Usage:
ROI2dataset <-prefix dsetname> [...] <-input ROI1 ROI2 ...>
[<-of ni_bi|ni_as|1D>]
[<-dom_par_id idcode>]
This program transforms a series of ROI files
to a node dataset. This data set will contain
the node indices in the first column and their
ROI values in the second column.
Duplicate node entries (nodes that are part of
multiple ROIs) will get ignored. You will be
notified when this occurs.
Mandatory parameters:
-prefix dsetname: Prefix of output dataset.
Program will not overwrite existing
datasets.
See also -label_dset alternate below.
-keep_separate: Output one column (sub-brick) for each ROI value
and/or
-nodelist NL: Prefix for a set of .1D files
-nodelist.nodups NL: that contain a list of node indices
in the order in which they appear in
an ROI. This way you can make use of the
directionality of an ROI line instead of just
treating it as a set of nodes.
For each integer label 'i' in the ROI files provided
with the -input option, you will get a file called
NL.i.1D listing the nodes in the order they were
encountered in an ROI file and across ROI files.
If you want duplicate node entries removed, then
use -nodelist.nodups instead.
For example, say you traced an ROI that consisted of some
arbitrary curved path and you want to get the nodes
forming the path in the order traversed while drawing.
First save the path drawn, say to trace.niml.roi,
then use the following command:
ROI2dataset -nodelist.nodups TRACE \
-input trace.niml.roi
Note: You can use the output of -nodelist as input to
ConvertDset's -node_select_1D option.
This is not the case for -nodelist because
ConvertDset's -node_select_1D does not allow for
duplicate node entries.
-nodelist_with_ROIval: Also add the ROIval as a second column in .1D
files output by -nodelist.
-input ROI1 ROI2....: ROI files to turn into a
data set. This parameter MUST
be the last one on command line.
Optional parameters:
All optional parameters must be specified before the -input parameters.
-label_dset dsetname: Write a label dataset, instead of a simple dataset.
Labeled datasets are treated differently in SUMA.
This option also sets the output format to NIML.
Note: Using -keep_separate with this option is legal, but
makes little sense. You can't view more than one
sub-brick in SUMA for Labeled datasets.
-h | -help: This help message
-of FORMAT: Output format of dataset. FORMAT is one of:
ni_bi: NIML binary
ni_as: NIML ascii (default)
1D : 1D AFNI format.
-dom_par_id id: Idcode of domain parent.
When specified, only ROIs have the same
domain parent are included in the output.
If id is not specified then the first
domain parent encountered in the ROI list
is adopted as dom_par_id.
1D roi files do not have domain parent
information. They will be added to the
output data under the chosen dom_par_id.
-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
are not part of any ROI will get
a default label of 0 unless you
specify your own padding label.
*** You may also set MAX_INDEX to
d:DSET.niml.dset which sets MAX_INDEX
to match DSET.niml.dset
-pad_label padding_label: Use padding_label (an integer) to
label nodes that do not belong
to any ROI. Default is 0.
This padding value is also used in the multi-column
format of option -keep_separate.
Compile Date:
Oct 31 2024
