Index

Software version described:

mris_label2annot

This command-line program amalgamates one or more label files, plus optionally a color lookup table, into a single annotation file. The concepts relating to label files and annotation files are described here: LabelsClutsAnnotationFiles.

Synopsis

mris_label2annot [Flagged args, see below]

Arguments

Positional Arguments

none

Flagged Arguments

Flag

<Args>

Description

--ctab

<ctab_file>

Colortable file. File that defines the structure names, their indices, and their color. This must have the same format as that found in $FREESURFER_HOME/FreeSurferColorLUT.txt.
The colortable file gets incorporated into the output annotation file. In addition, depending on other options, the names in colortable can be used by this program to find correspondingly-named label files. More details below.

--l

<label_file>

Repeat this flag and arg for each additional label file you want to include in the annotation file.

--ldir

<labeldir>

When seeking label files based on names in ctab, find the label files in labeldir. This has no effect on the files specified by --l

--ldir-default

Works like --ldir option, setting labeldir to the default label directory for the selected subject:

{SUBJECTS_DIR}/{SUBJECT}/label

--s or --subject

<subject>

FreeSurfer subject to work on

--a or --annot

<annot_name>

output annotation file The actual file will be called 'hemi.annot_name.annot', and it will be created in directory subject/label. To avoid overwriting possibly valuable data, the program will not overwrite an existing file by the same name.

--h or --hemi

<hemi>

hemisphere (lh or rh)

--no-unknown

Start label numbering at index 0 instead of index 1. Do not map unhit vertices (ie, vertices without a label) to 0.

--help

print_help

--version

print_version

--checkopts

checkoptsonly = 1

--debug

debug = 1

--nhits

<nhits_file>

This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2).

--nocheckopts

checkoptsonly = 0

--offset

<IndexOffset>

Add to label number to get CTAB index.

--sd

<SUBJECTS_DIR>

--noverbose

Turn off overlap and stat override messages.

--maxstatwinner

Keep label with highest 'stat' value.

--thresh

<thres>

threshold label by stats field.

--surf

<surfname>

Default is orig.

Description

This program is used to amalgamate one or more label files together into a single annotation file, usually including a color lookup table file. The concepts relating to label files and annotation files are described here: LabelsClutsAnnotationFiles.

Examples

Example 1

The following example is taken from mris_label2annot's help --GW

mris_label2annot --s bert --h lh 
  --ctab aparc.annot.ctab --a myaparc 
  --l lh.unknown.label 
  --l lh.bankssts.label
  --l lh.caudalanteriorcingulate.label 
  --nhits nhits.mgh

This will create lh.myaparc.annot in bert/labels using the three labels specified. Any vertices that have multiple labels will then be stored in nhits.mgh (as a volume-encoded surface file).

(Note: this nhits.mgh detail is a bit obscure. The idea of an nhits file is simply to provide a list of values giving the count of labels found for each vertex. This needs to be presented to tksurfer for display as a colored overlay. Here FS's MRI volume format is used just as a container for that 1 x vertex_count array of values. --GW)

To view, run: tksurfer bert lh inflated -overlay nhits.mgh -fthresh 1.5 Then File -> Label -> Import Annotation and select lh.myaparc.annot.

Bugs

None

See Also

mri_annotation2label, LabelsClutsAnnotationFiles

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Document Author/s

GrahamWideman

mris_label2annot (last edited 2017-12-20 11:54:21 by BramDiamond)