Per Doug, no longer distribute qdec binary and replace with script th…

…at will echo qdec is no longer supported.

scripts/CMakeLists.txt.ORIG

@@ -0,0 +1,336 @@
+install_configured(
+  annot2std
+  aparc2feat
+  aparc_stats_aseg
+  aparcstatsdiff
+  apas2aseg
+  aseg2feat
+  asegstatsdiff
+  avi2talxfm
+  bblabel
+  bbmask
+  bedpostx_mgh
+  beta2sxa
+  biasfield
+  bmedits2surf
+  browse-minc-header.tcl
+  bugr
+  build_desikan_killiany_gcs.csh
+  cblumwmgyri
+  check_recons.sh
+  check_subject
+  checkMCR.sh
+  clear_fs_env.csh
+  compute_interrater_variability.csh
+  compute_label_vals.csh
+  compute_label_volumes.csh
+  conf2hires
+  cor_to_minc
+  cp-dicom
+  csvprint
+  dcmdir-info-mgh
+  dcmsplit
+  dcmunpack
+  deface_subject
+  defect2seg
+  defect-seg
+  dicom-rename
+  dmri_bset
+  dmrirc.example
+  dmrirc.long.example
+  dmrirc.long.multiscan.example
+  dmrirc.multiscan.example
+  dt_recon
+  epidewarp.fsl
+  extract_talairach_avi_QA.awk
+  feat2segstats
+  feat2surf
+  findsession
+  fix_subject
+  fix_subject-lh
+  fix_subject-rh
+  fix_subject_corrected
+  fix_subject_corrected-lh
+  fix_subject_corrected-rh
+  fix_subject_on_seychelles
+  fixup_mni_paths
+  flirt.newdefault.20080811.sch
+  fname2ext
+  fname2stem
+  freesurfer
+  fsfirst.fsl
+  fs_install_mcr
+  fs_lib_check
+  fs_run_from_mcr
+  fs_time
+  fs_tutorial_data
+  fs_update
+  fscalc
+  fscalc.fsl
+  fsdcmdecompress
+  fsfget
+  fsl.5.0.2.xyztrans.sch
+  fsl_rigid_register
+  fsl_sub_mgh
+  fslregister
+  fsr-checkxopts
+  fsr-coreg  
+  fsr-getxopts
+  fsr-import
+  fsvglrun
+  fvcompare
+  gca-apply
+  gcainit
+  gcaprepone
+  gcatrain
+  gcatrainskull
+  get_label_thickness
+  getfullpath
+  grad_unwarp
+  groupstats
+  groupstatsdiff
+  gtmseg
+  help_xml_validate
+  inflate_subject
+  inflate_subject-lh
+  inflate_subject-rh
+  inflate_subject3
+  inflate_subject_new
+  inflate_subject_new-lh
+  inflate_subject_new-rh
+  inflate_subject_sc
+  irepifitvol
+  is-surface
+  isanalyze
+  IsLTA
+  isnifti
+  isolate_labels.csh
+  isolate_labels_keeporigval.csh
+  jkgcatrain
+  label_child
+  label_elderly_subject
+  label_subject
+  label_subject_flash
+  label_subject_mixed
+  labels_disjoint
+  labels_intersect
+  labels_union
+  listsubj
+  long_create_base_sigma
+  long_create_orig
+  longmc
+  lpcregister
+  make-segvol-table
+  make_average_subcort
+  make_average_subject
+  make_average_surface
+  make_average_volume
+  make_cortex_label
+  make_folding_atlas
+  make_hemi_mask
+  make_exvivo_filled
+  make_symmetric
+  make_upright
+  map_all_labels
+  map_all_labels-lh
+  map_central_sulcus
+  map_to_base
+  meanval
+  mergeseg
+  minc2seqinfo
+  mkheadsurf
+  mkima_index.tcl
+  mkmnc_index.tcl
+  mksubjdirs
+  mksurfatlas
+  mni152reg
+  morph_only_subject
+  morph_only_subject-lh
+  morph_only_subject-rh
+  morph_rgb-lh
+  morph_rgb-rh
+  morph_subject
+  morph_subject-lh
+  morph_subject-rh
+  morph_subject_on_seychelles
+  morph_tables-lh
+  morph_tables-rh
+  mri-func2sph
+  mri-funcvits
+  mri-sph2surf
+  mri_add_new_tp
+  mri_align_long.csh
+  mri_create_t2combined
+  mri_glmfit-sim
+  mri_mergelabels
+  mri_motion_correct
+  mri_motion_correct.fsl
+  mri_motion_correct2
+  mri_nu_correct.mni
+  mri_reorient_LR.csh
+  mris_preproc
+  mris_volsmooth
+  ms_refine_subject
+  orientLAS
+  parc_atlas_jackknife_test
+  pctsurfcon
+  plot_structure_stats.tcl
+  polyorder
+  print_unique_labels.csh
+  progressbar.tcl
+  rbbr
+  rcbf-prep
+  rebuild_gca_atlas.csh
+  rca-base-init
+  rca-long-tp-init
+  recon-all
+  recon-all-exvivo
+  recon-all.makefile
+  reconbatchjobs
+  reg-feat2anat
+  reg-mni305.2mm
+  reg2subject
+  register.csh
+  register_child
+  register_elderly_subject
+  register_subject
+  register_subject_flash
+  register_subject_mixed
+  reinflate_subject
+  reinflate_subject-lh
+  reinflate_subject-rh
+  remove_talairach
+  renormalize_subject
+  renormalize_subject_keep_editting
+  renormalize_T1_subject
+  reregister_subject_mixed
+  rtview
+  run-qdec-glm
+  run_mris_preproc
+  samseg2recon
+  seg2filled
+  segment_monkey
+  segment_subject
+  segment_subject_notal
+  segment_subject_notal2
+  segment_subject_old_skull_strip
+  segment_subject_sc
+  segment_subject_talmgh
+  segpons
+  setlabelstat
+  sfa2fieldsign
+  show_tal
+  skip_long_make_checks
+  slicedelay
+  sphere_subject
+  sphere_subject-lh
+  sphere_subject-rh
+  spm_t_to_b
+  spmmat2register
+  spmregister
+  sratio
+  stem2fname
+  surfreg
+  tal_compare
+  talairach
+  talairach2
+  talairach_mgh
+  talsegprob
+  test_recon-all.csh
+  test_tutorials.sh
+  thickdiffmap
+  tkmeditfv
+  tkregisterfv
+  tksurferfv
+  trac-all
+  trac-paths
+  trac-preproc
+  train-gcs-atlas
+  unpack_ima.tcl
+  unpack_ima1.tcl
+  unpack_mnc.tcl
+  unpackimadir
+  unpackimadir2
+  unpackmincdir
+  unpacksdcmdir
+  UpdateNeeded
+  usbtree
+  vertexvol
+  vno_match_check
+  vol2segavg
+  vol2subfield
+  vol2symsurf
+  vsm-smooth
+  wfilemask
+  wm-anat-snr
+  wmedits2surf
+  wmsaseg
+  xcerebralseg
+  xcorr
+  xfmrot
+  xhemi-tal
+  xhemireg
+  xsanatreg
+  DESTINATION bin
+)
+
+install_pyscript(
+  long_submit_jobs
+  long_qdec_table
+  long_submit_postproc
+  long_stats_tps
+  long_stats_slopes
+  long_mris_slopes
+  long_stats_combine
+  aparcstats2table
+  asegstats2table
+  tractstats2table
+  stattablediff
+  merge_stats_tables
+  fspalm
+  rca-config
+  rca-config2csh
+)
+
+install(FILES mri_nu_correct.mni.help.xml DESTINATION docs/xml)
+install_append_help(bbregister bbregister.help.xml bin)
+
+install_symlinks(fs_spmreg.glnxa64 irepifitvol.glnx64 TYPE programs DESTINATION bin)
+
+if(NOT MINIMAL)
+
+  # these tcl scripts should be excluded from a minimal distribution
+  install(PROGRAMS
+    allisons_surfaces.tcl
+    curv-flat.tcl
+    curv-views.tcl
+    dara_data.tcl
+    dipmovie-flat.tcl
+    eccen-flat.tcl
+    eccen-views.tcl
+    fs-flat.tcl
+    fs-make.tcl
+    fs-views.tcl
+    mk-fieldsign.tcl
+    offsetmovie.tcl
+    phasemovie.tcl
+    polar-flat.tcl
+    polar-views.tcl
+    readenv.tcl
+    real-flat.tcl
+    real-views.tcl
+    saveflat.tcl
+    saveviews.tcl
+    setdefpatchview.tcl
+    solmovie-flat.tcl
+    twocond-flat.tcl
+    twocond-masked-views.tcl
+    twocond-views.tcl
+    wrappers.tcl
+    fsgdfPlot.tcl
+    DESTINATION lib/tcl
+  )
+
+  install(PROGRAMS process_exvivo_diff_data_bay3.sh DESTINATION bin COMPONENT nmr EXCLUDE_FROM_ALL)
+
+endif()

scripts/qdec

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+echo "Please note that qdec is no longer supported and has been removed from the freesurfer distribution."
+echo "Use the \"command line\" stream instead (ie, mris_preproc, mris_surf2surf, mri_glmfit, and mri_glmfit-sim)."
+
+exit 1
+

tktools/CMakeLists.txt.ORIG

@@ -0,0 +1,36 @@
+project(tktools)
+
+# The tk GUIs - tkmedit, tkregister2, tksurfer, and qdec - are no
+# no longer maintained and cannot be built due to incompatibles across
+# systems and with modern vtk (which no longer offers tcl wrapping).
+# Eventually these programs can be completely deprecated, but for now
+# we have to option to install precompiled binaries in linux distributions.
+
+if(NOT APPLE)
+
+  install_symlinks(
+    qdec
+    tkmedit
+    tkregister2
+    tksurfer
+    TYPE programs
+    DESTINATION bin
+  )
+
+  install(PROGRAMS
+    scripts/tkanalyse.tcl
+    scripts/tkm_common.tcl
+    scripts/tkm_dialog.tcl
+    scripts/tkmedit.tcl
+    scripts/tkm_functional.tcl
+    scripts/tkm_graph.tcl
+    scripts/tkm_wrappers.tcl
+    scripts/tkregister2.tcl
+    scripts/tksurfer.tcl
+    scripts/tkUtils.tcl
+    DESTINATION tktools
+  )
+
+  install_tarball(resources.tar.gz DESTINATION lib)
+
+endif()