:orphan: .. _ahelp_@MakeLabelTable: *************** @MakeLabelTable *************** .. contents:: :local: | .. code-block:: none 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 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 ------------------------- See also @Atlasize script ------------------------- 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.