###################################################################
UPDATE: 22 Jul 2019
###################################################################

----------------------------------------------
Mask overlay using any combo of MGH annotation regions
----------------------------------------------

After an MGH surface annotation file has been read
with "D" on the "label:" line, you can use it to
mask currently displayed overlay data by
annotation idnum's.

Use an alternate shift-right-click on the "D"
button, which brings up two popups.  The first one
lists the idnum's of all the named regions.

In the second, you enter a space-separated list of
idnum's to show (any not listed are masked).

This is useful, for example, to see phase encoded
data from annotation regions (easier than with
colored annotation borders).

Once an annotation has been used to mask data, the
currently displayed data can optionally be written
out to a single label, or to per-area label files
by ticking either "extract_unmasked_flag" or
"extract_overlays_flag".  In the first case, this
writes a single label:

  rh-<infix>.label

while in the second case, each displayed region is
written into separate labels named by region name:

  rh-<infix>=<areaname>.label

The output by default goes to the subject's label
directory.

Those two operations are slightly out-of-place for
the label "D" button (display) as opposed to being
to being attached to the label "W" button (write),
but more convenient here.

----------------------------------------------
Csurf accepts inst/subj/funct paths with spaces
----------------------------------------------

After some hair-pulling, csurf/tksurfer/tkmedit
et al. now all work when the directory paths for
CSURF_DIR, SUBJECTS_DIR, or FUNCTIONALS_DIR
contain spaces.

In the process of fixing this, I noticed that the
standard MGH freesurfer 5.3 setup scripts
(FreeSurfer.{c}sh), and recon-all, *won't* work in
this case.  AFNI will work, when you add
AFNI_PATH_SPACES_OK=YES to its env.

The csurf compile script, mk0, won't work with
spaces in the $srcdir path because the configure
scripts for the external libraries (e.g., tcl/tk)
won't accept path spaces.  However, this doesn't
affect endusers.

Because this is not yet extensively tested, and
because spaces disable MGH freesurfer, you have
to add "force" to make csurf run when it detects
spaces in the paths to CSURF_DIR, SUBJECTS_DIR,
or FUNCTIONALS_DIR like so:

  csurf -f

----------------------------------------------
Truncphase upgrades (wrap, softer truncphase)
----------------------------------------------

The "truncph" tickbox and truncphase limits has
been upgraded to allow phase wrap (for
complex-valued data) -- that is, you can now use a
higher(0-1) phase value in the left box.

A new tickbox was also added just to the right of
"truncph", labeled "sft" (soft), that turns off
hard truncation (if ON) and instead ramps the
visible signal down to zero over 5% of the total
phase angle range beyond the set limits
(adjustable with new entry below truncation
limits).

This reduces the contrast and therefore the
distracting prominence of the (irrelevant) ragged
shape of the color edges at the truncation point.

----------------------------------------------
Fix Linux cmdline use of tksurfer, tkmedit, tkregister
----------------------------------------------

Very sorry to have just noticed that I broke
cmdline use of tksurfer, tkmedit, tkregister on
Linux (Jun2018) by incorrectly checking for
DYLD_LIBRARY_PATH instead of LD_LIBRARY_PATH.
Fixed.

----------------------------------------------
Easy re-run recon-all after edit orig.mgz
----------------------------------------------

A new tickbox, "start from edited orig.mgz" was
added to the panel for:

  MGHTools -> Run recon-all

Sometimes, the standard freesurfer pipeline will
fail to properly normalize all parts of an
otherwise good quality structural image (e.g.,
due to uncorrected variations in B1 transmit).  A
typical problem is that the anterior temporal
lobes are too dark, causing parts of them to be
lost in the reconstruction.

This can be quickly fixed by using spherical
hand-normalization to get this region bright
enough so that freesurfer can normalize it
properly.  Open orig.mgz for the subject in csurf
tkmedit using VOLUME, use [fn-]F3 to get the
hand-normalization controls, then use the "sph"
tickbox for spherical normalization (left-click:
linear, middle-click: Gaussian).  The selected
point sets the center of the normalization field,
"ffrac0:" sets the scale factor at the center
(e.g., 1.5), and "lim0:" and sets the radius (in
pixels) where the correction falls to 1.0 (no
change).

Use "TEST" to run the correction (e.g., with
different values) and put the result in the
COMPARE buffer.  To make the eventual effects more
visible "TRUNC" can be used to truncate the gray
matter (lower number).  Use "APPLY" to apply the
correction to the editable buffer, and finally
"SAVEIMG" to write it back out to orig.mgz

Then, to use the edited orig.mgz as a starting
point for recon-all, tick "start from edited
orig.mgz", select the edited subject from the
"new/redo subject:" dropdown, and click RECON-ALL.
This only skips step 1 (convert, conform, compute
Talairach), using the new option -all-skipstep1 of
the very slightly modifed recon-all script:

  $CSURF_DIR/bin/noarch/recon-all5.3b


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

ima2brik can append protocol name to numbered output files

fixed REDRAW crasher if annotmaskflag and no annotation loaded

rm check for _f in filename (do_fdr) so no err when csurf doesn't load stat

fix cmdline Linux use tk{surfer,medit,register}! (chk LD_LIB.. not DYLD_LIB..)

fix csurf: look for license.txt so don't block run recon-all on fs6/Centos7!

more surfcombine functions exposed

surfcombine read_{real,complex} swap error fixed!

surfcombine also accepts/writes curv-format wfiles

middle-click-W on "rgb:" line forces write transparent tiff

ctrl-R-REDRAW toggles overlay multiple single-voxel timecourses

fixpial script to correct big triangles at 'poles' of fsaverage surfs
[not in distro since extra 11M]

AVGSURF also fixes average avg pial defects at 'north/south' poles

re-compiled latest code for ancient PPC :-}



##########################################################################
UPDATE: 22 Jul 2019
##########################################################################

--[### end spaces-in-{CSURF,SUBJECTS,FUNCTIONALS}_DIR nightmare ###]
--tkmedit.tcl: pathspaces: listcmd_{surf,ims}: set "$list $m" =>lappend list $m
--csurf: refactor dyld/path spaces runafni proc for afni{cmd,allcmd,structcmd}
--csurf: afnicmd: omit empty dyld for namespace fix: env cmd uses as arg not env
--csurf: use AFNI_PATH_SPACES_OK=YES if detect FUNCTIONALS_DIR space (multiple)
--csurf: {l}backslashspaces runacmd args/listargs that could have spaces (~135)
--FreeSurfer.sh: fix lss,lsf,cds,cdf functions to accept spaces
--FreeSurfer.csh: fix lss,lsf,cds,cdf aliases to accept spaces
--mk0: unwind allow spaces edits to "tcltktix" (spaces break tcl configure's)
--mk0: (sh) allows space in srcdir path only for option "dist"
--mk0.csh: block all options if spaces in srcdir path, suggest mk0 (sh)
--N.B.: 10.12 tk{surfer/medit/strip} compiles coredump on 10.6 (converse OK)
--backslash-quote cat/gunzip/system args for paths w/spaces in following:
 => calcimg.c/fill.c/rawaverage.c/regcor.c/tkregister.c/wmfilter.c/tkstrip.c
--csurf: backslash spaces in runacmd pwd report
--csurf: medtestrender: backslash spaces in -real,-imag,-mask args for tkmedit
--csurf: backslash-quote maybe-space-containing DYLD cmdline passed to afni
--csurf: choosedir strips double-slash seen by file exists but not by tixDirTree
 [spaces now OK: opencmdsonlyfile,"Set {Subjects, Funct Sessions} Directory"]
 [spaces now OK: mknew{subject,funct},choose{subject,funct}dir,cpdir,avgsurfcmd]
--csurf: choosedir: strip curly braces in path-with-space added by glob (fixed!)
--csurf: MGHTools->RunRecon-all warn/cont. if space(s) in {FSURF,SUBJECTS}_DIR
--tksurfer.tcl: warn/catch mris_pmake ("Dijk" geodesic) fail w/spaces in PATH
--tksurfer.tcl: Dijk (mris_pmake) won't accept SUBJECTS_DIR spaces, add log/warn
--tksurfer.tcl: listcmd_{tcl,label,val,rgb} work (dblquoted auto-curly-braced)
--tksurfer.tcl: same fix for listcmd_{area,patch,lut}, select_{area,patch}
--tksurfer.tcl: path spaces: listcmd_curv, select_curv: set "..." => lappend
--tksurfer.c: [left some single-quoted system() args: OK unless change->runacmd]
--csurf: backslash spaces in tcl source file args
--csurf: backslash (proc) bindir/afnidir/mincdir/noarchdir spaces for runacmd sh
--wrappers.tcl: new proc: backslashspaces <path>
--tksurfer.c: backslash-quote cat/gunzip/system file args for paths with spaces
--tkmedit.c: backslash-quote cat/gunzip/system file args for paths with spaces
--bin/noarch/mk: add quotes to it make work with spaces in install dir path
--FreeSurferEnv.csh: LIB/PATH spaces now OK (use quoted lists, :q preserves q's)
--FreeSurferEnv.sh: LIB/PATH spaces now OK (use set/unset IFS)
--FreeSurferEnv.csh: if $path member w/space, don't touch (tmp fix, superseded)
--FreeSurferEnv.sh: allow $PATH bloat if memb have spaces (tmp fix, superseded)
--[### begin spaces-in-{CSURF,SUBJECTS,FUNCTIONALS}_DIR nightmare ###]
--csurf: better symbolic link ex. to fix path w/space (doesn't fix tix dirtree!)
--lib/help/csurf/tkmedit: rearrange, doc block double clicks, doc mask ctrls
--lib/help/tkmedit/{im2entry,im2read,seglabel}: update, doc block double clks
--tksurfer.tcl: do_annotmask checks overwrite if omnibus label (not multi)
--lib/help/tksurfer/label_read: update
--tksurfer.c: redraw crasher: set_{real,cmplx}_color didn't chk brainregion/cnt
--tksurfer.tcl: add $extract_unmasked_flag tickbox: write_val_unmasked_vertices
--tksurfer.c: add funct: write_val_unmasked_vertices
--tksurfer.tcl: rm chk _f in filename (do_fdr) so no err when csurf noload stat
--csurf: add View Functional Data tickbox for softtruncphaseflag ("Sft")
--csurf: readheader (READ HEADER) init alignscanparms(brightness) 1.0 if align
--ima2brik: inclprot trimleft 08's to block octal in format (fix past scan07)
--csurf: add "start from edited orig.mgz" tick to Run MGH recon-all panel
--bin/noarch/recon-all5.3b: copy of recon-all w/new opt: -all-skipstep1
--mk0{.csh}: insttmp/dist append tarfile date to README.txt
--ima2brik: add -afniprot, -niftiprot to insert protocol names in output BRIKs
--tkregister.c: fix look for DYLD_LIBRARY_PATH on Linux (broke cmdline use!)
--tkmedit.c: fix look for DYLD_LIBRARY_PATH on Linux (broke cmdline use!)
--tksurfer.c: fix look for DYLD_LIBRARY_PATH on Linux (broke cmdline use!)
--mk0{.csh}: also include my license.txt
--csurf: check CSURF_DIR for .license *or* license.txt (fs6.0 on centos7)
--surfcombine.c: expose additional functs, better documentation stack ops
--surfcombine.c: read_binary_values: fread -> freadFloat (!)
--lib/help/tksurfer/truncphasesoft: update (re-use softtruncphase tick help)
--tksurfer.tcl: add unlabaled entry next to invph tick for $softtruncwidth
--tksurfer.tcl: "invphase" -> "invph" to make room (update relevant helpfiles)
--tksurfer.c: add/export softtruncwidth (width of lin ramp-to-zero)
--mk0{.csh}: add new helpfile: truncphasesoft
--csurf: new $softtruncphase helpfile: truncphasesoft
--lib/help/tksurfer/{truncphase,rgb_write,rgb_write2}: update
--tksurfer.tcl: overload mid-click-WN on "rgb:" line to force write transparent
--tksurfer.tcl: overload mid-click-W on "rgb:" line to force write transparent
--tksurfer.tcl: add "s" tickbox for $softtruncphaseflag, "truncphase"->"truncph"
--tksurfer.c: add/export softtruncphaseflag (lin ramp-to-zero beyond limits)
--annot2roi.tcl: warn opposite hemisphere not yet done
--surfcombine: add write_{real,complex}_cv
--surfcombine: prohibit mixing orig (subset OK) with curv (full) valfiles
--surfcombine.c: stacksize: 100->300
--surfcombine.c: read_binary_values() also accepts curvfiles
--lib/help/tksurfer/truncphase{flag,min,max}: update
--tksurfer.tcl: ticking colscale=1=heat resets truncphase{min,max} to orig def
--tksurfer.tcl: truncphase{flag,max,min} allow wrapped phase limits if complex
--tksurfer.c: all set_complex_color's accept wrapped truncphase limits
--lib/help/tksurfer/label: update
--csurf: AVGSURF also fixes fsaverage pial 'poles' (for final disp, not sample)
--[don't fix less-used fsaverage surfs w/'pole' defects: orig, white]
--bin/noarch/fixpial: script to fix giant triangles in fsaverage pial
--lib/help/tksurfer/{label_read,label_write}: update
--tksurfer.tcl: setfile label w/relative now defaults to subject (was funct!)
--tksurfer.tcl: mask annot popup can write labels (not in "W" but convenient)
--tksurfer.c: add funct: write_val_idnum_vertices <idnum>
--lib/help/tksurfer/redraw: update
--tksurfer.tcl: wire toggle multitimecourseflag to ctrl-mid-REDRAW
--csurf: setup align/funct page sets iscandir so AFNI button goes to right dir
--lib/help/tksurfer/{label_toggle,label_read,hbutt}: update
--tksurfer.tcl: annotmaskctrls opens current MGH annot ctab in helpwin
--tksurfer.c: read_mgh_annot: write MGH ctab in scripts (vs. overwrite in label)
--tksurfer.tcl: annotmaskctrls/do_annotmask: pick annot idnum(s) to not mask
--tksurfer.tcl: bind pick annot idnum vis ctrls popup to "D" butt (shift-R-clk)
--tksurfer.tcl: bind annotmaskflag to label tickbox (5th overload: shift-R-clk)
--tksurfer.c: set_{real,complex}_color: if annotmaskflag use brainreg maskflag
--tksurfer.c: add funct: set_idnums_visibility <0,1> => brainregion[i].maskflag
--tksurfer.c: add funct: set_idnum_visibility <idnum> <0,1> => .maskflag
--tksurfer.c: add annotmaskflag (enable masking by annot regions)
--lib/help/csurf/makenewfunct: update
--lib/help/tkmedit/im2read: update

##########################################################################
PREVIOUS UPDATE: 08 Feb 2019
##########################################################################
--lib/help/tkmedit/roiup_write: update
--tkmedit.tcl: overload "W" button on "roiup:" line with write_allsegids
--tkmedit.c: add write_allsegids
--csurf: fix afni crash new Mac: add DYLD if exists /opt/X11/lib/flat_namespace
--lib/help/tkmedit/roiup_time: update
--tkmedit.tcl: overload "T" on "roiup:" line to run write_segid_timecourses
--tkmedit.c: add write_segid_timecourses <idnum> (first load segmentation)
--csurf: block all abspath paradigmdir's in deconvcmd, rawaveragecmd (concat)
--lib/help/csurf/setuprand: suggest only stim1Ds dir inside each scandir
--FreeSurferEnv.{c}sh: Mac: if exists /opt/X11/lib/flat_namespace add to DYLD_
--tkregister.tcl: fix cmd typo disabling SAGMIRR! (showvisble -> showvisible)
--tkmedit.c: thin gray dividers for all3views
--tksurfer.tcl: "clo" button R-click help
...