2023.1204:

Below is a list of all current AFNI handouts.  I'd like to trim this down,
triaging the contents of afni_handouts into 3 categories:
   keep in the main afni_handouts/ directory—things we teach using
   move into a (new) afni_handouts/supplements/ directory
        - things we don't teach with, but are still useful
   remove from afni_handouts/ altogether: outdated, unnecessary

We can label these using handy colorcoding.


m  3dQwarp.pdf
m  Qwarp.pdf

d  AFNI_2018_12_SCNU_5day_schedule.pdf
d  AFNI_2019_03_NIH_5day_schedule.pdf
d  AFNI_2019_04_UWMilwaukee_5day_schedule_rev.pdf
d  AFNI_2019_10_NIH_3day_schedule_Kansas.pdf
d  AFNI_2019_11_NIH_5day_schedule.pdf
d  AFNI_2020_03_LIBR_5day_schedule.pdf
d  AFNI_2020_03_NIH_5day_schedule.pdf
d  AFNI_2023_10_NIH_5day_schedule.pdf
d  AFNI_Mar2019_dti_1day_schedule.pdf
m  AFNI_global_datasets.pdf
m  AFNI_interactive2.pdf
k  AFNIintergoals.txt (rename to afni03_commands.txt)
d  BML.pdf (can be removed, is just part of a slide presentation)
d  Cox-Abstract.pdf
m  Cox_Poster_HBM2013.pdf (rename to supplements/ohbm_2023_cox_glen_warping.pdf)
d  DTI.pdf : remove (just placeholder for schedule)
m  Driving_Afni+Suma.pdf
m  ExptDsgn.pdf
k  FATCAT_01_background_dti.pdf
k  FATCAT_02_dti_tracking_intro.pdf
k  FATCAT_03_dti_tracking_funcs.pdf
k  FATCAT_04_netw_stats_mvm.pdf
k  FATCAT_05_suppl_trcomp.pdf
k  FATCAT_HO.pdf
m  FMRI_basics.pdf
m  PPI.pdf
d  ROI.pdf (can be removed, is just part of a slide presentation)
k  RegressionHandsOn.pdf
m  SliceTiming.pdf
m  SomeScripts.pdf
d  TORTOISE_Okan.pdf
m  Warping-for-EPI.pdf (rename to supp/notes_on_warping_for_epi.pdf)
k  advanced_vis_notes.txt
k  afni00_unix.pdf
k  afni01_intro.pdf
m  afni02_to3d.pdf
k  afni03_interactive.pdf
m  afni04_fmri.pdf      (todo: rename afni22 to afni04)
k  afni05_regression.pdf
m  afni06_decon.pdf

k  afni07_ETAC.pdf
d  ETAC_clone.pdf
m  afni_clustering_etac.pdf
m  Clusters_2017.pdf

k  afni07_advanced.pdf
m  afni09_render.pdf
m  afni09_render_work.txt
k  afni10_volreg_talairach.pdf
k  afni10_volreg_talairach_extras.pdf
k  afni11_roi.pdf
k  afni11_roi_cmds.txt (todo: rename to commands)
k  afni14_alignment.pdf
k  afni14_alignment_cmds_3dvolreg.txt (todo: rename to commands)
m  afni15_templates_atlases.pdf (todo: rename something back to this)
k  afni16_start_to_finish.pdf
m  afni17_ht03.pdf
k  afni20_instastuff.pdf
k  afni22_indiana.pdf (todo: rename to afni04)

k  afni23_restingstate.pdf
m  RestingState.pdf (afni23*.pdf is prob most recent)
m  RestingState_Denoising.pdf (see afni23)
m  BiasSources_RS-FMRI.pdf (see afni23)

d  RestingAFNI.pdf
m  Connectivity.pdf
m  afni24_GroupAna.pdf (been superceded by afni32*pdf)
m  afni25_GroupAna_HO.pdf (been superceded by afni35*pdf)
m  afni26_ROI-based-modeling.pdf (been superceded by afni32*pdf, also)
k  afni30_vol_dset_basics.pdf
m  afni31_sidedness_tests.pdf
k  afni32_group_analysis.pdf
k  afni35_GroupAna_HO.pdf
m  afni40_plm_GroupAna.pdf
k  afni41_results_reporting.pdf
m  afni_proc.pdf
d  bootcamp_schedule_dti_2018_10_22.pdf
d  bootcamp_schedule_dti_2019_11_prelim.pdf
d  bootcamp_schedule_dti_2020_04_03.pdf
m  brainhack_afni_driving.txt
d  colorbar2.pdf
k  contributor_connections.niml.dset
m  deface_anat.csh
k  dir_struct.pdf (rename to afni00_unix_tree.pdf)
m  driving_afni_images.tcsh
d  effect.pdf (can be removed, is just part of a slide presentation)
d  global_process_commands.txt
d  global_process_outline.txt
   index.html
d  intro_notes.txt
d  outRBA.pdf (can be removed, is just part of a slide presentation)
k  suma.pdf
k  suma_fatcat.pdf
k  suma_keystrokes.txt
m  zebrafish_suma.mpg

   **maybe make a separate dir for these, for self-learning/reference?
   move under new directory: reference
   afni19_jazz.pdf
   afni19_jazz_answers.pdf
   afni19_jazz_hints.pdf
   MiscRoundup.pdf
   JewelBox.pdf         (misc/jewel very similar)
   QuickTasks.doc.pdf
   QuickTasks.pptx.pdf
   afni_tips.pdf

   move under new directory: nih_info
   nih_campus_map_highlightsC.pdf
   nih_campus_map_highlights_2023_10.pdf
   nihmap.gif

cleanup commands:
   mkdir keep delete supplements reference nih_info
   mv nih* nih_info
   mv *jazz* MiscRoundup.pdf JewelBox.pdf QuickTasks.* afni_tips.pdf reference/
   rm index.html
   grep '^k ' ../afni_handouts.cleanup.txt
   grep '^k ' ../afni_handouts.cleanup.txt | awk '{print $2}'
   mv `grep '^k ' ../afni_handouts.cleanup.txt | awk '{print $2}'` keep
   find . | grep afni35
   mv afni35_GroupAna_HO.pdf keep/
   vi ../afni_handouts.cleanup.txt
   fg
   j
   grep '^m ' ../afni_handouts.cleanup.txt | awk '{print $2}'
   mv `grep '^m ' ../afni_handouts.cleanup.txt | awk '{print $2}'` supplements
   grep '^d ' ../afni_handouts.cleanup.txt | awk '{print $2}'
   mv `grep '^d ' ../afni_handouts.cleanup.txt | awk '{print $2}'` delete/
   ls -l
   mv afni50_templates_atlases.pdf chauffeur_demo.txt keep
   history >> ../afni_handouts.cleanup.txt

   # more renaming to do, but start with this
   cd keep
   mv AFNIintergoals.txt afni03_commands.txt
   mv dir_struct.pdf afni00_unix_tree.pdf

   # and restore
   mv keep/* .
   rmdir keep