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 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)
- -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.
- -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
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
-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 failingOptions in usage 2 are mutually exclusive
- -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
- Example:
- @MakeLabelTable -LT_to_atlas_PL aparc.a2009s+aseg_rank.niml.lt
into an ATLAS
- -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 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
-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.