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)
-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.
