AFNI program: @MakeLabelTable
Output of -help
Script used to create a label table
Usage: @MakeLabelTable <-labeltable LABELTABLE>
[-atlas_pointlist ATLAS_POINTLIST>
[<-lab_r LAB MIN MAX> <-lab_r LAB MIN MAX> <...>]
[<-lab_v LAB KEY> <-lab_v LAB VAL> <...>]
[<-lab_file FILE cLAB cVAL>]
[<-dset DSET>]
-labeltable LABELTABLE: Name of output label table
-atlas_pointlist ATLAS_POINTLIST: Instead of a label table
produce an atlas point list
-lab_r LAB MIN MAX: Define a label LAB its minimum key MIN
and its maximum value MAX.
For example: -lab_r GM 5 7 generates in the labeltable:
"5" "GM01"
"6" "GM02"
"7" "GM03"
-lab_v LAB KEY: Define a label LAB and its value KEY
For example: -lab_v WM 8 generates in the labeltable:
"8" "WM"
-lab_file_delim COL_DELIM: Set column delimiter for -lab_file option
Default is ' ' (space), but you can set
your own. ';' for example. Note that the
delimiter is passed directly to awk's -F
Note: This option must be set BEFORE -lab_file option
on the command line.
-lab_file FILE cLAB cVAL: Labels and keys are in text file FILE.
cLAB is the index of column containing labels
vVAL is the index of column containing keys
(1st column is indexed at 0)
index can have leading zeros now, but they will
be converted to non-leading zeros (e.g. 001->1)
-longnames cLONGNAME: Additionally, allow for another column of long
names for regions, e.g. amygdala for AMY
cLONGNAME is the starting column for the longname continuing
to the last name of the output (0-based column index).
Using this option requires using '-atlas_pointlist ..'
-last_longname_col cLASTLONGNAME: limit longnames to nth column
-dset DSET: Attach the label table (or atlas point list) to
dataset DSET
-centers : Compute center of mass location for each ROI
requires simple blobbish ROIs to work
-centertype TYPE: Choose Icent, Dcent or cm for different ways
to compute centers. See 3dCM for details
-centermask DSET: Calculate center of mass locations for each ROI
using a subset of voxels. Useful for atlases with
identical labels in both hemispheres.
See 3dCM -mask for details
-skip_novoxels : Skip regions without voxels
Note that you cannot use the same key for multiple labels.
When redundancies occur, the script preserves just one entry.
Example:
@MakeLabelTable -lab_r CSF 1 3 -lab_r GM 5 7 -lab_v WM 8 \
-labeltable example1
Usage mode 2: Get information about an existing labeltable
@MakeLabelTable <-labeltable LABELTABLE>
<[-lkeys LABEL] | [-rkeys LABEL] | [-all_labels] | [-all_keys]>
-all_labels: Return a listing of the labels
-all_keys: Return a listing of all keys
-lkeys LABEL: Return the keys whose labels match LABEL
-rkeys LABEL: Return the range (min max) of keys whose
labels match LABEL
-klabel KEY: Return the label associated with KEY
-match_label LABEL: Return labels matching LABEL
-labeltable_of_dset DSET: Dump the labeltable from DSET
-word_label_match: Use word matching (grep's -w )
With this option, 'Out' matches 'Out.l1'
but no longer matches 'OutSk'
-quiet_death: Do not give error messages when failing
Options in usage 2 are mutually exclusive
Usage mode 3: Transform Label Tables to Atlas Point Lists or CSV and exit
@MakeLabelTable [<-LT_to_atlas_PL LABELTABLE>]
[<-dset_LT_to_atlas_PL DSET POINTLIST]
[<-LT_to_CSV LABELTABLE>
-LT_to_atlas_PL LABELTABLE: Transform Label Table LABELTABLE to
Atlas Point List
-dset_LT_to_atlas_PL DSET POINTLIST: Get Label Table in
DSET and write it out as an
Atlas Point List to POINTLIST
-LT_to_CSV LABELTABLE: Transform Label Table LABELTABLE to a CSV format
-LT_to_qCSV LABELTABLE: Transform Label Table LABELTABLE to a quoted CSV format
Example:
@MakeLabelTable -LT_to_atlas_PL aparc.a2009s+aseg_rank.niml.lt
Usage mode 4: Turn a labeled dataset or an integral valued dset
into an ATLAS
@MakeLabelTable [<-atlasize_labeled_dset SOME_LABELED_ROI_DSET>]
[<-atlas_file ATLAS_NIML_FILE]
[<-atlas_name ATLAS_NAME>] [-replace]
-atlasize_labeled_dset SOME_LABELED_ROI_DSET: Change a labeled
ROI dataset into an atlas
-atlas_file ATLAS_NIML_FILE: Specify the name of the NIML file
where atlas attributes are stored.
Default is ./SessionAtlases.niml which
is a good choice for single subject atlases
-atlas_name ATLAS_NAME: Atlas is named based on the prefix, by
default. You can override that with this
option.
-atlas_description ATLAS_DESC: Atlas description, which appears
in afni's whereami_afni window. Default is
'My Atlas'
-replace: If ATLAS_NAME is already in ATLAS_NIML_FILE, the script
will fail to proceed unless you instruct it to do so
this option
-add_atlas_dset ATLAS_DSET: Use if you have an atlas that you want
added to an atlas_file.
Example:
@MakeLabelTable -atlasize_labeled_dset SOME_LABELED_ROI_DSET
or you can specify the keys in a file:
@MakeLabelTable -lab_file FILE cLAB cVAL \
-atlas_pointlist apl \
-dset target_dset \
-atlas_file SessionAtlases.niml
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See also @Atlasize script
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Global Help Options:
--------------------
-h_web: Open webpage with help for this program
-hweb: Same as -h_web
-h_view: Open -help output in a GUI editor
-hview: Same as -hview
-all_opts: List all of the options for this script
-h_find WORD: Search for lines containing WORD in -help
output. Seach is approximate.
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Mon Sep 29 10:46:42 PM EDT 2025