Usage: A program to find the convex hull, or perform a delaunay triangulation
of a set of points.
This program is a wrapper for the qhull, and qdelaunay programs.
see copyright notice by running suma -sources.
ConvexHull
usage 1: < -input VOL >
< -isoval V | -isorange V0 V1 | -isocmask MASK_COM >
[<-xform XFORM>]
usage 2: < i_TYPE input surface >
[<-sv SURF_VOL>]
usage 3: < -input_1D XYZ >
[<-q_opt OPT>]
common optional:
[< -o_TYPE PREFIX>]
[< -debug DBG >]
Mandatory parameters, choose one of three usage modes:
Usage 1:
You must use one of the following two options:
-input VOL: Input AFNI (or AFNI readable) volume.
You must use one of the following iso* options:
-isoval V: Create isosurface where volume = V
-isorange V0 V1: Create isosurface where V0 <= volume < V1
-isocmask MASK_COM: Create isosurface where MASK_COM != 0
For example: -isocmask '-a VOL+orig -expr (1-bool(a-V))'
is equivalent to using -isoval V.
NOTE: -isorange and -isocmask are only allowed with -xform mask
See -xform below for details.
Usage 2:
-i_TYPE SURF: Use the nodes of a surface model
for input. See help for i_TYPE usage
below.
Usage 3:
-input_1D XYZ: Construct the triangulation of the points
contained in 1D file XYZ. If the file has
more than 3 columns, use AFNI's [] selectors
to specify the XYZ columns.
-q_opt OPT: Meshing option OPT can be one of.
convex_hull: For convex hull of points (default)
triangulate_xy: Delaunay triangulation using x y coords
These three options are only useful with -q_opt triangulate_xy
-proj_xy: Project points onto plane whose normal is the third principal
component. Then rotate projection so that plane in parallel to
Z = constant.
-orig_coord: Use original coordinates when writing surface, not
transformed ones.
-these_coords COORDS.1D: Use coordinates in COORDS.1D when
writing surface.
Optional Parameters:
Usage 1 only:
-xform XFORM: Transform to apply to volume values
before searching for sign change
boundary. XFORM can be one of:
mask: values that meet the iso* conditions
are set to 1. All other values are set
to -1. This is the default XFORM.
shift: subtract V from the dataset and then
search for 0 isosurface. This has the
effect of constructing the V isosurface
if your dataset has a continuum of values.
This option can only be used with -isoval V.
none: apply no transforms. This assumes that
your volume has a continuum of values
from negative to positive and that you
are seeking to 0 isosurface.
This option can only be used with -isoval 0.
Usage 2 only:
-sv SURF_VOL: Specify a surface volume which contains
a transform to apply to the surface node
coordinates prior to constructing the
convex hull.
All Usage:
-o_TYPE PREFIX: prefix of output surface.
where TYPE specifies the format of the surface
and PREFIX is, well, the prefix.
TYPE is one of: fs, 1d (or vec), sf, ply.
Default is: -o_ply
Specifying input surfaces using -i or -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
stl: STL format, ascii or binary.
This format of no use for much of the surface-based
analyses. Objects are defined as a soup of triangles
with no information about which edges they share. STL is only
useful for taking surface models to some 3D printing
software.
mni: MNI .obj format, ascii only.
Only vertex, triangulation, and node normals info is preserved.
byu: BYU format, ascii.
Polygons with more than 3 edges are turned into
triangles.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
gii: GIFTI XML surface format.
obj: OBJ file format for triangular meshes only. The following
primitives are preserved: v (vertices), f (faces, triangles
only), and p (points)
Note that if the surface filename has the proper extension,
it is enough to use the -i option and let the programs guess
the type from the extension.
You can also specify multiple surfaces after -i option. This makes
it possible to use wildcards on the command line for reading in a bunch
of surfaces at once.
-onestate: Make all -i_* surfaces have the same state, i.e.
they all appear at the same time in the viewer.
By default, each -i_* surface has its own state.
For -onestate to take effect, it must precede all -i
options with on the command line.
-anatomical: Label all -i surfaces as anatomically correct.
Again, this option should precede the -i_* options.
More variants for option -i:
-----------------------------
You can also load standard-mesh spheres that are formed in memory
with the following notation
-i ldNUM: Where NUM is the parameter controlling
the mesh density exactly as the parameter -ld linDepth
does in CreateIcosahedron. For example:
suma -i ld60
create on the fly a surface that is identical to the
one produced by: CreateIcosahedron -ld 60 -tosphere
-i rdNUM: Same as -i ldNUM but with NUM specifying the equivalent
of parameter -rd recDepth in CreateIcosahedron.
To keep the option confusing enough, you can also use -i to load
template surfaces. For example:
suma -i lh:MNI_N27:ld60:smoothwm
will load the left hemisphere smoothwm surface for template MNI_N27
at standard mesh density ld60.
The string following -i is formatted thusly:
HEMI:TEMPLATE:DENSITY:SURF where:
HEMI specifies a hemisphere. Choose from 'l', 'r', 'lh' or 'rh'.
You must specify a hemisphere with option -i because it is
supposed to load one surface at a time.
You can load multiple surfaces with -spec which also supports
these features.
TEMPLATE: Specify the template name. For now, choose from MNI_N27 if
you want to use the FreeSurfer reconstructed surfaces from
the MNI_N27 volume, or TT_N27
Those templates must be installed under this directory:
/home/afniHQ/.afni/data/
If you have no surface templates there, download
https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI_N27.tgz
and/or
https://afni.nimh.nih.gov/pub/dist/tgz/suma_TT_N27.tgz
and/or
https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI152_2009.tgz
and untar them under directory /home/afniHQ/.afni/data/
DENSITY: Use if you want to load standard-mesh versions of the template
surfaces. Note that only ld20, ld60, ld120, and ld141 are in
the current distributed templates. You can create other
densities if you wish with MapIcosahedron, but follow the
same naming convention to enable SUMA to find them.
SURF: Which surface do you want. The string matching is partial, as long
as the match is unique.
So for example something like: suma -i l:MNI_N27:ld60:smooth
is more than enough to get you the ld60 MNI_N27 left hemisphere
smoothwm surface.
The order in which you specify HEMI, TEMPLATE, DENSITY, and SURF, does
not matter.
For template surfaces, the -sv option is provided automatically, so you
can have SUMA talking to AFNI with something like:
suma -i l:MNI_N27:ld60:smooth &
afni -niml /home/afniHQ/.afni/data/suma_MNI_N27
Specifying a Surface Volume:
-sv SurfaceVolume [VolParam for sf surfaces]
If you supply a surface volume, the coordinates of the input surface.
are modified to SUMA's convention and aligned with SurfaceVolume.
You must also specify a VolParam file for SureFit surfaces.
Specifying output surfaces using -o or -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
stl: STL format, ascii or binary (see also STL under option -i_TYPE).
byu: BYU format, ascii or binary.
mni: MNI obj format, ascii only.
gii: GIFTI format, ascii.
You can also enforce the encoding of data arrays
by using gii_asc, gii_b64, or gii_b64gz for
ASCII, Base64, or Base64 Gzipped.
If AFNI_NIML_TEXT_DATA environment variable is set to YES, the
the default encoding is ASCII, otherwise it is Base64.
obj: No support for writing OBJ format exists yet.
Note that if the surface filename has the proper extension,
it is enough to use the -o option and let the programs guess
the type from the extension.
[-novolreg]: Ignore any Rotate, Volreg, Tagalign,
or WarpDrive transformations present in
the Surface Volume.
[-noxform]: Same as -novolreg
[-setenv "'ENVname=ENVvalue'"]: Set environment variable ENVname
to be ENVvalue. Quotes are necessary.
Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'"
See also options -update_env, -environment, etc
in the output of 'suma -help'
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
Global Options (available to all AFNI/SUMA programs)
-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.
Compile Date:
Oct 31 2024
