################################################################################################# https://pages.ucsd.edu/~msereno/csurf/fsaverage-labels/CsurfMaps1-parcellation/simple-annot/README.txt ################################################################################################# 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 [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.