-------------------------------------------
USING MGH ANNOTATION FILES (*.annot)
-------------------------------------------
Summary of main operations that can be quickly
performed using an MGH annotation (multi-label)
file (e.g., $hemi-CsurfMaps1.annot or
$hemi-HCP-MMP1.annot) or a Brain Voyager
patches-of-interest file (*.poi).  This is the
*shift*-right click help :-}


-------------------------------------------
Display fsaverage or indiv-subject MGH annotation file
-------------------------------------------

  select *.annot from "label:" dropdown
  "D" (display)
  -----
  adjust label transparency with "tran"
  shift-middle-click tick left of "label:" => toggle borders
  ctrl-shift-middle-click tick => white dots as borders
  ctrl-shift-right-click tick => prune white dots
  double-middle-click region => col/idnum/name popup

-------------------------------------------
Display subset of areas in MGH annotation file
-------------------------------------------

  select *.annot from "label:" dropdown
  "D" (display)
  -----
  shift-R-click D    [pop-up: idnums/names/cols]
  type in space-separated list idnums to show
  READY
  type "all" to restore all

-------------------------------------------
Resample an fsaverage annot to an indiv subject
-------------------------------------------

This is for fsaverage annotations that have not
already been resampled by standard freesurfer
recon-all (e.g., Van Essen parcellation,
$hemi.HCP-MMP1.annot, in directory,
$CSURF_DIR/fsaverage-ADDITIONS/label):

  open indiv subject
  select "annot2roi.tcl" from "tcl:" dropdown
  GO
  select fsaverage .annot from "annot:" dropdown on popup
  RUN SCRIPT   (uses mri_surf2surf)

-------------------------------------------
Dump out surface data for single annotation area:
-------------------------------------------

  load some data into indiv subject or fsaverage
  load annotation file
  click in one area
  shift-middle-click-W on "label:" line

-------------------------------------------
Dump out surface data for *all* annotation areas:
-------------------------------------------

  load some data into subject
  load annotation file
  shift-left-click-W on "label:" line

-------------------------------------------
Construct fsaverage annotation file from set of labels:
-------------------------------------------

  make a bunch of labels in fsaverage named like this:
     $SUBJECTS_DIR/fsaverage/label/rh-V1_upper.label
  follow label-making hints bottom of R-click "label:" help
  make ASCII FreeSurfer LUT file referencing label infixes
    => N.B.: choose unique colors and id numbers
#----------- cut here -----------------------------------
#!ascii , CsurfColorLUT.txt (in $CSURF_DIR/lib/lut)
#--------------------------------------------------------
#id  region		R	G	B	A
#--------------------------------------------------------
0    Unknown		0	0	0	0
1    V1_lower		150	0	10	0
2    V1_upper		150	0	120	0
4    V3_lower		0	50	200	0
. . . [etc]
#----------- cut here -----------------------------------
  ctrl-middle-click-W on "label:" line
  enter name of your LUT file in pop-up

-------------------------------------------
Display all annotation region(s) on 2D slice
-------------------------------------------

  open fsaverage or indiv-sub in *tkmedit* (VOLUME)
  F4 to get big tkmedit panel
  select annot file from "annot:" dropdown
  click R (read)
    => "line:" entry controls thickness colored ribbon

-------------------------------------------
Display *one* annotation region(s) on 2D slice
-------------------------------------------

  also display annotation on surface (SURFACE)
  double-mid-click region for popup with region idnum
  ------------------
  open fsaverage or indiv-sub in tkmedit (VOLUME)
  F4 to get big tkmedit panel
  select annot file from "annot:" dropdown
  click R (read)
  type in idnum to tkmedit "an:" in SURFPAINT, <Return>
    => e.g., see where 3b (idnum=9) actually is in slices :-}
    => "line:" entry controls thickness colored ribbon

-------------------------------------------
Make indiv subj 3D AFNI ROIs from fsaverage annotation
-------------------------------------------

  open indiv subj functional in View Functional Data
  select "annot2roi.tcl" from  "tcl:" dropdown
  GO
  select fsaverage .annot from "annot:" dropdown on popup
  click to select tick: "Make_3D_AFNI_ROIs_flag"
  RUN SCRIPT (uses mri_surf2surf, tksurfer funct)
    => result is single-subject functional-resolution ROI for
            each surface region, plus, an all-in-one ROI file
    => can erode each region 1+ layers of vtxs before => 3D
    => can adjust normal search parameters before => 3D

