_Ct+orig
20 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WRITE_1D_AS_PREFIX allows writing 1D or surface data given the prefix
For example, setting this to YES will allow writing surface data to NIfTI.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_GIFTI_VERB sets the verbose level in the gifti I/O library
The default is 1, 0 is quiet, and values go up to 7.
07 Mar 2008, RW Cox, Dataset#N, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_DATASETN_NMAX sets number of datasets allowed
New environment variable AFNI_DATASETN_NMAX sets the number of datasets
allowed in Dataset#N plugin, from 9..49. This is for Shruti.
06 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added three variables affecting the surface controller
* SUMA_ShowOneOnly: Sets '1 Only' on or off. On by default
* SUMA_GraphHidden: Update open graphs even if corresponding dset
is hidden.* SUMA_ColorMapRotationFraction: Fraction of
colormap to rotate
up or down with arrow keys.
See suma -environment for a complete list.
28 Feb 2008, ZS Saad, suma-general, level 3 (MAJOR), type 3 (NEW_ENV)
Support for GIFTI surface format reading
04 Feb 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_NEWSESSION_SWITCH in afni_func.c == switch to new session?
03 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_SEE_OVERLAY environment variable.
* Turn overlay on when user first-time switches Overlay, and turn TTatlas
colors on when user pops up atlas color chooser panel.
27 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_DISABLE_TEAROFF environment variable.
auto-generated by afni_history on Sep 29 2025