###################################################################
UPDATE:  30 Sep 2026
###################################################################

-------------------------------------------------------------------
Summary:
  (1) ARM compile for MacOS 26 (Tahoe) w/AFNI
  (2) calculate/display rawdata time-series covariance
  (3) sample flat patch .val data to x-y grid and back
-------------------------------------------------------------------

-------------------------------------------
(1) ARM compile for MacOS 26 (Tahoe)
-------------------------------------------

The Mac upgrade from MacOS 25 (Sequoia) to MacOS
26 (Tahoe) broke all X11/GLX/OpenGL apps running
on XQuartz (e.g., glxgears).  Intrepid programmers
(Peter Molfese, above my pay grade) tracked down
some of the problems and prepared a homebrew 'tap'
of work-around X11/GLX/GL libraries (mesa25.3.4 -
N.B.: early mesa26 regressed to broken on Tahoe,
fixed on later mesa26).

I compiled all the csurf programs on Tahoe against
his fixed libs, so tksurfer, etc, should now run
(tested up to Tahoe/macOS 26.7.1):

    https://pages.ucsd.edu/~msereno/csurf/csurf0.8-arm-260930.tgz

To avoid having to unquarantine a downloaded
tarfile on Mac, here is how to download and unpack
in one step:

    cd <install_dir>
    curl -sSL 'https://pages.ucsd.edu/~msereno/csurf/csurf0.8-arm-260930.tgz' | tar xfz -

To recursively unquarantine an already unpacked
csurf, do:

    cd <directory_that_contains_csurf_dir>
    sudo xattr -r -d com.apple.quarantine csurf

The arm64 distribution includes the fixed
X11/GLX/GL mesa libraries within it, so it should
just work on Tahoe, even with a broken XQuartz and
without homebrew installed.  Just cd into the
unpacked csurf and first run FreeSurferEnv.{c}sh
as usual, so that csurf apps can find the fixed
X11/GL libraries.

This distribution contains AFNI bins used by csurf.
On Mac, this is macos_10.12_local (x86_64), which
I tested runs on ARM on MacOS 26/Tahoe w/Rosetta2.
If this AFNI doesn't work for some reason, you can
link csurf to your working AFNI with:

  cd csurf           # wherever you installed it
  mv afni afni~      # just in case
  mkdir -p afni/bin  # make a fresh dir visible to csurf
  cd afni/bin        # cd into it
  ln -s <fullpath_to_dir_containing_afni> Darwin-arm64  # make link to yours

N.B.: The arm64 Tahoe distribution has only been
tested on apple silicon running Tahoe, so I don't
know if it will run on ARM/Sequoia or earlier OS's.
If you have any info on this, please email me!

N.B.: The arm64 Tahoe distribution *won't* work on
an Intel machine running Tahoe (these are
arm64-only binaries).  I don't yet have -arch
x86_64 csurf/library compiles working on my
ARM/Tahoe machine, and unfortunately, I don't have
access to an Intel/Tahoe machine for testing.


-------------------------------------------
(2) calculate/display rawdata covariance
-------------------------------------------

New (very) basic functionality to calculate and
display rawdata time series covariance has been
added.  There are 4 new C/tcl functions:

  calc_rawdata_covar
  write_rawdata_covar
  read_rawdata_covar
  copy_rowcovar_val

These functions can be accessed via the buttonbar
from a R-click on the "X" (cross-corr) button on
the "label:" line.

The first step is to set up a new functional
session with a scandir containing a raw time
series data BRIK and register that rawdata to a
subject in the standard way (makes register.dat).

Then read the rawdata BRIK into tksurfer using the
alternate set of 3D buttons on the "val:" line:

 (1) click "val:" to toggle it to "val3d:"
 (2) click "RD" to get rawdata popup
 (3) select rawdata BRIK from popup "val3d:" dropdown
 (4) click "READ RAWDATA and REGISTRATION"

Next, click "label:" to get NormSamp controls and
set the sampling method and sampling point, using
either mm or fraction of cortical thickness:

  if normdfracflag unticked (mm above orig GM/WM surface),
  set normdsamp, normdmax equal (e.g., 1.0 [mm])

  if normdfracflag ticked (fraction of cort thickness above GM/WM),
  set normdfracsamp, normdfracmax equal (e.g., 0.6 [=60%])

Next, R-click the "X" button on the "label:" line
to get a button-bar popup, and click "Calculate
RawData Covariance" on the popup (there will be an
error if you are sampling a range, not a point,
along the surface normals).

This procedure first finds 'representative' or
'unique' vertices.  That is, for each sampled 3D
voxel, find the surface vertex closest to the 3D
positional average of all the vertices that
sampled that voxel (to avoid having duplicate
entries in the covariance matrix). N.B.: to see
the 'representative' vertices, click "UQ" on the
"val3d:" line after "Calculate RawData Covariance"
has run.

The C/tcl functions run by "Calculate RawData
Covariance" are:

  rawdatasubbrik_to_paintable 0   # extract first frame of rawdata
  paint_surface 0                 # 'paint' to surf to find sample voxels
  find_uniqsamp_vertices          # find voxel-unique 'representative' vtxs
  calc_rawdata_covar              # calculate covariance matrix

N.B.: you can do the first three operations
manually one at a time from the tksurfer interface
as follows:

  (1) click "MAKE FIRST VOL PAINTABLE (for uniq)" on popup
  (2) click "PA" button on "val3d:" line (does paint)
  (3) click "UQ" button on "val3d:" line (does unique vertices)

(these will be harmlessly redone by "Calculate
RawData Covariance").

Each covariance matrix entry (for a pair of
vertices, v1 and v2) is computed in the usual way
as follows (sum is across t):

           Sum[(v1 - v1_avg) * (v2 - v2_avg)]
corr =   -------------------------------------
                       n - 1

which results in a symmetric matrix with variances
along the diagonal.

To view individual rows of the covariance matrix,
click "Display Correlation for CurrVertex" on the
Label "X" popup, after selecting a 'seed' vertex
(the actual seed will be the 'representative'
vertex closest to your selected vertex).  The
first time this runs, the colscale will be set to
sane values to display the correlations:

  set overlayflag 1
  set truncphaseflag 0
  set complexvalflag 0
  set statmaskampflag 0
  set colscale 11
  set fslope 0.1
  set fthresh 5.0
  set fmid 10.0

Since the (large) covariance matrix (about 13K by
13K) only contains 'representative' vertices, the
correlation data is first interpolated on the
surface with smooth_val_sparse (the "sp" option
for the SMOOTH button).  During this smoothing,
the values at 'representative' vertices are fixed
and only the undefined vertices in between are
interpolated (20 steps).

Finally, to export the covariance matrix to the
current scandir to analyze it with external tools,
use the "Write RawData Covariance" button on the
R-click "X" popup.  This will write out two files
in the current scandir with standard names.  The
first file:

  $hemi-CovarianceMatrix.float

is the covariance matrix, written as a string of
floats in standard freesurfer byte order (MSB).
Use AFNI 4swap to convert to Intel (LSB) byte
order to read the binary data into an external
program, for example:

  4swap rh-CovarianceMatrix.float

The indices of the rows and columns of this matrix
are sequentially numbered 'representative'
vertices, which are a subset of full vertex
subset.  So, in addition to the covariance matrix,
an ASCII file of the original full surface vertex
numbers of these 'representative' vertices is also
written to:

  $hemi-CovarianceMatrixVnums.txt

Since it takes a minute to calculate the large
covariance matrix, you can read a previously
calculated matrix into tksurfer with "Read RawData
Covariance" on the R-click "X" buttonbar popup.

Finally, a new popup to select/query vertices by
vertex number and dispay time series is available
by R-clicking the REDRAW button and clicking the
bottom "Select Vertex By Number Popup" button
(mainly for debugging).  The buttons are:

  CURRENTLY SELECTED VTX   (from display window click)
  SELECT VERTEX BY NUMBER
  SHOW VERTEX TIMECOURSE
  SHOW UNIQSAMP VERTICES


-------------------------------------------
(3) sample flat patch .val data to grid and back
-------------------------------------------

new popup:
  from R-click on "W" button on "label:" line

new C/tcl functs:
  write_flatval_to_grid <gridmm> <fillholes> <maxdatadistmm>
  read_gridval_to_surf <fillholes> <maxdatadistmm>

----------------
Surface -> Grid:
----------------

The first button on the popup allows sampling
vertexwise .val data that is currently loaded on a
flat surface to a regular x-y grid -- e.g., to
process it with an external program expecting a
grid.

The grid size is set by the $gridmm entry (default
value 0.6mm similar to average surface edge size).
The bounding box of the grid is calculated from
min/max values of any displayed vertices.

For each vertex, the .val at that vertex is
assigned to the closet grid point.

The grid of resampled .val's is written out as a
headerless freesurfer MSB (most significant byte
first) 32-bit float binary file with a standard
hemisphere-specific name to the subject's label
directory:

  $hemi-ValToGrid.MSBfloat

In order to be able to read the grid data
(possibly modified), back onto the same flat
surface (see bottom button on popup), a second
ASCII/text file is written containing the surface
vertex numbers closest to each grid point:

  $hemi-ValToGridNearest.txt

This file is written in the same order as the
binary MSB float file (x is the inner loop).  Its
first line is a "#" comment, which contains the
subject, patch, x and y grid dimensions and the
grid spacing (gridmm).

The sampling process can result in holes in the
grid since each point in the surface is assigned
to only one grid point.  Ticking $fillholesflag
causes a (slower 1-2min, multithreaded) search,
where grid holes are filled with the .val from
the closest vertex, as long as it is less than
$maxdatadistmm (default=1.5mm) away from the grid
point hole.

N.B.: use AFNI 4swap to convert freesurfer MSB
float files to LSB float files for processing in
external programs.

----------------
Grid -> Surface:
----------------

The second button on the popup allows sampling a
regular x-y grid of MSB float .val data onto a
flat surface.

The float data file (and the nearest vertex ASCII
file) will previously have been written out by the
C/tcl function, write_flatval_to_grid (SAMPLE SURF
VAL TO GRID FILE button on the popup).

The two hemisphere specific input files have
standard names, and are read from the subject's
label directory:

  $hemi-ValToGrid.MSBfloat
  $hemi-ValToGridNearest.txt

The float data may have been subsequently modified
by an external program before reading it back onto
the flat surface for viewing.

For each grid point, vertex, the .val at that
point is assigned to the vertex number for that
grid point found in the second ASCII input file.

The currently displayed subject and flat surface
must match what is found in the first "#" comment
header line in the $hemi-ValToGridNearest.txt
file.

The sampling process can result in holes on the
surface since each point in the grid is assigned
to only one surface vertex.  Ticking
$fillholesflag causes a (slower 1-2min,
multithreaded) search, where surface holes are
filled with the .val from the closest grid point,
as long as it is less than $maxdatadistmm
(default=0.5mm for a 0.6mm grid) away from the
surface vertex hole.

N.B.: to view the data on a different (e.g.,
inflated_avg) surface, just switch to any other
surface in tksurfer after reading in the grid
data.

N.B.: use AFNI 4swap to convert between LSB (most
Intel/ARM) and MSB (freesurfer) float file files.


-----------------------------------------------
Bug fixes, small changes
----------------------------------------------

tksurfer interface stays up even if no GLX win (all computation works)

draw areanames now respects annotmaskflag (show subset of areas)

UQ popup reports sampvtxcnt, uniqvtxcnt, vtxs per voxel

NormSamp popup: enable/disable relevant parms: normdfracflag, bokflag

new R-clk-REDRAW accessible "Select Vertex by Number Popup"


##########################################################################
UPDATE: 30 Sep 2026
##########################################################################

---------------- 30Sep2026 csurf0.8 tarballs ------------------------------
--csurf: sphavgcxcmd,volavgcxcmd: $use3dttestplusplusflag: 3dttest++ vs 3dttest
--csurf: sphavgcxcmd,volavgcxcmd - if $use3dttestplusplusflag, use 3dttest++
--csurf: startup: 3dttest notfound lookfor 3dttest++, set use3dttestplusplusflag
--mk0: update 'mk0 afni' tarfile fish out: get 3dttest++ if no 3dttest
--mk0: Rosetta2/ARM: add 10.12_local libs precompiled, libs -> afni bin
--mk0 (04s): update afni download to current state afni site
--tksurfer.c: draw_areanames() now respects annotmaskflag (show subset of areas)
--tkmedit.c: make linearflag respect contrast reversed (bwslope is negative)
--brik2cor.c: add invthresh to skip inverting almost-zeros
--tkmedit.c: HOR/SAG TRUNC to real 0 (=COR), not sqmap[0] (only vis midpt<0.15)
--tksurfer.tcl: if not openglwindowflag say non-graphics cmds still work
--tksurfer.c: don't exit if can't open glx window (non-graphics cmds still work)
--tksurfer.c: rename read_gridval_to_surf -> read_gridval_to_flat symm. w/write
--tksurfer.c: fillpix updated 1.0 -> 0.5 on read 512^3 dateset
   [tmprelease 260825]
--tksurfer.c: read_gridval_to_surf requires same flat patch and subject
--tksurfer.c: require same flat patch on read grid to surface
--lib/help/tksurfer/label_{write,read2val}: update
--tksurfer.tcl: write/read grid now put up same popup, with two offset helpwins
--wrappers.tcl: helpwin early exit/raise returns "raise" instead of window name
--tksurfer.c,tcl: new multithread read_gridval_to_surf fillholes/maxdatadistmm
--tksurfer.c,tcl: rm broken read_gridval_to_surf fillholes (was onlynearvtx=0)
--tksurfer.c: multithread fillholesflag option in write_flatval_to_grid 8m->2m
--tksurfer.tcl: add labelR_grid (runs read_gridval_to_surf (also prev popup)
--tksurfer.tcl: samp2gridctrls/do_samp2grid (runs write_flatval_to_grid)
--tksurfer.tcl: checklabelfile bug fails on some 5,6 args label (how long?!)
--tksurfer.c: compute_avg_edgewidth() skips border/ripped esp. better flat est.
--tksurfer.c: add/export: write_flatval_to_grid(), read_gridval_to_surf()
--mk0: 04r: action "clean", libtool vs ranlib for strtod fix XC12 on Catalina
--mk0: 04q: strtod ranlib fix Xcode12 ahead-load Catalina vs. BigSur+ -> faile
--mk0: 04p: insttmp edits FreeSurferEnv.{sh,csh} to copy state in mk0
--mk0,mk,getonearch,Makefile: systbrew->optloc, csurfbrew->csurfloc
--FreeSurferEnv.{sh,csh}: v18: add $uselocalx11gl parallel to mk0
--csurf: chk ./tardate-YYMMDD.txt to set $tarfiledate if notfound in README.txt
--mk0: save second copy of tardate file to $srcdir
--mk0: "mk0 csurf" reports commands that will run, "mk0 dist" explains itself
--mk0: compile/link mesa26 software render on 10.15 -> fail (still Frameworks!)
--mk0: change 'mk0 onearch' etc to more sensible 'mk0 csurf'
--mk0: add $uselocalx11gl ($macxllgl:systbrew->csurfbrew (brew cp in csurf))
--csurfsrc/dist/precompiled/X11GL/include/Darwin-<arch>: find min req'd X11 incl
--getonearch,mk: cleanup,doc,overrides: mk0->mk->getonearch->exportvars->make
--tksurfer.tcl: CS buttonbar: title correction: Val "R" -> Val "CS"
--update-csurf: download and untar at once (avoids Mac Gatekeeper quarantine)
--FreeSurferEnv.{c}sh: Darwin-arm86->Darwin-arm64 :-} (fixed 260622 tarfiles)
   [tmprelease 260622]
--tksurfer.c: accept/ignore -fontfile if gcc/no-font so won't quit w/bad opt
--tksurfer.c: raise mup/etc+=0.01 to fix label holes in Linux VirtualBox
--mkcsurflist,update-csurf: now recognize csurf0.8-arm-YYMMDD.tgz
      ------- MacOS 26 Tahoe (release=25) compile working ---------
--FreeSurferEnv.{c}sh: v17: cleanup old, align sh/csh versions
--mk0: add new mpeg_{play,encode} patches for Tahoe
--mk0: arm64 insttmp adds precompiled mesa-25.3.4 libs $CSURF_DIR/X11GL
--mk0: dist incl's 60M precompiled mesa-25.3.4: dist/precompiled/X11GL
--mk0: MacOS 26 Tahoe compile working w/precompiled brew
--{tkmedit/tkregister/tkstrip}.c -- clean up "unsed but set" warnings
--Makefile tkregister: ifeq(${macCGLparms),1) for optional gcc ... -DmacGLparms
--mk: use getonearch to export $macCGLparms 0|1 (CGL parms gone post-Catalina)
--getonearch: also report 0|1 for $macCGLparms (CGL parms gone post-Catalina)
--tkregister.c: doublebuffer *or* singlebuffer OK
--tkregister.c: #ifdef macCGLparms, include CGLSetParameter swapInterval
--tkregister.c: MacOS 26 (Tahoe): CGLSetParameter swapInterval no longer exists
--tkregister.c: CGLSetParameter swapInterval req'd up to at least MacOS 10.15
--tkmedit.c: doublebuffer *or* singlebuffer OK/equivalent
--Makefile tkmedit/tkregister/tkstrip: same lib/incl logic as Makefile tksurfer
--tksurfer Makefile: add $macx11gl (xquartz vs. systbrew vs. csurfbrew) logic
--mk: get $macx11gl from getonearch, export it to makefile env
--getonearch: can now output $macx11gl, proc arm -> $oneproc=arm64 (was x86_64)
--tksurfer.c: fix many 'set but not used' and 'misleading indentation' warnings
--tksurfer.c: fix samevtxthickflag no-op in move_along_normal,bug intro'd Jun'24
--tksurfer.tcl: harmonize read_{mgh,poi,obj,gifti}_to_annot set transparency
--tksurfer.c: read_{gifti,obj,poi}_to_annot: init avgx,y,z (drawnames crashers)
--tksurfer.c: read_{gifti,obj,poi}_to_annot: forgot find_regionvtx_nearest_avg
--tksurfer.c: add getkernelreleasenum(),override doublebufferflag Tahoe+/kern>24
--mk0: mk0 <badtarg> now gives error (vs. silence)
 ftgl: use homebrew GL libs (same as GLX programs, tksurfer etc), patch demo
 tiff/ezxml/freetype: worked as is
 tix: use consistent (e.g., homebrew) X11 (not just GL) libs
 tix: awk "#include <ctype.h>" to generic/tix{GrUtl,ImgXpm}.c for isspace
 tix: X11 link to *tk* dir already on tix -L path: fix no find -lX11 Mac
 tk/tix: use same X11 libs as libftgl, GLX progs (tksurfer etc)
 tk: use consistent (e.g., homebrew) X11 (not just GL) libs
 tk: patch missing _fixstrtod: add fixstrtod.o to Makefile GENERIC_OBJS
 tk: patch missing _fixstrtod: cp tcl-compiled fixstrtod.o into tk
 tcl: ranlib strtod.o, fixstrtod.o to fix dup'd symbols
 tcl: typedef int->long ptrdiff_t tclInt.h fix tclUnixTime.c redef xc12.4+
 use tcl8.5/tk8.5/tix8.4 (vs. 8.6) for less interface adjust, less tix patch
--mk0: add $kernelreleasenum, homebrew mesa-25.3.4 X11+GL if BigSur+
--wheel.c: first successful port w/homebrew tap patched mesa-25.3.4 (GL + X11!)
      ------- begin MacOS 26 Tahoe (release=25) compile ------------
--tksurfer.c: append hemi, selectedvtx to edit.dat on SEND PNT for xhemi corr
--tksurfer.tcl: do sampclustctrls after "RD" readrawdata remind set sample point
--lib/help/tksurfer/label_corr: update
--[prev 3 a bit overkill :-} ]
--tksurfer.tcl: MAKE FIRST VOL PAINTABLE reports buff mismatch (won't get here)
--tksurfer.tcl: READ RAWDATA err on rawdata_tdim=1 (HEAD read sets rawdata_tdim)
--tksurfer.c: rawdatasubbrik_to_paintable reports mismatched dims vs. just err
--[prev blocks err: read 3D BRIK, calc covar, re-read 4D BRIK, make PAINTABLE
--tksurfer.c: read_rawdata sets rawdataloaded=0 if rawdata_tdim from HEAD is 1
--tksurfer.tcl: fix forgot logcmd for rawdatasubbrik_to_paintable
   [tmprelease 260525]
--tksurfer.tcl: add $isession to top of READ RAWDATA BRIK and REGISTRATION popup
--lib/help/tksurfer/val3d_raw: update
--tksurfer.tcl: calc covar catches non-zero sample points with normsearch OFF
--tksurfer.tcl: rawdata: "MAKE FIRST VOL PAINTABLE" rawdatasubbrik_to_paintable
--tksurfer.tcl: paint_real_or_complex OK if rawdataframerealloaded=1
--tksurfer.c: add/exp rawdataframerealloaded set by rawdatasubbrik_to_paintable
--tksurfer.tcl: add "SHOW UNIQSAMP VERTICES" to "SELECT VERTEX BY NUMBER" popup
--tksurfer.c: extra-safe NULL ptr check in rawdatasubbrik_to_paintable
   [tmprelease 260522]
--tksurfer.c: fix left-out returns in show_timecourse error checks!!
   [tmprelease 260521]
--lib/help/tksurfer/{label_corr,redraw}: update
--ksurfer.tcl: add "SHOW VERTEX TIMECOURSE" button to select-by-vtx-num popup
--tksurfer.c: functify show_timecourse and export to tcl
--tksurfer.tcl: R-click "REDRAW" button: add "Select Vertex By Number Popup"
--tksurfer.tcl: R-click "X" buttonbar: add "Read RawData Covariance"
--tksurfer.c: add/export read_rawdata_covar (a bit overkill)
--tksurfer.tcl: green selbgcol for hacked-in popup comboboxes (mkannot,rawdata)
--tksurfer.c: rawdatasubbrik_to_paintable now accepts short read by read_rawdata
--tksurfer.tcl: R-clk "X" buttonbar: add "Display Correlation for CurrVertex"
--tksurfer.tcl: R-clk "X" buttonbar: add "{Calc,Write} RawData Covariance"
--tksurfer.c: add/export copy_rowcovar_val() (find nearest uniqvtx to selected)
--tksurfer.c: add/export calc_rawdata_covar(), write_rawdata_covar()
--tksurfer.c: new tmp covar mat globals: covarmat{,_dim,_vnum,loaded}
--tksurfer.c: sampvtxcnt, uniqvtxcnt made global for tcl report
--tksurfer.tcl: R-clk menu "label:" line "X" refreshes corr over label/annot
--tksurfer.tcl: NormSamp popup: enable/disable parms: normdfracflag, bokflag
--tksurfer.tcl: UQ popup reports sampvtxcnt, uniqvtxcnt, vtxs per voxel
--tksurfer.c: sampvtxcnt, uniqvtxcnt made global for tcl report

##########################################################################
UPDATE: 02 May 2026
##########################################################################

---------------- 02May2026 csurf0.8 tarballs ------------------------------
--lib/help/tksurfer/{save,goto}_pnt: update
--tksurfer.c: sensibly rename: *vindex -> *selectedptr (in 2 functs below)
--tksurfer.c: same fix as below for (script-only) select_talairach_point
   [tmprelease 260429]
--tksurfer.c: funct below passed &selected(def=-1) so deref rngchk brks 1stcall
--tksurfer.c: rm bad select_orig_vertex_coords err chk *vindex - broke 1st GOTO
...