Usage:
FSread_annot <-input ANNOTFILE>
[-FScmap CMAPFILE]
[-FScmaprange iMin iMax]
[-FSversion VER]
[-col_1D annot.1D.col]
[-roi_1D annot.1D.roi]
[-cmap_1D annot.1D.cmap]
[show_FScmap]
[-help]
Reads a FreeSurfer annotation file and outputs
an equivalent ROI file and/or a colormap file
for use with SUMA.
Required options:
-input ANNOTFILE: Binary formatted FreeSurfer
annotation file.
AND one of the optional options.
Optional options:
-FScmap CMAPFILE: Get the colormap from the Freesurfer
colormap file CMAPFILE.
Colormaps inside the ANNOTFILE would be
ignored. See also MakeColorMap's fscolut* options.
With FSversion set to 2009, if FScmap is not set,
the program will attempt to locate
FreeSurferColorLUT.txt based on the environment
variable $FREESURFER_HOME
You can use FS_DEFAULT to force the program to load
FreeSurfer's $FREESURFER_HOME/FreeSurferColorLUT.txt
-FScmaprange iMin iMax: CMAPFILE contains multiple types of labels
The annotation values in ANNOTFILE can map to multiple
labels if you do not restrict the range with
iMin and iMax. That is because annotation values
encode color in RGB which is used to lookup a name
and integer label from CMAPFILE. The same color is
used for multiple labels.
When an external CMAPFILE is needed (a2009 versions),
the programs uses a default of [13100 13199] for lh,
[14100 14199] for rh surfaces.
If CMAPFILE is set to FS_DEFAULT in a2005 versions,
the programs uses a default of [3100 3199] for lh,
[4100 4199] for rh surfaces.
-FSversion VER: VER is the annotation file vintage. Choose from 2009,
or 2005. The program will attempt to guess from the name
ANNOTFILE and would default to 2005.
-hemi HEMI: Specify hemisphere. HEMI is one of lh or rh.
Program guesses by default
-col_1D annot.1D.col: Write a 4-column 1D color file.
The first column is the node
index followed by r g b values.
This color file can be imported
using the 'c' option in SUMA.
If no colormap was found in the
ANNOTFILE then the file has 2 columns
with the second being the annotation
value.
-roi_1D annot.1D.roi: Write a 5-column 1D roi file.
The first column is the node
index, followed by its index in the
colormap, followed by r g b values.
This roi file can be imported
using the 'Load' button in SUMA's
'Draw ROI' controller.
If no colormap was found in the
ANNOTFILE then the file has 2 columns
with the second being the annotation
value.
-dset annot.niml.dset: Write the annotation and colormap as a
niml formatted Label Dset. This type of dset
gets special treatment in SUMA.
-cmap_1D annot.1D.cmap: Write a 4-column 1D color map file.
The first column is the color index,
followed by r g b and flag values.
The name of each color is inserted
as a comment because 1D files do not
support text data.
-show_FScmap: Show the info of the colormap in the ANNOT file.
-dset DSET: Write out a niml formatted label dataset which is handled
in a special way in SUMA. If AFNI_NIML_TEXT_DATA is set
to YES, then output is ASCII NIML.
Compile Date:
Oct 17 2024
