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LATEST EMAIL UPDATE: 13 Dec 2013
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The main update is that the "w" option in the cross subjects
panel to run AFNI 3dttest for real-valued data (one condition at
a time...) now works :-} (it wasn't properly painting back to a
single subject or running surfclust).

These are designed to be used alongside the standard MGH
freesurfer (csurf can conveniently run recon-all), but also
include tools for making hi-res surfaces (512^3, 0.5mm^3).

A larger, also updated, linux tarfile (~270M) that also includes
the very old (ca. 2001) surface-making binaries is here:

  zakros:/home/inverse/freesurfer/tarballs/FreeSurfer0.8-131213.tgz
  buc05:/usr0/freesurfer/dist/FreeSurfer0.8-131213.tgz

To install:

  cd <dir-where-csurf-currently-installed>
  mv csurf csurf-YYMMDD
  tar xvfz csurf0.8-{mac,linux}-YYMMDD.tgz

Here is a summary of the  updates (full details appended).

### 13 Dec 2013 (fix xsub t-test, offscreen render, fix help panels, cleanup)
  1) cross subject t-test (AFNI 3dttest) painted and surfclust'd w/phasetype="w"
  2) MGHTools->Register now also runs mris_sphere for all-manual morph
  3) csurf Preferences menu item to change namefile (for 3D xsub thalamus avg)
  4) paint accepts short BRIKs (for DWI 'stats')
  5) tksurfer alt/cmd-k makes bigger surface cursor (also color neighbor edges)
  6) fix render offscreen (for extra hi-res, new R-click help at rgb WRITE)
  7) higher max vertex count (1M->4M) allowed for init orig tessellation
  8) live surfclust parms controls added (on pop-up from R-click "label:")
  9) updated 36 help panels

cheers,
marty


### UPDATE: 13 Dec 2013 -- details
--lib/help/csurf/setupsphavg: document phasetype=w updates
--tksurfer.tcl: block {patch,curv,area} config -value callback (even disabled!)
--tksurfer.tcl: setfile {patch,curv,area} blks select_{curv.patch,area} callbak
--csurf: putback mk{3d,flat}script setfile's (blk'd callback tksurfer.tcl works)
--tk{surfer,medit,register,strip}.c -- flush report run interface,cmdli scripts
--csurf: add mris_sphere (all default) to MGH Register sequence
--bresize.c: help a little better: TODO: both-way example!
--csurf: samp2subj pass1: if real, don't skip surf2surf
--csurf: samp2subj pass2: if real, don't skip surfclust (N.B. tstat => _h)
--csurf: samp2subj pass2: if real, look for AFNI -tstat- not csurf-intern -stat-
--csurf: mghsphereregcmd warns missing morph register targ (.tif)
--lib/help/tkmedit/valn2up: vals typo
--tksurfer.c: fix crash: raise_window w/o open gl window open
--tksurfer.tcl: TODO: setfile mk abbrev trigs select_{curv.patch,area} callback
--tksurfer.tcl: tixcombo -variable {curv,patch,area}abbrev so setfile updates
--tksurfer.tcl: make select_patch act like viewcuts on read *.3d
--setdefpatchview.tcl: don't apply flat xforms to *.patch.3d (we want viewcuts)
--lib/tcl/{curv,eccen.fs,polar,real,twocond}-flat.tcl: readenv bef. setdefpatch
--lib/help/tksurfer/{scripts,rgb,tksurfer} -- funcs/vars, offscreen render, "S"
--tksurfer.tcl: rm hack to for old fixcolors missing entries ending in .e*
--wrappers.tcl: fix fixcolors to (mostly) check widget class
--lib/tcl/movie360.tcl: add diag 360 rotation, zoom-and-back
--lib/help/csurf/{csurf,makenewfunct}
--csurf: rearrange Preferences menu, add more separators
--csurf: Preferences -> Change Subj for Curr Session to change namefile
--lib/help/csurf/smoothcurvinflatesulchires => new helpfile, edited non-hires
--tksurfer.tcl: 3toggle inset: disk(but=rect) => rect(but=off) => off(but=disk)
--lib/help/tksurfer/cuts: add remake cuts w/label trick
--lib/tcl/setdefpatchview.tcl: accept $type*.patch.flat* to set patch view vars
--tksurfer.tcl: patch:match $hemi.$type*.patch.$suff*, curv:match $hemi.$type*
--lib/help/csurf/tksurfer -> bigcursor hotkey doc
--tksurfer.tcl: bind toggle bigcursor to Cmd/Alt-k
--tksurfer.c: change bigcursorflag to draw edges to each neighbor, bind Mod-k
--paint.c: accept AFNI short BRIK (for DWI), require BRICK_FLOAT_FACS=0
--tksurfer.c: eventloop: Tk_GetNumMainWindows(), static global window vars
--tksurfer.c: lower occluding white offscreen map window (not filled on Linux)
--tksurfer.c: fix openglxwindow renderoffscreen, XMoveWindow hack for Mac
--tksurfer.c: separate close_window(), export to tcl
--lib/help/tkmedit/all -> usage of ALL w/spherical ramp
--csurf: fix: add close $id accidentally rm'd below into writearrayparms (!)
--FreeSurferEnv.sh: fix execute-prevention test (no "-bash" broke Mac 10.7 bash)
--mk0: update helpfile list
--csurf: in medtestrender: sub{real,image} => up{real,imag}
--csurf: def missing tkmedit rawdata arg stimcycles (e.g., surfavg, notfour)
--libhelp/tkmedit:rm vals,vals_{write,read},mskn2s,valn2s,msks,msks_{read,write}
--lib/help/tkmedit: sfmid,sfslope,sfthresh
--lib/help/tkmedit: valup,valup_{write,read},valn_read,valn2up,smoothstats
                    roi_time,maskn2up,maskup,maskup_{read,write},mask_ck,fwhm
--tkmedit.tcl: use renamed functs/vars
--tkmedit.c: rename all subsamp/substat/2sub var/functs to upsamp/upstat/2up
--tksurfer.tcl: add alt-shift-arrow translate_brain help/keybindings
--lib/help/tksurfer/{xrot,yrot,xtrans,ytrans}
--lib/help/csurf/{rc-VOLUME,tksurfer}: doc tkmedit cmdline, tksurfer shift-arr
--csurf: pass nondef -wmfillthresh to tkmedit so edit->wht OK below wmfillthresh
--tkmedit.c: accept -wmfillthresh (def=2=WM_MIN_VAL), edit->wht if below
--tksurfer.c: add Shift-arrow -> translate keybindings (vs. no-shift -> rotate)
--surf.c: 1M->4M def maxvertices/maxfaces (bucky3), check overflow, add maxopts
--csurf: log csurf.dat writes (accid. deleted close $id here, fixed above!!)
--csurf: save/pass -wmfillthresh parm to reconditioned fill
--csurf: statbrikstem accepts *Coef*+orig.BRIK (in add. to *+orig_?+orig.BRIK)
--csurf: forcebrik LSB -> MSB HEAD fix message written to cmds-only file
--csurf: Preferences to open/close file into which only cmds are dumped
--FreeSurfer0.8: add lib/Linux-i386/{GLU,libjpeg so's} (!)
--FreeSurferEnv.csh,sh: replace lsb_release with parse /etc/issue, auto rh9
--wrappers.tcl: rm lsb_release (was crashing Fedora15!)
--tkmedit.c: correct FWHM report for 512^3
--fill.c: expose optional -wmfillthresh parm for smoothed upsamp wm (bucky3)
--lib/help/tksurfer/val3d_{paint,clust}
--tksurfer.tcl: add clust parms to NormSamp,Cluster Controls for live surfclust