3dSurf2Vol - map data from a surface domain to an AFNI volume domain
usage: 3dSurf2Vol [options] -spec SPEC_FILE -surf_A SURF_NAME \
-grid_parent AFNI_DSET -sv SURF_VOL \
-map_func MAP_FUNC -prefix OUTPUT_DSET
This program is meant to take as input a pair of surfaces,
optionally including surface data, and an AFNI grid parent
dataset, and to output a new AFNI dataset consisting of the
surface data mapped to the dataset grid space. The mapping
function determines how to map the surface values from many
nodes to a single voxel.
Surfaces (from the spec file) are specified using '-surf_A'
(and '-surf_B', if a second surface is input). If two
surfaces are input, then the computed segments over node
pairs will be in the direction from surface A to surface B.
The basic form of the algorithm is:
o for each node pair (or single node)
o form a segment based on the xyz node coordinates,
adjusted by any '-f_pX_XX' options
o divide the segment up into N steps, according to
the '-f_steps' option
o for each segment point
o if the point is outside the space of the output
dataset, skip it
o locate the voxel in the output dataset which
corresponds to this segment point
o if the '-cmask' option was given, and the voxel
is outside the implied mask, skip it
o if the '-f_index' option is by voxel, and this
voxel has already been considered, skip it
o insert the surface node value, according to the
user-specified '-map_func' option
Surface Coordinates:
Surface coordinates are assumed to be in the Dicom
orientation. This information may come from the option
pair of '-spec' and '-sv', with which the user provides
the name of the SPEC FILE and the SURFACE VOLUME, along
with '-surf_A' and optionally '-surf_B', used to specify
actual surfaces by name. Alternatively, the surface
coordinates may come from the '-surf_xyz_1D' option.
See these option descriptions below.
Note that the user must provide either the three options
'-spec', '-sv' and '-surf_A', or the single option,
'-surf_xyz_1D'.
Surface Data:
Surface domain data can be input via the '-sdata_1D'
or '-sdata' option. In such a case, the data is with
respect to the input surface.
Note: With -sdata_1D, the first column of the file
should contain a node's index, and following columns are
that node's data. See the '-sdata_1D' option for more info.
Option -sdata takes NIML or GIFTI input which contain
node index information in their headers.
If the surfaces have V values per node (pair), then the
resulting AFNI dataset will have V sub-bricks (unless the
user applies the '-data_expr' option).
Mapping Functions:
Mapping functions exist because a single volume voxel may
be occupied by multiple surface nodes or segment points.
Depending on how dense the surface mesh is, the number of
steps provided by the '-f_steps' option, and the indexing
type from '-f_index', even a voxel which is only 1 cubic
mm in volume may have quite a few contributing points.
The mapping function defines how multiple surface values
are combined to get a single result in each voxel. For
example, the 'max' function will take the maximum of all
surface values contributing to each given voxel.
Current mapping functions are listed under the '-map_func'
option, below.
------------------------------------------------------------
examples:
1. Map a single surface to an anatomical volume domain,
creating a simple mask of the surface. The output
dataset will be fred_surf+orig, and the orientation and
grid spacing will follow that of the grid parent. The
output voxels will be 1 where the surface exists, and 0
elsewhere.
3dSurf2Vol \
-spec fred.spec \
-surf_A pial \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-map_func mask \
-prefix fred_surf
2. Map the cortical grey ribbon (between the white matter
surface and the pial surface) to an AFNI volume, where
the resulting volume is restricted to the mask implied by
the -cmask option.
Surface data will come from the file sdata_10.1D, which
has 10 values per node, and lists only a portion of the
entire set of surface nodes. Each node pair will be form
a segment of 15 equally spaced points, the values from
which will be applied to the output dataset according to
the 'ave' filter. Since the index is over points, each
of the 15 points will have its value applied to the
appropriate voxel, even multiple times. This weights the
resulting average by the fraction of each segment that
occupies a given voxel.
The output dataset will have 10 sub-bricks, according to
the 10 values per node index in sdata_10.1D.
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-sdata_1D sdata_10.1D \
-map_func ave \
-f_steps 15 \
-f_index points \
-prefix fred_surf_ave
3. The inputs in this example are identical to those in
example 2, including the surface dataset, sdata_10.1D.
Again, the output dataset will have 10 sub-bricks.
The surface values will be applied via the 'max_abs'
filter, with the intention of assigning to each voxel the
node value with the most significance. Here, the index
method does not matter, so it is left as the default,
'voxel'.
In this example, each node pair segment will be extended
by 20% into the white matter, and by 10% outside of the
grey matter, generating a "thicker" result.
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-sdata_1D sdata_10.1D \
-map_func max_abs \
-f_steps 15 \
-f_p1_fr -0.2 \
-f_pn_fr 0.1 \
-prefix fred_surf_max_abs
4. This is similar to example 2. Here, the surface nodes
(coordinates) come from 'surf_coords_2.1D'. But these
coordinates do not happen to be in Dicom orientation,
they are in the same orientation as the grid parent, so
the '-sxyz_orient_as_gpar' option is applied.
Even though the data comes from 'sdata_10.1D', the output
AFNI dataset will only have 1 sub-brick. That is because
of the '-data_expr' option. Here, each applied surface
value will be the average of the sines of the first 3
data values (columns of sdata_10.1D).
3dSurf2Vol \
-surf_xyz_1D surf_coords_2.1D \
-sxyz_orient_as_gpar \
-grid_parent 'fred_func+orig[0]' \
-sdata_1D sdata_10.1D \
-data_expr '(sin(a)+sin(b)+sin(c))/3' \
-map_func ave \
-f_steps 15 \
-f_index points \
-prefix fred_surf_ave_sine
5. In this example, voxels will get the maximum value from
column 3 of sdata_10.1D (as usual, column 0 is used for
node indices). The output dataset will have 1 sub-brick.
Here, the output dataset is forced to be of type 'short',
regardless of what the grid parent is. Also, there will
be no scaling factor applied.
To track the numbers for surface node #1234, the '-dnode'
option has been used, along with '-debug'. Additionally,
'-dvoxel' is used to track the results for voxel #6789.
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-sdata_1D sdata_10.1D'[0,3]' \
-map_func max \
-f_steps 15 \
-datum short \
-noscale \
-debug 2 \
-dnode 1234 \
-dvoxel 6789 \
-prefix fred_surf_max
6. Draw some surface ROIs, and map them to the volume. Some
voxels may contain nodes from multiple ROIs, so take the
most common one (the mode), as suggested by R Mruczek.
ROIs are left in 1D format for the -sdata_1D option.
setenv AFNI_NIML_TEXT_DATA YES
ROI2dataset -prefix rois.1D.dset -input rois.niml.roi
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-sdata_1D rois.1D.dset \
-map_func mode \
-f_steps 10 \
-prefix rois.from.surf
------------------------------------------------------------
REQUIRED COMMAND ARGUMENTS:
-spec SPEC_FILE : SUMA spec file
e.g. -spec fred.spec
The surface specification file contains the list of
mappable surfaces that are used.
See @SUMA_Make_Spec_FS and @SUMA_Make_Spec_SF.
Note: this option, along with '-sv', may be replaced
by the '-surf_xyz_1D' option.
-surf_A SURF_NAME : specify surface A (from spec file)
-surf_B SURF_NAME : specify surface B (from spec file)
e.g. -surf_A smoothwm
e.g. -surf_A lh.smoothwm
e.g. -surf_B lh.pial
This parameter is used to tell the program with surfaces
to use. The '-surf_A' parameter is required, but the
'-surf_B' parameter is an option.
The surface names must uniquely match those in the spec
file, though a sub-string match is good enough. The
surface names are compared with the names of the surface
node coordinate files.
For instance, given a spec file that has only the left
hemisphere in it, 'pial' should produce a unique match
with lh.pial.asc. But if both hemispheres are included,
then 'pial' would not be unique (matching rh.pial.asc,
also). In that case, 'lh.pial' would be better.
-sv SURFACE_VOLUME : AFNI dataset
e.g. -sv fred_anat+orig
This is the AFNI dataset that the surface is mapped to.
This dataset is used for the initial surface node to xyz
coordinate mapping, in the Dicom orientation.
Note: this option, along with '-spec', may be replaced
by the '-surf_xyz_1D' option.
-surf_xyz_1D SXYZ_NODE_FILE : 1D coordinate file
e.g. -surf_xyz_1D my_surf_coords.1D
This ascii file contains a list of xyz coordinates to be
considered as a surface, or 2 sets of xyz coordinates to
considered as a surface pair. As usual, these points
are assumed to be in Dicom orientation. Another option
for coordinate orientation is to use that of the grid
parent dataset. See '-sxyz_orient_as_gpar' for details.
This option is an alternative to the pair of options,
'-spec' and '-sv'.
The number of rows of the file should equal the number
of nodes on each surface. The number of columns should
be either 3 for a single surface, or 6 for two surfaces.
sample line of an input file (one surface):
11.970287 2.850751 90.896111
sample line of an input file (two surfaces):
11.97 2.85 90.90 12.97 2.63 91.45
-grid_parent AFNI_DSET : AFNI dataset
e.g. -grid_parent fred_function+orig
This dataset is used as a grid and orientation master
for the output AFNI dataset.
-map_func MAP_FUNC : surface to dataset function
e.g. -map_func max
e.g. -map_func mask -f_steps 20
This function applies to the case where multiple data
points get mapped to a single voxel, which is expected
since surfaces tend to have a much higher resolution
than AFNI volumes. In the general case data points come
from each point on each partitioned line segment, with
one segment per node pair. Note that these segments may
have length zero, such as when only a single surface is
input.
See "Mapping Functions" above, for more information.
The current mapping function for one surface is:
mask : For each xyz location, set the corresponding
voxel to 1.
The current mapping functions for two surfaces are as
follows. These descriptions are per output voxel, and
over the values of all points mapped to a given voxel.
mask2 : if any points are mapped to the voxel, set
the voxel value to 1
ave : average all values
nzave : ave, but ignoring any zero values
count : count the number of mapped data points
min : find the minimum value from all mapped points
max : find the maximum value from all mapped points
max_abs: find the number with maximum absolute value
(the resulting value will retain its sign)
median : median of all mapped values
nzmedian: median, but ignoring any zero values
mode : apply the most common value per voxel
(minimum mode, if they are not unique)
(appropriate where surf ROIs overlap)
nzmode : mode, but ignoring any zero values
-prefix OUTPUT_PREFIX : prefix for the output dataset
e.g. -prefix anat_surf_mask
This is used to specify the prefix of the resulting AFNI
dataset.
------------------------------
SUB-SURFACE DATA FILE OPTIONS:
-sdata_1D SURF_DATA.1D : 1D sub-surface file, with data
e.g. -sdata_1D roi3.1D
This is used to specify a 1D file, which contains
surface indices and data. The indices refer to the
surface(s) read from the spec file.
The format of this data file is a surface index and a
list of data values on each row. To be a valid 1D file,
each row must have the same number of columns.
-sdata SURF_DATA_DSET: NIML, or GIFTI formatted dataset.
------------------------------
OPTIONS SPECIFIC TO SEGMENT SELECTION:
(see "The basic form of the algorithm" for more details)
-f_steps NUM_STEPS : partition segments
e.g. -f_steps 10
default: -f_steps 2 (or 1, the number of surfaces)
This option specifies the number of points to divide
each line segment into, before mapping the points to the
AFNI volume domain. The default is the number of input
surfaces (usually, 2). The default operation is to have
the segment endpoints be the actual surface nodes,
unless they are altered with the -f_pX_XX options.
-f_index TYPE : index by points or voxels
e.g. -f_index points
e.g. -f_index voxels
default: -f_index voxels
Along a single segment, the default operation is to
apply only those points mapping to a new voxel. The
effect of the default is that a given voxel will have
at most one value applied per voxel pair.
If the user applies this option with 'points' or 'nodes'
as the argument, then every point along the segment will
be applied. This may be preferred if, for example, the
user wishes to have the average weighted by the number
of points occupying a voxel, not just the number of node
pair segments.
Note: the following -f_pX_XX options are used to alter the
locations of the segment endpoints, per node pair.
The segments are directed, from the node on the first
surface to the node on the second surface. To modify
the first endpoint, use a -f_p1_XX option, and use
-f_pn_XX to modify the second.
-f_p1_fr FRACTION : offset p1 by a length fraction
e.g. -f_p1_fr -0.2
e.g. -f_p1_fr -0.2 -f_pn_fr 0.2
This option moves the first endpoint, p1, by a distance
of the FRACTION times the original segment length. If
the FRACTION is positive, it moves in the direction of
the second endpoint, pn.
In the example, p1 is moved by 20% away from pn, which
will increase the length of each segment.
-f_pn_fr FRACTION : offset pn by a length fraction
e.g. -f_pn_fr 0.2
e.g. -f_p1_fr -0.2 -f_pn_fr 0.2
This option moves pn by a distance of the FRACTION times
the original segment length, in the direction from p1 to
pn. So a positive fraction extends the segment, and a
negative fraction reduces it.
In the example above, using 0.2 adds 20% to the segment
length past the original pn.
-f_p1_mm DISTANCE : offset p1 by a distance in mm.
e.g. -f_p1_mm -1.0
e.g. -f_p1_mm -1.0 -f_pn_fr 1.0
This option moves p1 by DISTANCE mm., in the direction
of pn. If the DISTANCE is positive, the segment gets
shorter. If DISTANCE is negative, the segment will get
longer.
In the example, p1 is moved away from pn, extending the
segment by 1 millimeter.
-f_pn_mm DISTANCE : offset pn by a distance in mm.
e.g. -f_pn_mm 1.0
e.g. -f_p1_mm -1.0 -f_pn_fr 1.0
This option moves pn by DISTANCE mm., in the direction
from the first point to the second. So if DISTANCE is
positive, the segment will get longer. If DISTANCE is
negative, the segment will get shorter.
In the example, pn is moved 1 millimeter farther from
p1, extending the segment by that distance.
-stop_gap : stop when a zero gap has been hit
This limits segment processing such that once a non-zero
mask value has been encountered, the segment will be
terminated on any subsequent zero mask value.
The goal is to prevent mixing masked cortex regions.
------------------------------
GENERAL OPTIONS:
-cmask MASK_COMMAND : command for dataset mask
e.g. -cmask '-a fred_func+orig[2] -expr step(a-0.8)'
This option will produce a mask to be applied to the
output dataset. Note that this mask should form a
single sub-brick.
This option follows the style of 3dmaskdump (since the
code for it was, uh, borrowed from there (thanks Bob!)).
See '3dmaskdump -help' for more information.
-data_expr EXPRESSION : apply expression to surface input
e.g. -data_expr 17
e.g. -data_expr '(a+b+c+d)/4'
e.g. -data_expr '(sin(a)+sin(b))/2'
This expression is applied to the list of data values
from the surface data file input via '-sdata_1D'. The
expression is applied for each node or node pair, to the
list of data values corresponding to that node.
The letters 'a' through 'z' may be used as input, and
refer to columns 1 through 26 of the data file (where
column 0 is a surface node index). The data file must
have enough columns to support the expression. It is
valid to have a constant expression without a data file.
-datum DTYPE : set data type in output dataset
e.g. -datum short
default: based on the map function
(was grid_parent, but that made little sense)
This option specifies the data type for the output data
volume. Valid choices are byte, short and float, which
are 1, 2 and 4 bytes for each data point, respectively.
The default is based on the map function, generally
implying float, unless using mask or mask2 (byte), or
count or mode (short).
-debug LEVEL : verbose output
e.g. -debug 2
This option is used to print out status information
during the execution of the program. Current levels are
from 0 to 5.
-dnode DEBUG_NODE : extra output for that node
e.g. -dnode 123456
This option requests additional debug output for the
given surface node. This index is with respect to the
input surface (included in the spec file, or through the
'-surf_xyz_1D' option).
This will have no effect without the '-debug' option.
-dvoxel DEBUG_VOXEL : extra output for that voxel
e.g. -dvoxel 234567
This option requests additional debug output for the
given volume voxel. This 1-D index is with respect to
the output data volume. One good way to find a voxel
index to supply is from output via the '-dnode' option.
This will have no effect without the '-debug' option.
-hist : show revision history
Display module history over time.
-help : show this help
If you can't get help here, please get help somewhere.
-noscale : no scale factor in output dataset
If the output dataset is an integer type (byte, shorts
or ints), then the output dataset may end up with a
scale factor attached (see 3dcalc -help). With this
option, the output dataset will not be scaled.
-sxyz_orient_as_gpar : assume gpar orientation for sxyz
This option specifies that the surface coordinate points
in the '-surf_xyz_1D' option file have the orientation
of the grid parent dataset.
When the '-surf_xyz_1D' option is applied the surface
coordinates are assumed to be in Dicom orientation, by
default. This '-sxyz_orient_as_gpar' option overrides
the Dicom default, specifying that the node coordinates
are in the same orientation as the grid parent dataset.
See the '-surf_xyz_1D' option for more information.
-version : show version information
Show version and compile date.
------------------------------------------------------------
Author: R. Reynolds - version 3.10 (June 22, 2021)
(many thanks to Z. Saad and R.W. Cox)
