Index of /sereno/csurf/fsaverage-labels/CsurfMaps1-parcellation/simple-annot
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https://pages.ucsd.edu/~msereno/csurf/fsaverage-labels/CsurfMaps1-parcellation/simple-annot/README.txt
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Lightweight (simple-annot) versions of full annotation
The eight files in here:
% ls -al
-rw-r--r-- 1 sereno 655383 Jan 1 16:00 CsurfMaps1_newcurv-lh.w
-rw-r--r-- 1 sereno 655383 Jan 1 16:00 CsurfMaps1_newcurv-rh.w
-rw-r--r-- 1 sereno 504152 Jan 1 16:52 CsurfMaps1_old3byte-lh.w
-rw-r--r-- 1 sereno 501744 Jan 1 16:00 CsurfMaps1_old3byte-rh.w
-rw-r--r-- 1 sereno 6254705 Jan 1 16:00 lh-CsurfMaps1_MNI152.label
-rw-r--r-- 1 sereno 6262280 Jan 1 16:00 lh-CsurfMaps1_MNI305.label
-rw-r--r-- 1 sereno 6096170 Jan 1 16:00 rh-CsurfMaps1_MNI152.label
-rw-r--r-- 1 sereno 6100257 Jan 1 16:00 rh-CsurfMaps1_MNI305.label
can be placed in the "label" subdirectory of the FreeSurfer average
subject, fsaverage.
N.B.: these files are already included in the updated fsaverage subject
tarfiles here:
https://pages.ucsd.edu/~msereno/csurf/fsaverage-ADDITIONS.tgz (just adds)
https://pages.ucsd.edu/~msereno/csurf/fsaverage.tgz (fs5.3 + adds)
These files are lightweight valfile and labelfile versions of the left
and right hemisphere CsurfMaps1 MGH annotation files:
lh-CsurfMaps1.annot
rh-CsurfMaps1.annot
taken from the publication:
Sereno MI, Sood MR and Huang R-S (2022)
Topological Maps and Brain Computations From Low to High.
Frontiers in System Neuroscience 16:787737
https://pages.ucsd.edu/~msereno/papers/MapsLowToHigh22.pdf
(doi: 10.3389/fnsys.2022.787737)
Each file contains vertexwise integer annotation region ID numbers of the
parcellation (stored as floating point 'values'). The files are provided
in freesurfer binary valuefile (wfile) format and ASCII label format.
Binary wfiles (*.w)
The binary *.w files are provided in two different freesurfer format
versions -- "old3byte" and "newcurv". Details of binary these file
formats are shown below. Byte sizes are in brackets, repeating groups
indicated by "...", and byteorder MSB (most significant byte first,
'bigendian'). There are MATLAB utilities (read_wfile.m, read_curv.m)
in the standard freesurfer/matlab directory for reading these MSB binary
files into MATLAB.
----------------------------------------------
valfile/wfile -- only vertices w/non-zero values
----------------------------------------------
[magic: none]
header: latency[2],vertexcnt[3]
data: {vtxnum[3],floatval[4]}, ...
----------------------------------------------
----------------------------------------------
newcurv -- all vertices, implicitly numbered
----------------------------------------------
[magic: -1 # i.e., 16777215 read in 3bytes]
header: -1[3],vcnt[4],fcnt[4],valspervtx[4]
data: floatcurv[4], ...
----------------------------------------------
ASCII label files (*.label)
The ASCII *.label files are also provided in two versions, which
have included vertex x,y,z coordinates as either MNI 305 coordinates
(freesurfer standard) or MNI 152 coordinates. Each x,y,z point is moved
outward along the local surface normal from the "orig" surface vertex
by a fraction of 0.4 (40%) of the cortical thickness at each vertex.
Viewing files in csurf
These valfiles files don't look like typical MRI data, so to best
display/verify the integer values in csurf, you can make a random
color lookup table with the csurf-supplied program, mkrandlut (in
$CSURF_DIR/bin/noarch):
mkrandlut <minval> <maxval> <step> [rseed]
Since the CsurfMaps1 parcellation has 117 regions (plus 0=Unknown),
execute the following commands in a shell to write a val2rgb.lut file
to the cwd:
cd $SUBJECTS_DIR/fsaverage/scripts
$CSURF_DIR/bin/noarch/mkrandlut 0 117 1
Then click upper middle "Col:" in tksurfer to get the colscale popup,
select color scale 12 ("lt"), and read the val2rgb.lut file with "R"
on the tksurfer "lut:" line.