SurfLocalStat - compute local statistics on a surface
Local statistics are those computed over the neighborhood of
each node, possibly restricted to a mask.
Neighborhoods and distances are defined on a triangulated surface
mesh. They will differ between smoothwm and pial, for example.
The neighborhood of a given node is defined by nodes within a
specified distance of the given node (along the surface).
For each node's neighborhood, statistics are computed from data
values associated with those nodes, such as MRI intensities,
beta weights or ROI index values.
usage:.
-hood R = Neighborhood of node n consists of nodes within R
-nbhd_rad R = distance from n as measured by the shortest
distance along the mesh.
(-hood and -nbhd_rad are equivalent)
-prefix PREFIX = Prefix of output data set.
-stat sss = Compute the statistic named 'sss' on the values
extracted from the region around each voxel:
* mean = average of the values
* mode = most common value
* num = number of the values in the region:
with the use of -mask or -automask,
the size of the region around any given
voxel will vary; this option lets you
map that size. It may be useful if you
plan to compute a t-statistic (say) from
the mean and stdev outputs.
* FWHM = compute (like 3dFWHM) image smoothness
inside each voxel's neighborhood. Results
are in 3 sub-bricks: FWHMx, FHWMy, and FWHM.
Places where an output is -1 are locations
where the FWHM value could not be computed
(e.g., outside the mask).
* ALL = all of the above, in that order
More than one '-stat' option can be used.
------------------------------------------------------------
examples:
1. count the number of nodes in each node's local neighborhood
(the -input data will not matter in this case)
SurfLocalstat -hood 5 -stat num \
-i_gii std.141.lh.smoothwm.gii \
-input std.141.lh.thickness.niml.dset \
-prefix std.141.lh.local_nnode.niml.dset
2. smooth locally, output the mean over each neighbornood
SurfLocalstat -hood 5 -stat mean \
-i_gii std.141.lh.smoothwm.gii \
-input std.141.lh.thickness.niml.dset \
-prefix std.141.lh.local_mean_5.niml.dset
3. perform modal smoothing on a FreeSurfer parcellation dataset
- smooth in small neighborhoods of 'radius' 2mm
- use 3dRank to first convert to a more usable form (can improve)
- include suma commands to compare input vs output
3dRank -prefix std.141.lh.aparc.a2009s_RANK.niml.dset \
-input std.141.lh.aparc.a2009s.annot.niml.dset
SurfLocalstat -hood 2 -stat mode \
-i_gii std.141.lh.smoothwm.gii \
-input std.141.lh.aparc.a2009s_RANK.niml.dset \
-prefix std.141.lh.aparc.RANK_smooth_2.niml.dset
suma -spec std.141.FT_lh.spec -sv FT_SurfVol.nii \
-input std.141.lh.aparc.a2009s_RANK.niml.dset &
suma -spec std.141.FT_lh.spec -sv FT_SurfVol.nii \
-input std.141.lh.aparc.RANK_smooth_2.niml.dset &
------------------------------------------------------------
general and global options:
[-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.
------------------------------------------------------------
surface input/output 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 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
SUMA dataset input options:
-input DSET: Read DSET1 as input.
In programs accepting multiple input datasets
you can use -input DSET1 -input DSET2 or
input DSET1 DSET2 ...
NOTE: Selecting subsets of a dataset:
Much like in AFNI, you can select subsets of a dataset
by adding qualifiers to DSET.
Append #SEL# to select certain nodes.
Append [SEL] to select certain columns.
Append {SEL} to select certain rows.
The format of SEL is the same as in AFNI, see section:
'INPUT DATASET NAMES' in 3dcalc -help for details.
Append [i] to get the node index column from
a niml formatted dataset.
* SUMA does not preserve the selection order
for any of the selectors.
For example:
dset[44,10..20] is the same as dset[10..20,44]
Also, duplicate values are not supported.
so dset[13, 13] is the same as dset[13].
I am not proud of these limitations, someday I'll get
around to fixing them.
SUMA mask options:
-n_mask INDEXMASK: Apply operations to nodes listed in
INDEXMASK only. INDEXMASK is a 1D file.
-b_mask BINARYMASK: Similar to -n_mask, except that the BINARYMASK
1D file contains 1 for nodes to filter and
0 for nodes to be ignored.
The number of rows in filter_binary_mask must be
equal to the number of nodes forming the
surface.
-c_mask EXPR: Masking based on the result of EXPR.
Use like afni's -cmask options.
See explanation in 3dmaskdump -help
and examples in output of 3dVol2Surf -help
NOTE: Unless stated otherwise, if n_mask, b_mask and c_mask
are used simultaneously, the resultant mask is the intersection
(AND operation) of all masks.
SUMA communication options:
-talk_suma: Send progress with each iteration to SUMA.
-refresh_rate rps: Maximum number of updates to SUMA per second.
The default is the maximum speed.
-send_kth kth: Send the kth element to SUMA (default is 1).
This allows you to cut down on the number of elements
being sent to SUMA.
-sh <SumaHost>: Name (or IP address) of the computer running SUMA.
This parameter is optional, the default is 127.0.0.1
-ni_text: Use NI_TEXT_MODE for data transmission.
-ni_binary: Use NI_BINARY_MODE for data transmission.
(default is ni_binary).
-feed_afni: Send updates to AFNI via SUMA's talk.
-np PORT_OFFSET: Provide a port offset to allow multiple instances of
AFNI <--> SUMA, AFNI <--> 3dGroupIncorr, or any other
programs that communicate together to operate on the same
machine.
All ports are assigned numbers relative to PORT_OFFSET.
The same PORT_OFFSET value must be used on all programs
that are to talk together. PORT_OFFSET is an integer in
the inclusive range [1025 to 65500].
When you want to use multiple instances of communicating programs,
be sure the PORT_OFFSETS you use differ by about 50 or you may
still have port conflicts. A BETTER approach is to use -npb below.
-npq PORT_OFFSET: Like -np, but more quiet in the face of adversity.
-npb PORT_OFFSET_BLOC: Similar to -np, except it is easier to use.
PORT_OFFSET_BLOC is an integer between 0 and
MAX_BLOC. MAX_BLOC is around 4000 for now, but
it might decrease as we use up more ports in AFNI.
You should be safe for the next 10 years if you
stay under 2000.
Using this function reduces your chances of causing
port conflicts.
See also afni and suma options: -list_ports and -port_number for
information about port number assignments.
You can also provide a port offset with the environment variable
AFNI_PORT_OFFSET. Using -np overrides AFNI_PORT_OFFSET.
-max_port_bloc: Print the current value of MAX_BLOC and exit.
Remember this value can get smaller with future releases.
Stay under 2000.
-max_port_bloc_quiet: Spit MAX_BLOC value only and exit.
-num_assigned_ports: Print the number of assigned ports used by AFNI
then quit.
-num_assigned_ports_quiet: Do it quietly.
Port Handling Examples:
-----------------------
Say you want to run three instances of AFNI <--> SUMA.
For the first you just do:
suma -niml -spec ... -sv ... &
afni -niml &
Then for the second instance pick an offset bloc, say 1 and run
suma -niml -npb 1 -spec ... -sv ... &
afni -niml -npb 1 &
And for yet another instance:
suma -niml -npb 2 -spec ... -sv ... &
afni -niml -npb 2 &
etc.
Since you can launch many instances of communicating programs now,
you need to know wich SUMA window, say, is talking to which AFNI.
To sort this out, the titlebars now show the number of the bloc
of ports they are using. When the bloc is set either via
environment variables AFNI_PORT_OFFSET or AFNI_PORT_BLOC, or
with one of the -np* options, window title bars change from
[A] to [A#] with # being the resultant bloc number.
In the examples above, both AFNI and SUMA windows will show [A2]
when -npb is 2.
