3dinfo¶
Prints out sort-of-useful information from a 3D dataset’s header
Usage: 3dinfo [-verb OR -short] dataset [dataset …]¶
-verb means to print out lots of stuff
-VERB means even more stuff [including slice time offsets]
-short means to print out less stuff [now the default]
-no_hist means to omit the HISTORY text
-h: Mini help, at time, same as -help in many cases.
-help: The entire help output
-HELP: Extreme help, same as -help in majority of cases.
-h_view: Open help in text editor. AFNI will try to find a GUI editor
-hview : on your machine. You can control which it should use by
setting environment variable AFNI_GUI_EDITOR.
-h_web: Open help in web browser. AFNI will try to find a browser.
-hweb : on your machine. You can control which it should use by
setting environment variable AFNI_GUI_EDITOR.
-h_find WORD: Look for lines in this programs's -help output that match
(approximately) WORD.
-h_raw: Help string unedited
-h_spx: Help string in sphinx loveliness, but do not try to autoformat
-h_aspx: Help string in sphinx with autoformatting of options, etc.
-all_opts: Try to identify all options for the program from the
output of its -help option. Some options might be missed
and others misidentified. Use this output for hints only.
Alternative Usage 1 (without either of the above options):¶
Output a large block of text per dataset. This has multiple options:
-label2index label dataset : output index corresponding to label¶
example: 3dinfo -label2index aud#0_Coef stats.FT+tlrc
Prints to stdout the index corresponding to the sub-brick with
the name label, or a blank line if label not found.
The ONLY output is this sub-brick index.
This is intended for used in a script, as in this tcsh fragment:
set face = `3dinfo -label2index Face#0 AA_Decon+orig`
set hous = `3dinfo -label2index House#0 AA_Decon+orig`
3dcalc -a AA_Decon+orig"[$face]" -b AA_Decon+orig"[$hous]" ...
* Added per the request and efforts of Colm Connolly.
-niml_hdr dataset : output entire NIML-formatted header¶
example: 3dinfo -niml_hdr stats.FT+tlrc
Prints to stdout the NIML-formatted equivalent of the .HEAD file.
-subbrick_info dataset : output only sub-brick part of info¶
example: 3dinfo -subbrick_info stats.FT+tlrc
Prints to stdout only the part of the full '3dinfo -VERB. output
that includes sub-brick info. The first such line might look like:
-- At sub-brick #0 'Full_Fstat' datum type is float: 0 to 971.2
Alternate Usage 2:¶
3dinfo <OPTION> [OPTION ..] dataset [dataset ...]
Outputs a specific piece of information depending on OPTION.
This can form a table of outputs per dataset.
Options producing one value (string)¶
-exists: 1 if dset is loadable, 0 otherwise
This works on prefix also.
-id: Idcodestring of dset
-is_labeltable: 1 if dset has a labeltable attached.
-is_atlas: 1 if dset is an atlas.
-is_atlas_or_labeltable: 1 if dset has an atlas or has a labeltable.
-is_nifti: 1 if dset is NIFTI format, 0 otherwise
-is_slice_timing_nz: is there slice timing, and is it not uniformly 0
-dset_extension: show filename extension for valid dataset (e.g. .nii.gz)
-storage_mode: show internal storage mode of dataset (e.g. NIFTI)
-space: dataset's space
-gen_space: datasets generic space
-av_space: AFNI format's view extension for the space
-nifti_code: what AFNI would use for an output NIFTI (q)sform_code
-is_oblique: 1 if dset is oblique
-handedness: L if orientation is Left handed, R if it is right handed
-obliquity: Angle from plumb direction.
Angles of 0 (or close) are for cardinal orientations
-prefix: Return the prefix
-prefix_noext: Return the prefix without extensions
-ni: Return the number of voxels in i dimension
-nj: Return the number of voxels in j dimension
-nk: Return the number of voxels in k dimension
-nijk: Return ni*nj*nk
-nv: Return number of points in time or the number of sub-bricks
-nt: same as -nv
-n3: same as -ni -nj -nk
-n4: same as -ni -nj -nk -nv
-nvi: The maximum sub-brick index (= nv -1 )
-nti: same as -nvi
-ntimes: Return number of sub-bricks points in time
This is an option for debugging use, stay away from it.
-max_node: For a surface-based dset, return the maximum node index
-di: Signed displacement per voxel along i direction, aka dx
-dj: Signed displacement per voxel along j direction, aka dy
-dk: Signed displacement per voxel along k direction, aka dz
-d3: same as -di -dj -dk
-adi: Voxel size along i direction (abs(di))
-adj: Voxel size along j direction (abs(dj))
-adk: Voxel size along k direction (abs(dk))
-ad3: same as -adi -adj -adk
-voxvol: Voxel volume in cubic millimeters
-oi: Volume origin along the i direction
-oj: Volume origin along the j direction
-ok: Volume origin along the k direction
-o3: same as -oi -oj -ok
-dcx: volumetric center in x direction (DICOM coordinates)
-dcy: volumetric center in y direction (DICOM coordinates)
-dcz: volumetric center in z direction (DICOM coordinates)
-dc3: same as -dcx -dcy -dcz
-tr: The TR value in seconds.
-dmin: The dataset's minimum value, scaled by fac
-dmax: The dataset's maximum value, scaled by fac
-dminus: The dataset's minimum value, unscaled.
-dmaxus: The dataset's maximum value, unscaled.
-smode: Dset storage mode string.
-header_name: Value of dset structure (sub)field 'header_name'
-brick_name: Value of dset structure (sub)field 'brick_name'
-iname: Name of dset as input on the command line
-orient: Value of orientation string.
For example, LPI means:
i direction grows from Left(negative) to Right(positive).
j direction grows from Posterior (neg.) to Anterior (pos.)
k direction grows from Inferior (neg.) to Superior (pos.)
-extent: The spatial extent of the dataset along R, L, A, P, I and S
-Rextent: Extent along R
-Lextent: Extent along L
-Aextent: Extent along P
-Pextent: Extent along P
-Iextent: Extent along I
-Sextent: Extent along S
-all_names: Value of various dset structures handling filenames.
Options producing one value per sub-brick¶
-fac: Return the float scaling factor
-label: The label of each sub-brick
-datum: The data storage type
-min: The minimum value, scaled by fac
-max: The maximum value, scaled by fac
-minus: The minimum value, unscaled.
-maxus: The maximum value, unscaled.
Options producing multiple values (strings of multiple lines)¶
You can specify the delimiter between sub-brick parameters with
-sb_delim DELIM. Default DELIM is "|"
-labeltable: Show label table, if any
-labeltable_as_atlas_points: Show label table in atlas point format.
-atlas_points: Show atlas points list, if any
-history: History note.
-slice_timing: Show slice timing.
Options affecting output format¶
-header_line: Output as the first line the names of attributes
in each field (column)
-hdr: Same as -header_line
-sb_delim SB_DELIM: Delimiter string between sub-brick values
Default SB_DELIM is "|"
-NA_flag NAFLAG: String to use when a field is not found or not
applicable. Default is "NA"
-atr_delim ATR_DELIM: Delimiter string between attributes
Default ATR_DELIM is the tab character.
Options for displaying ijk_to_xyz matrices¶
A set of functions for displaying the matrices that tell us where
the data actually is in space! These 4x4---well 3x4, in practice,
because the bottom row of the matrix *must* be (0, 0, 0, 1)---
can be related to the NIFTI sform and qform matrices (which are LPI
native), but these aform_* matrices are RAI (DICOM) native.
There are several types of matrices. Linear affine are the most general
(containing translation, rotation, shear and scaling info), followed by
orthogonal (no shear info; only translation, rotation and scale),
followed by cardinal (no rotation info; only translation and scale).
The 'scale' info is the voxel sizes. The 'translation' determines the
origin location in space. The 'rotation' describes a, well, rotation
relative to the scanner coords---this is the dreaded 'obliquity'. The
'shear'... well, that could also be present, but it is not common, at
least to describe just-acquired data: it would tilt the axes away from
being mutually 90 deg to each other (i.e., they wouldn't be
orthogonal); this would likely just result from an alignment process.
Note: the NIFTI sform can be linear affine, in general; in practice, it
is often just orthogonal. The NIFTI qform is a quaternion representation
of the orthogonalized sform; if sform is orthogonal, then they contain
the same information (common, but not required).
The aform_real matrix is AFNI's equivalent of the NIFTI sform; it *can*
encode general linear affine mappings. (In practice, it rarely does so.)
The aform_orth is the orthogonalized aform_real, and thus equivalent
to the NIFTI qform. If aform_real is orthogonal (no shear info), then
these two matrices are equal. The aform_card is the cardinalized form of
the aform_orth; NIFTI does not have an equivalent. AFNI typically uses
this matrix to display your data on a rectangle that is parallel to your
computer screen, without any need to regrid/resample the data (hence, no
blurring introduced). This can be though of displaying your dataset in
a way that you *wish* your subject had been oriented. Note that if
there is no obliquity in the acquired data (that is, aform_orth does not
contain any rotation relative to the scanner coords), then
aform_card == aform_orth.
The aform_card is an AFNI convenience (ha!) matrix, it does not have an
equivalent in the NIFTI stable of matrices.
-aform_real: Display full 3x4 'aform_real' matrix (AFNI's RAI equivalent
of the sform matrix in NIFTI, may contain obliquity info),
with comment line first.
-aform_real_oneline: Display full 'aform_real' matrix (see '-aform_real')
as 1 row of 12 numbers. No additional comment.
-aform_real_refit_ori XXX: Display full 3x4 'aform_real' matrix (see
'-aform_real')
*if* the dset were reoriented (via 3drefit) to
new orient XXX. Includes comment line first.
-is_aform_real_orth: if true, aform_real == aform_orth, which should be
a very common occurrence.
-aform_orth: Display full 3x4 'aform_orth' matrix (AFNI's RAI matrix
equivalent of the NIFTI quaternion, which may contain
obliquity info), with comment line first.
This matrix is the orthogonalized form of aform_real,
and veeery often AFNI-produced dsets, we will have:
aform_orth == aform_real.
-perm_to_orient YYY: Display 3x3 permutation matrix to go from the
dset's current orientation to the YYY orient.
Options requiring dataset pairing at input¶
3dinfo allows you to make some comparisons between dataset pairs.
The comparison is always done in both directions whether or not
the answer can be different. For example:
3dinfo -same_grid dset1 dset2
will output two values, one comparing dset1 to dset2 and the second
comparing dset2 to dset1. With -same_grid, the answers will always
be identical, but this might be different for other queries.
This behaviour allows you to mix options requiring dataset pairs
with those that do not. For example:
3dinfo -header_line -prefix -n4 -same_grid \
DSET1+orig DSET2.nii DSET3.nii DSET4.nii
-same_grid: Output 1 if the grid is identical between two dsets
0 otherwise.
For -same_grid to be 1, all of -same_dim, -same_delta,
-same_orient, -same_center, and -same_obl must return 1
-same_dim: 1 if dimensions (nx,ny,nz) are the same between dset pairs
-same_delta: 1 if voxels sizes are the same between dset pairs
-same_orient: 1 if orientation is the same between dset pairs
-same_center: 1 if geometric center is the same between dset pairs
-same_obl: 1 if obliquity is the same between dset pairs
-same_all_grid: Equivalent to listing all of -same_dim -same_delta
-same_orient, -same_center, and -same_obl on the
command line.
-val_diff: Output the sum of absolute differences of all voxels in the
dataset pair. A -1.0 value indicates a grid mismatch between
volume pairs.
-sval_diff: Same as -val_diff, but the sum is divided (scaled) by the
total number of voxels that are not zero in at least one
of the two datasets.
-monog_pairs: Instead of pairing each dset with the first, pair each
couple separately. This requires you to have an even
number of dsets on the command line
Examples with csh syntax using datasets in your afni binaries directory¶
0- First get some datasets with which we'll play
set dsets = ( `apsearch -list_all_afni_P_dsets` )
1- The classic
3dinfo $dsets[1]
2- Produce a table of results using 1-value-options for two datasets
3dinfo -echo_edu -prefix_noext -prefix -space -ni -nj -nk -nt \
$dsets[1-2]
3- Use some of the options that operate on pairs, mix with other options
3dinfo -echo_edu -header_line -prefix -n4 -same_grid $dsets[1-4]
++ Compile date = Oct 17 2024 {AFNI_24.3.03:linux_ubuntu_24_64}
