Usage: SurfToSurf <-i_TYPE S1> [<-sv SV1>]
<-i_TYPE S2> [<-sv SV1>]
[<-prefix PREFIX>]
[<-output_params PARAM_LIST>]
[<-node_indices NODE_INDICES>]
[<-proj_dir PROJ_DIR>]
[<-data DATA>]
[<-node_debug NODE>]
[<-debug DBG_LEVEL>]
[-make_consistent]
[<-dset DSET>]
[<-mapfile MAP_INFO>]
This program is used to interpolate data from one surface (S2)
to another (S1), assuming the surfaces are quite similar in
shape but having different meshes (non-isotopic).
This is done by projecting each node (nj) of S1 along the normal
at nj and finding the closest triangle t of S2 that is intersected
by this projection. Projection is actually bidirectional.
If such a triangle t is found, the nodes (of S2) forming it are
considered to be the neighbors of nj.
Values (arbitrary data, or coordinates) at these neighboring nodes
are then transferred to nj using barycentric interpolation or
nearest-node interpolation.
Nodes whose projections fail to intersect triangles in S2 are given
nonsensical values of -1 and 0.0 in the output.
Mandatory input:
Two surfaces are required at input. See -i_TYPE options
below for more information.
Optional input:
-prefix PREFIX: Specify the prefix of the output file.
The output file is in 1D format at the moment.
Default is SurfToSurf
-output_params PARAM_LIST: Specify the list of mapping
parameters to include in output
PARAM_LIST can have any or all of the following:
NearestTriangleNodes: Use Barycentric interpolation (default)
and output indices of 3 nodes from S2
that neighbor nj of S1
NearestNode: Use only the closest node from S2 (of the three
closest neighbors) to nj of S1 for interpolation
and output the index of that closest node.
NearestTriangle: Output index of triangle t from S2 that
is the closest to nj along its projection
direction.
DistanceToSurf: Output distance (signed) from nj, along
projection direction to S2.
This is the parameter output by the precursor
program CompareSurfaces
ProjectionOnSurf: Output coordinates of projection of nj onto
triangle t of S2.
NearestNodeCoords: X Y Z coordinates of closest node on S2
Data: Output the data from S2, interpolated onto S1
If no data is specified via the -data option, then
the XYZ coordinates of SO2's nodes are considered
the data.
-data DATA: 1D file containing data to be interpolated.
Each row i contains data for node i of S2.
You must have one row for each node making up S2.
In other terms, if S2 has N nodes, you need N rows
in DATA.
Each column of DATA is processed separately (think
sub-bricks, and spatial interpolation).
You can use [] selectors to choose a subset
of columns.
If -data option is not specified and Data is in PARAM_LIST
then the XYZ coordinates of SO2's nodes are the data.
-dset DSET: Treat like -data, but works best with datasets, preserving
header information in the output.
-dset and -data are mutually exclusive.
Also, -dset and parameter Data cannot be mixed.
-node_indices NODE_INDICES: 1D file containing the indices of S1
to consider. The default is all of the
nodes in S1. Only one column of values is
allowed here, use [] selectors to choose
the column of node indices if NODE_INDICES
has multiple columns in it.
-proj_dir PROJ_DIR: 1D file containing projection directions to use
instead of the node normals of S1.
Each row should contain one direction for each
of the nodes forming S1.
-closest_possible OO: Flag allowing the substitution of the projection
result with the closest node that could be found
along any direction.
0: Don't do that, direction results only.
1: Use closest node if projection fails to hit target
2: Use closest node if it is at a closer distance.
3: Use closest and don't bother with projections.
-make_consistent: Force a consistency check and correct triangle
orientation of S1 if needed. Triangles are also
oriented such that the majority of normals point
away from center of surface.
The program might not succeed in repairing some
meshes with inconsistent orientation.
-mapfile MAP_INFO: Use the mapping from S2 to S1 that is stored in
MAP_INFO. MAP_INFO is a file containing the mapping
parameters between surfaces S2 and S1.
It is generated automatically by SurfToSurf when
-mapfile is not used, and saved under PREFIX.niml.M2M.
Reusing the MAP_INFO file allows for faster execution
of SurfToSurf the next time around, assuming of course
that the two surfaces involved are the same, and that
only the input data differs.
MAP_INFO is also generated by MapIcosahedron.
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.
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 17 2024
Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov
