AFNI program: 3dAutobox
Output of -help
++ 3dAutobox: AFNI version=AFNI_24.3.10 (Dec 17 2024) [64-bit]
Usage: 3dAutobox [options] DATASET
Computes size of a box that fits around the volume.
Also can be used to crop the volume to that box.
The default 'info message'-based terminal text is a set of IJK coords.
See below for options to display coordinates in other ways, as well as
to save them in a text file. Please note in particular the difference
between *ijk* and *ijkord* outputs, for scripting.
OPTIONS: ~1~
-prefix PREFIX :Crop the input dataset to the size of the box, and
write an output dataset with PREFIX for the name.
*If -prefix is not used, no new volume is written out,
just the (x,y,z) extents of the voxels to be kept.
-input DATASET :An alternate way to specify the input dataset.
The default method is to pass DATASET as
the last parameter on the command line.
-noclust :Don't do any clustering to find box. Any non-zero
voxel will be preserved in the cropped volume.
The default method uses some clustering to find the
cropping box, and will clip off small isolated blobs.
-extent :Write to standard out the spatial extent of the box
-extent_xyz_quiet :The same numbers as '-extent', but only numbers and
no string content. Ordering is RLAPIS.
-extent_ijk :Write out the 6 auto bbox ijk slice numbers to
screen:
imin imax jmin jmax kmin kmax
Note that resampling would affect the ijk vals (but
not necessarily the xyz ones).
-extent_ijk_to_file FF
:Write out the 6 auto bbox ijk slice numbers to
a simple-formatted text file FF (single row file):
imin imax jmin jmax kmin kmax
(same notes as above apply).
-extent_ijk_midslice :Write out the 3 ijk midslices of the autobox to
the screen:
imid jmid kmid
These are obtained via: (imin + imax)/2, etc.
-extent_ijkord :Write out the 6 auto bbox ijk slice numbers to screen
but in a particular order and format (see 'NOTE on
*ijkord* format', below).
NB: This ordering is useful if you want to use
the output indices in 3dcalc expressions.
-extent_ijkord_to_file FFORRD
:Write out the 6 auto bbox ijk slice numbers to a file
but in a particular order and format (see 'NOTE on
*ijkord* format', below).
NB: This option is quite useful if you want to use
the output indices in 3dcalc expressions.
-extent_xyz_to_file GG
:Write out the 6 auto bbox xyz coords to
a simple-formatted text file GG (single row file):
xmin xmax ymin ymax zmin zmax
(same values as '-extent').
-extent_xyz_midslice :Write out the 3 xyz midslices of the autobox to
the screen:
xmid ymid zmid
These are obtained via: (xmin + xmax)/2, etc.
These follow the same meaning as '-extent'.
-npad NNN :Number of extra voxels to pad on each side of box,
since some troublesome people (that's you, LRF) want
this feature for no apparent reason.
** With this option, it is possible to get a dataset
thatis actually bigger than the input.
** You can input a negative value for NNN, which will
crop the dataset even more than the automatic method.
-npad_safety_on :Constrain npad-ded extents to be within dset. So,
each index is bounded to be in range [0, L-1], where L
is matrix length along that dimension.
NOTE on *ijkord* format ~1~
Using any of the '-*ijkord*' options above will output pairs of ijk
indices just like the regular ijk options, **but** they will be ordered
in a way that you can associate each of the i, j, and k indices with
a standard x, y and z coordinate direction. Without this ordering,
resampling a dataset could change what index is associated with which
coordinate axis. That situation can be confusing for scripting (and
by confusing, we mean 'bad').
The output format for any '-*ijkord*' options is a 3x3 table, where
the first column is the index value (i, j or k), and the next two
columns are the min and max interval boundaries for the autobox.
Importantly, the rows are placed in order so that the top corresponds
to the x-axis, the middle to the y-axis and the bottom to the z-axis.
So, if you had the following table output for a dset:
k 10 170
i 35 254
j 21 199
... you would look at the third row for the min/max slice values
along the z-axis, and you would use the index 'j' to refer to it in,
say, a 3dcalc expression.
Note that the above example table output came from a dataset with ASL
orientation. We can see how that fits, recalling that the first,
second and third rows tell us about x, y and z info, respectively; and
that i, j and k refer to the first, second and third characters in the
orientation string. So, the third (z-like) row contains a j, which
points us at the middle character in the orientation, which is S, which
is along the z-axis---all consistent! Similarly, the top (x-like) row
contains a k, which points us at the last char in the orientation,
which is L and that is along the x-axis---phew!
The main point of this would be to extra this information and use it
in a script. If you knew that you wanted the z-slice range to use
in a 3dcalc 'within()' expression, then you could extract the 3rd row
to get the correct index and slice ranges, e.g., in tcsh:
set vvv = `sed -n 3p FILE_ijkord.txt`
... where now ${vvv} will have 3 values, the first of which is the
relevant index letter, then the min and max slice range values.
So an example 3dcalc expression to keep values only within
that slice range:
3dcalc \
-a DSET \
-expr "a*within(${vvv[1]},${vvv[2]},${vvv[3]})" \
-prefix DSET_SUBSET
++ Compile date = Dec 17 2024 {AFNI_24.3.10:linux_ubuntu_24_64}
This page auto-generated on
Tue Dec 17 06:52:28 PM EST 2024