-help, -h :see helpfile (here, in fact)
-hview :popup help
-ver :see version number
-ulay UUU :name of underlay dset (required); can be 3D or 4D
set, depending on the circumstances. For 4D,
though, strongly consider using "@djunct_4d_imager".
-olay OOO :name of overlay dset (opt).
-mode_4D :for each viewing plane (sag, cor, axi) one slice
is selected across all volumes in a 4D data set
(e.g., using one of the "-set_* .." opts, below).
A montage of those slices is made for any ulay UUU
and olay OOO selected. Note that with this
option:
+ the user cannot thresold by statistic with the
"-thr_olay_p2stat .." opt (-> because different
stats in a volume might have different conversions)
+ when using this opt, at least on of UUU and OOO
*must* have >1 volumes.
+ if one of the ulay/olay volumes has only one brick,
it will be viewed in the same way across the entire
montage (i.e., as if it were a constant volume
throughout 'time').
-olay_off :explicitly state you are not using olay (opt);
if not used and no olay is given, then the user
just gets prompted to be sure they haven't
forgotten the olay dset.
-prefix PPP :prefix for output files (required).
-ulay_range UMIN UMAX :specify min and max range values of ulay dset;
if a "%" is on both numbers, then treat the
numerical part of UMIN and UMAX as percentiles
from which to calculate actual values; otherwise,
treat UMIN and UMAX as values directly. (def:
UMIN=0% and UMAX=98%). (See DR: SET_ULAY_RANGE)
Also, see "Special Ulay Range" and "Combining %ile
values..." in NOTES, below.
-ulay_range_nz UMIN UMAX
:same as the preceding opt, but when "%" is on both
numbers, here the percentiles are only calculated
over the *non-zero* voxels. The above one is more
in line with the AFNI GUI default behavior for
percentile calcs (though GUI by default works
slicewise). If %ile values are not given, then
both this and the above option produce identical
results for the same UMIN and UMAX values. (See
DR: SET_ULAY_RANGE) "Special Ulay Range" and
"Combining %ile values..." in NOTES, below.
-globalrange GR :specify how lookup range for matching ulay values
is done (def: VOLUME);
(see ENV: AFNI_IMAGE_GLOBALRANGE)
Ignored if '-ulay_range* ..' is set.
Note for '-mode_4D': this setting applies to the
resliced volume (i.e., the one made of one slice
of each subbrick). See "Combining %ile
values..." in NOTES, below.
-func_range FR :specify upper value FR of the olay dset to be
matched to top of colorbar (def: calc 98%ile non-zero
value of dset and use that).
-func_range_perc_nz FRP
:alternative to "-func_range ..."; specify a
percentile value FRP to use to make the upper
value of the olay dset to be matched to the top of
the colorbar (def: calc 98%ile non-zero value of dset
and use that). NB: this percentile range is always
among *non-zero* voxel values with this option; see
below.
-func_range_perc FRP :same as above option, but this is a percentile
among *all* voxel values, not just those with
non-zero values.
-func_resam RES :set the resampling mode for dsets; valid values
are: NN Li Cu Bk
(def: NN; hey, voxels are voxels).
(See DR: SET_FUNC_RESAM)
-thr_olay THR :threshold the olay dset at THR (def: 0, or
unthreshold). If you are thresholding a statistic
brick, then you should see the "-thr_olay_p2stat ..."
option, below. (See DR: SET_THRESHNEW)
-thrflag 'fff' :further control of how the THR value is interpreted
(def: "*"). (See DR: SET_THRESHNEW)
-thr_olay_p2stat PP :an alternative way to specify a voxelwise
threshold (i.e., instead of "-thr_olay ..."), when
thresholding based on a statistic; you can specify
the p-value you want, and using internal header
information, the appropriate value for whatever
statistic is in the statistic brick will be
calculated and applied; you likely need to use
"-set_subbricks i j k" with this, where 'k' would
be the index of the statistic brick (and likely
'j' would be the index of the associated
coefficient/beta brick; 'i' would be the brick of
the underlay volume, and if there is only a single
volume there, it could just be either '0' or
'-1'). And see next option '-thr_olay_pside', below.
-thr_olay_pside SS :(required if using '-thr_olay_p2stat ..') specify the
sidedness of the testing for the conversion of
p-to-stat. Valid values for SS at present include:
bisided
2sided
1sided
-cbar CCC :specify a new colorbar, where CCC can be any of the
cbars in the standard AFNI list (def: Plasma).
-pbar_posonly :for color range specification, default is to use
both positive and negative values; enter this flag
to use only the positive range. (See DR:
SET_PBAR_ALL)
-pbar_saveim PBS :if an olay is used, then you can save the color pbar
(=colorbar) that is used in plotting. PBS is the
name of the file (including path), with allowed
extensions jpg, png, or ppm.
When this option is used, a text file of the same
name as PBS but with extension 'txt' will also be
saved, containing three values: the bottom and top
values of the functional range (i.e., of the
colorbar), and the threshold value (if no thr is
specified, then it is 0). See also '-pbar_dim ..'
for relation pbar optioning. (See DR: PBAR_SAVEIM)
-pbar_dim PBD :if '-pbar_saveim ..' is used to save the color pbar
of the olay, then this option can specify the
orientation of the colorbar image and its pixel
dimensions. This is done by specifying the
'dimstring' part of the PBAR_SAVEIM input (see DR:
PBAR_SAVEIM). The default value is '64x512H',
which means to have a vertical cbar that is 64
pixels wide and 512 pixels tall which is then
tipped horizontally on its side; to leave it vertical
just don't put an 'H' at the end.
-cbar_ncolors NC :set colorscale mode (def: 99) (See DR:
SET_PBAR_ALL, the 2nd usage case, description
about '99').
-cbar_topval TOPV :set colorscale mode (def: 1) (See DR:
SET_PBAR_ALL, the 2nd usage case, description
about 'topval').
-opacity OO :enter an "opacity factor" for the olay, where OO is
an integer in the interval [0, 9], with the 9 being
opaque (see DR).
-blowup BB :enter a "blowup factor", where BB is an integer
in the interval [1, 8]. Increases spatial resolution
in the output by a factor of BB (see DR; def: 2).
-set_xhairs XX :specify type and/or existence of crosshairs in the
image (see DR: SET_XHAIRS).
-delta_slices DS DC DA :when montaging, (DS, DC, DA) is the integer
number of slices to use as spacing between views
along the (sag, cor, axi) axes, respectively
(def: automatically calculate to ~evenly fit the
number of selected montage slices along this
axis). (See DR: "mont=PxQ:R"; basically, each D?
is the 'R' value along the given axis). Users
can specify a delta_slice value along *some* axis
and leave other(s) to be chosen automatically, by
specifying a D? value >0 for their own value, and
given any other D? value -1. For example:
-delta_slices 40 -1 -1
would specify every 40th slice along the sag axis,
while the cor and axi spacing would be automatically
calculated.
-set_subbricks i j k :for 3D image viewing, specify subbricks being
viewed in the ulay, olay and threshold dsets (def:
"-1 -1 -1", which means ignore these values).
This is the way to specify different overlay and
threshold subbricks for displaying, such as using
the "beta" or "coefficient" for color and the
"statistic" as the threshold level. (See DR:
SET_SUBBRICKS)
-save_ftype FTYPE :type of file as which to save images; key types are
listed in the Driver description (def: PNG) (See
DR: SAVE_ALLJPEG, SAVE_ALLPNG, SAVE_MPEG,
SAVE_AGIF, SAVE_JPEG, SAVE_PNG; for which the user
would enter just the non-"SAVE_" part, just as
"PNG", "MPEG", etc.)
-set_ijk II JJ KK :Set the controller coordinates to the given
triple, which are integer index selectors along
the three spatial axes. This essentially
specifies the middle image in the montage (def:
for each coordinate, choose middle slice along
axis).
-set_dicom_xyz XX YY ZZ :Set the controller coordinates to the given
triple, which are the (x, y, z) coordinates in
AFNI's favorite RAI DICOM notation. (def: for
each coordinate, choose middle slice along axis).
-box_focus_slices REF :Use a dset REF to define a narrow range of
where slices cover. This is done by autoboxing the
REF dset (with '3dAutobox -noclust', so if it
hasn't been masked already, it's not useful), and
using the midpoint of the box's FOV as the new
center; also, the montage slices are chosen to be
evenly spread within the box FOV, though they
*still* show the unboxed dataset. This is
different than cropping (see '-crop*' below for
that); this is only to try to avoid showing empty
slices and such. If the ulay is a template dset,
you might make REF that template. Just for '3D'
dset viewing
NEW: enter a keyword for the argument REF,
instructing the program to make a focus box from
the ulay or olay: AMASK_FOCUS_ULAY or
AMASK_FOCUS_OLAY, respectively. Mask is just made
using default 3dAutomask (with '-clfrac 0.2', to
err on the side of inclusivity)-- may not be
perfect, but provide some useful focus while
hopefully not cutting off regions that should
still be included.
-montx MX :in creating a montage, the number of image panels in
a row, i.e., the number of columns (def: 3); the
total number of panels per axis is: MX*MY (see
below "-monty ..."). (See DR: "mont=PxQ:R";
basically, MX is the 'P' value).
-monty MY :in creating a montage, the number of image panels in
a column, i.e., the number of rows (def: 3); the
total number of panels per axis is: MX*MY (see
above "-montx ..."). (See DR: "mont=PxQ:R";
basically, MY is the 'Q' value).
-montgap MG :in creating a montage, one can put a border (or "gap")
between the image panels. This is specified as a
number of pixels with which to insert between images
(def: 0). (See DR: "mont=PxQ:R" additional option
":G:C"; basically, MG is the 'G' value).
-montcolor MC :in creating a montage, one can put a border (or "gap")
between the image panels (see "-montgap", above);
one can also specify a color for this gap, using
the present option (def: 'black'). (See DR:
"mont=PxQ:R" additional option ":G:C"; basically,
MC is the 'C' value).
-olay_alpha {Yes|No} :In addition to representing olay values as colors
with a threshold, one also apply opacity
information to 'soften' the effect of
thresholding; see DR: SET_FUNC_ALPHA for a
description of this behavior (def: "No", which is
just standard thresholding stuff).
-olay_boxed {Yes|No} :a partner parameter for the fancy alpha-based olay
viewing; put a box around supra-threshold
voxels/clusters. Default value is "No". (see DR:
SET_FUNC_BOXED)
-image_zoom_nn_no :the default zoom is set to NN mode, so no smoothing
occurs (see ENV: AFNI_IMAGE_ZOOM_NN). This option
changes behavior internally to set this variable
to have the value "NO".
-crop_axi_x CAX1 CAX2,
-crop_axi_y CAY1 CAY2 :crop axial image(s) to be between voxels CAX1 and
CAX2 along the x-axis (inclusive) and CAY1 and CAY2
along the y-axis. These values are integer row and
column numbers.
(See DR: "crop=x1:x2,y1:y2"; CAX1 is x1, etc.;
def: no cropping -- CAX1=0, CAX2=0, etc.)
-crop_sag_x CSX1 CSX2,
-crop_sag_y CSY1 CSY2 :same as other '-crop_*' above, but for sagittal
images.
-crop_cor_x CCX1 CCX2,
-crop_cor_y CCY1 CCY2 :same as other '-crop_*' above, but for coronal
images.
-zerocolor ZC :Change the default 'background' ulay color of zero
values (def: "Black"); ZC can be set to any allowed
AFNI value (see ENV: AFNI_IMAGE_ZEROCOLOR). This
option is mainly for G. Chen, who flaunts convention
whenever possible.
-label_mode LM :control labels, ON/OFF and location (def: 1);
(see ENV: AFNI_IMAGE_LABEL_MODE)
-label_size LS :control labels, size (def: 3);
(see ENV: AFNI_IMAGE_LABEL_SIZE)
-label_color LC :control labels, color (def: white);
(see ENV: AFNI_IMAGE_LABEL_COLOR)
-label_setback LB :control labels, offset from edge (def: 0.01);
(see ENV: AFNI_IMAGE_LABEL_SETBACK)
-label_string LSTR :control labels, string automatically appended
to the slice (def: "");
(see ENV: AFNI_IMAGE_LABEL_STRING)
-image_label_ijk :If this option is used, then the image label will
be based on the slice index rather than the
spatial (mm) coordinate; thanks, Bob.
(see ENV: AFNI_IMAGE_LABEL_IJK)
-pass :does nothing (no, really).
-do_clean :by default, the temporary directory of copying
files and such is not removed; using this option
means that that working directory *is* removed.
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