Usage: SurfaceMetrics <-Metric1> [[-Metric2] ...]
<-SURF_1>
[-tlrc] [<-prefix prefix>]
Outputs information about a surface's mesh
-Metric1: Replace -Metric1 with the following:
-vol: calculates the volume of a surface.
Volume unit is the cube of your surface's
coordinates unit, obviously.
Volume's sign depends on the orientation
of the surface's mesh.
Make sure your surface is a closed one
and that winding is consistent.
Use SurfQual to check the surface.
If your surface's mesh has problems,
the result is incorrect.
Volume is calculated using Gauss's theorem,
see [Hughes, S.W. et al. 'Application of a new
discrete form of Gauss's theorem for measuring
volume' in Phys. Med. Biol. 1996].
-conv: output surface convexity at each node.
Output file is prefix.conv. Results in two columns:
Col.0: Node Index
Col.1: Convexity
This is the measure used to shade sulci and gyri in SUMA.
C[i] = Sum(dj/dij) over all neighbors j of i
dj is the distance of neighboring node j to the tangent plane at i
dij is the length of the segment ij
Note: This option produces a .1D file, and a NIML dataset with
similar content.
-closest_node XYZ_LIST.1D: Find the closest node on the surface
to each XYZ triplet in XYZ_LIST.1D
Note that it is assumed that the XYZ
coordinates are in RAI (DICOM) per AFNI's
coordinate convention. For correspondence
with coordinates observed in SUMA and AFNI
be sure to use the proper -sv parameter for
the surface and XYZ coordinates in question.
Output file is prefix.closest.1D. Results in 8 columns:
Col.0: Index of closest node.
Col.1: Distance of closest node to XYZ reference point.
Col.2..4: XYZ of reference point (same as XYZ_LIST.1D, copied
here for clarity).
Col.5..7: XYZ of closest node (after proper surface coordinate
transformation, including SurfaceVolume transform.
-area: output area of each triangle.
Output file is prefix.area. Results in two columns:
Col.0: Triangle Index
Col.1: Triangle Area
-tri_sines/-tri_cosines: (co)sine of angles at nodes forming
triangles.
Output file is prefix.(co)sine. Results in 4 columns:
Col.0: Triangle Index
Col.1: (co)sine of angle at node 0
Col.2: (co)sine of angle at node 1
Col.3: (co)sine of angle at node 2
-tri_CoSines: Both cosines and sines.
-tri_angles: Unsigned angles in radians of triangles.
Col.0: Triangle Index
Col.1: angle at node 0
Col.2: angle at node 1
Col.3: angle at node 2
-node_angles: Unsigned angles in radians at nodes of surface.
Col.0: Node Index
Col.1: minimum angle at node
Col.2: maximum angle at node
Col.3: average angle at node
-curv: output curvature at each node.
Output file is prefix.curv. Results in nine columns:
Col.0: Node Index
Col.1-3: vector of 1st principal direction of surface
Col.4-6: vector of 2nd principal direction of surface
Col.7: Curvature along T1
Col.8: Curvature along T2
Col.9: Curvature magnitude sqrt(c7*c7+c8*c8)
Curvature algorithm by G. Taubin from:
'Estimating the tensor of curvature of surface
from a polyhedral approximation.'
Note: This option produces a .1D file, a NIML dataset with similar
content, and Displayable Objects (DO) file containing
the principal directions at each node. You can load these objects
with SUMA's 'Alt+Ctrl+s' option.
-edges: outputs info on each edge.
Output file is prefix.edges. Results in five columns:
Col.0: Edge Index (into a SUMA structure).
Col.1: Index of the first node forming the edge
Col.2: Index of the second node forming the edge
Col.3: Number of triangles containing edge
Col.4: Length of edge.
-node_normals: Outputs segments along node normals.
Segments begin at node and have a default
magnitude of 1. See option 'Alt+Ctrl+s' in
SUMA for visualization.
Note: This option produces a .1D file and a Displayable Objects
file containing the principal directions at each node.
You can load these objects with SUMA's 'Alt+Ctrl+s' option.
-face_normals: Outputs segments along triangle normals.
Segments begin at centroid of triangles and
have a default magnitude of 1. See option
'Alt+Ctrl+s' in SUMA for visualization.
-normals_scale SCALE: Scale the normals by SCALE (1.0 default)
For use with options -node_normals and -face_normals
-coords: Output coords of each node after any transformation
that is normally carried out by SUMA on such a surface.
Col. 0: Node Index
Col. 1: X
Col. 2: Y
Col. 3: Z
-sph_coords: Output spherical coords of each node.
-sph_coords_center x y z: Shift each node by x y z
before calculating spherical
coordinates. Default is the
center of the surface.
Both sph_coords options output the following:
Col. 0: Node Index
Col. 1: R (radius)
Col. 2: T (azimuth)
Col. 3: P (elevation)
-boundary_nodes: Output nodes that form a boundary of a surface
i.e. they form edges that belong to one and only
one triangle.
-boundary_triangles: Output triangles that form a boundary of a surface
i.e. they contain edges that belong to one and only
one triangle.
-internal_nodes: Output nodes that are not a boundary.
i.e. they form edges that belong to more than
one triangle.
You can use any or all of these metrics simultaneously.
(-SURF_1): An option for specifying the surface.
(For option's syntax, see 'Specifying input surfaces'
section below).
-sv SurfaceVolume [VolParam for sf surfaces]: Specify a surface volume
for surface alignment. See ConvertSurface -help for
more info.
-tlrc: Apply Talairach transform to surface.
See ConvertSurface -help for more info.
-prefix prefix: Use prefix for output files.
(default is prefix of inSurf)
-quiet: Quiet
Options for applying arbitrary affine transform:
[xyz_new] = [Mr] * [xyz_old - cen] + D + cen
-xmat_1D mat: Apply transformation specified in 1D file mat.1D.
to the surface's coordinates.
[mat] = [Mr][D] is of the form:
r11 r12 r13 D1
r21 r22 r23 D2
r31 r32 r33 D3
or
r11 r12 r13 D1 r21 r22 r23 D2 r31 r32 r33 D3
-ixmat_1D mat: Same as xmat_1D except that mat is replaced by inv(mat)
NOTE: For both -xmat_1D and -ixmat_1D, you can replace mat with
one of the special strings:
'RandShift', 'RandRigid', or 'RandAffine' which would create
a transform on the fly.
-seed SEED: Use SEED to seed the random number generator for random
matrix generation
-xcenter x y z: Use vector cen = [x y z]' for rotation center.
Default is cen = [0 0 0]'
-polar_decomp: Apply polar decomposition to mat and preserve
orthogonal component and shift only.
For more information, see cat_matvec's -P option.
This option can only be used in conjunction with
-xmat_1D
-h: Show most of the options
-help: Show all of the options
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 surfaces using -t* options:
-tn TYPE NAME: specify surface type and name.
See below for help on the parameters.
-tsn TYPE STATE NAME: specify surface type state and name.
TYPE: Choose from the following (case sensitive):
1D: 1D format
FS: FreeSurfer ascii format
PLY: ply format
MNI: MNI obj ascii format
BYU: byu format
SF: Caret/SureFit format
BV: BrainVoyager format
GII: GIFTI format
NAME: Name of surface file.
For SF and 1D formats, NAME is composed of two names
the coord file followed by the topo file
STATE: State of the surface.
Default is S1, S2.... for each surface.
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 a surface specification (spec) file:
-spec SPEC: specify the name of the SPEC file.
As with option -i, you can load template
spec files with symbolic notation trickery as in:
suma -spec MNI_N27
which will load the all the surfaces from template MNI_N27
at the original FreeSurfer mesh density.
The string following -spec is formatted in the following manner:
HEMI:TEMPLATE:DENSITY where:
HEMI specifies a hemisphere. Choose from 'l', 'r', 'lh', 'rh', 'lr', or
'both' which is the default if you do not specify a hemisphere.
TEMPLATE: Specify the template name. For now, choose from MNI_N27 if
you want surfaces from the MNI_N27 volume, or TT_N27
for the Talairach version.
Those templates must be installed under this directory:
/home/afniHQ/.afni/data/
If you have no surface templates there, download one of:
https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI_N27.tgz
https://afni.nimh.nih.gov/pub/dist/tgz/suma_TT_N27.tgz
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.
This parameter is optional.
The order in which you specify HEMI, TEMPLATE, and DENSITY, does
not matter.
For template surfaces, the -sv option is provided automatically, so you
can have SUMA talking to AFNI with something like:
suma -spec MNI_N27:ld60 &
afni -niml /home/afniHQ/.afni/data/suma_MNI_N27
Specifying a surface using -surf_? method:
-surf_A SURFACE: specify the name of the first
surface to load. If the program requires
or allows multiple surfaces, use -surf_B
... -surf_Z .
You need not use _A if only one surface is
expected.
SURFACE is the name of the surface as specified
in the SPEC file. The use of -surf_ option
requires the use of -spec option.
[-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
