Usage:
ConvertDset -o_TYPE -input DSET [-i_TYPE] [-prefix OUT_PREF]
Converts a surface dataset from one format to another.
Mandatory parameters:
-o_TYPE: TYPE of output datasets
where TYPE is one of:
niml_asc (or niml): for ASCII niml format.
niml_bi: for BINARY niml format.
1D: for AFNI's 1D ascii format.
1Dp: like 1D but with no comments
or other 1D formatting gimmicks.
1Dpt: like 1Dp but transpose the output.
gii: GIFTI format default .
gii_asc: GIFTI format with ascii DataArrays.
gii_b64: GIFTI format with Base 64 encoded DataArrays.
gii_b64gz: GIFTI format with B64 encoding and gzipping.
For stderr and stdout output use one of:
1D_stderr, 1D_stdout, niml_stderr, or niml_stdout,
1Dp_stdout, 1Dp_stderr, 1Dpt_stdout, 1Dpt_stderr
Actually, this parameter is not that mandatory, the program
can look at extensions on the prefix to guess the output
format. If the prefix has no extension and o_TYPE is not
specified, then the output format is the same as that of the
input.
-input DSET: Input dataset to be converted.
See more on input datasets below.
-dset_labels 'SB_LABEL_0 SB_LABEL_1 ...'
Label the columns (sub-bricks) of the output dataset
You must have as many labels as you have sub-bricks in
the output dataset. Optional parameters:
-add_node_index: Add a node index element if one does not exist
in the input dset. With this option, the indexing
is assumed to be implicit (0,1,2,3.... for rows 0,1
2,3,...). If that is not the case, use -node_index_1D
option below.
** NOTE: It is highly recommended you use one of -node_index_1D
or -add_node_index when going from 1D format to NIML
GIFTI formats.
-node_index_1D INDEX.1D: Specify file containing node indices
Use this to provide node indices with
a .1D dset. In many cases for .1D data
this option is DSET.1D'[0]'
-node_select_1D MASK.1D: Specify the nodes you want to keep in the
output.
The order of the rows in the output dataset
reflects the order of the nodes in MASK.1D.
Note that the presence of duplicate nodes in
MASK.1D is not allowed, so if MASK.1D came
from ROI2dataset's -nodelist, recreate it with
option -nodelist.nodups instead.
Also, node indices that do not have data in the
input dataset will be ignored.
When in doubt, use the 1D output format along
with -prepend_node_index_1D and spot check your
results.
-prepend_node_index_1D: Add a node index column to the data, rather
than keep it as part of the metadata.
-pad_to_node MAX_INDEX: Output a full dset from node 0
to node MAX_INDEX (a total of
MAX_INDEX + 1 nodes). Nodes that
get no value from input DSET are
assigned a value of 0
If MAX_INDEX is set to 0 it means you want
to pad the maximum node in the input dataset.
** Notice that padding gets done at the very end.
** Instead of directly setting MAX_INDEX to an integer you
can set MAX_INDEX to something like:
ld120 (or rd17) which sets MAX_INDEX to be the maximum
node index on an Icosahedron with -ld 120. See
CreateIcosahedron for details.
d:DSET.niml.dset which sets MAX_INDEX to the maximum node found
in dataset DSET.niml.dset.
-labelize CMAP: Turn the dataset into a labeled set per the colormap in
CMAP. A CMAP can easily be generated with MakeColorMap's
options -usercolorlutfile and -suma_cmap.
-graphize: Turn the dataset into a SUMA graph dataset.
See input format constraints under -onegraph and -multigraph
-graph_nodelist_1D NODEINDLIST.1D NODELIST.1D: Two files specifying the
indices and the coordinates of the graph's
nodes. In sum you need I X Y Z (RAI mm).
but the I comes from NODEINDLIST.1D and the
X Y Z coordinates from NODELIST.1D
If you have everything in one file, use
the same filename twice with proper column
selectors.
-graph_full_nodelist_1D NODELIST.1D: Same as above, but without the need
for NODEINDLIST.1D. In that case, indices
will implicitly go from 0 to N-1, with N
being the number of nodes.
-graph_named_nodelist_txt NODENAMES.txt NODELIST.1D: Two files used to
specify graph node indices, string labels,
and their coordinates.
In sum you need I LABEL X Y Z (RAI mm).
The I and LABEL come from NODENAMES.txt and
the X Y Z coordinates from NODELIST.1D
Also, you can assign to each graph node a group ID
and nodes with the same group ID can be
displayed with the same color in SUMA.
To do so, add a third column to
NODENAMES.txt so that you have: I LABEL GID
with GID being the integer group ID.
Color selection for the different group IDs
is done automatically with ConvertDset, but
you can set your own by appending three
more columns to NODENAMES.txt to have:
I LABEL GID R G B
with R, G, and B values between 0 and 1.0
-graph_XYZ_LPI: Coords in NodeList.1D are in LPI instead of RAI
-graph_edgelist_1D EDGELIST.1D: i j indices of graph nodes defining edge
with each row matching the input dset row.
This option only works with -multigraph
This option also marks the graph as being
a sparse matrix, even if a square matrix
is provided.
-onegraph: Expect input dataset to be one square matrix defining the
graph (default).
-multigraph: Expect each column in input dataset to define an entire
graph. Each column in this case should be a column-stacked
square matrix.
-i_TYPE: TYPE of input datasets
where TYPE is one of:
niml: for niml data sets.
1D: for AFNI's 1D ascii format.
dx: OpenDX format, expects to work on 1st
object only.
If no format is specified, the program will
guess using the extension first and the file
content next. However the latter operation might
slow operations down considerably.
-prefix OUT_PREF: Output prefix for data set.
Default is something based
on the input prefix.
-split N: Split a multi-column dataset into about N output datasets
with all having the same number of columns, except perhaps
for the last one. Confused? try:
ConvertDset -i v2s.lh.TS.niml.dset -split 3 \
-prefix Split3
3dinfo -n4 -label Split3.000* v2s.lh.TS.niml.dset\
-no_history: Do not include a history element in the output
Notes:
-This program will not overwrite pre-existing files.
-The new data set is given a new idcode.
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.
[-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.
Examples:
1- Plot a node's time series from a niml dataset:
ConvertDset -input DemoSubj_EccCntavir.niml.dset'#5779#' \
-o_1D_stdout | 1dplot -nopush -stdin
2- Change a dataset to a labeled dataset using the colormap generated
in Example 5 of MakeColorMap's help
ConvertDset -i you_look_marvellous.niml.dset \
-o you_look_labeled.niml.dset -labelize toylut.niml.cmap
The advantage of having a labeled dataset is that you can see the label
of a node when you click on it in SUMA, and you can extract
regions based on their labels. For example, with the dataset created
above you can run the following command to extract a mask of the
nodes labeled 'Small_Face' with something like:
3dcalc -a you_look_labeled.niml.dset'<Small_Face>' \
-expr 'a' -prefix Small_Face.only
This assumes of course that your colormap toylut.niml.cmap does have
an entry labeled 'Small_Face'
Compile Date:
Oct 17 2024
Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov
