#!/bin/tcsh # for olay, default will be "show all"-- update fatcats to call for # 98%iles of non-zeros! # update fatcats for ulays, as well! @global_parse `basename $0` "$*" ; if ($status) exit 0 # ----------------------------------------------------------------- # Multipurpose, driven viewer. Meant to be used for auto QC in # scripts. # # This function constructed by: PA Taylor (NIMH, NIH, USoA) # # Dec, 2016: # + conception and start. # # Jan, 2017: # + add I/O. # # Jan, 2017b: # + if ulay/olay are in different files, have tmp readdir. # + default now to proceed if no olay given but also no # '-olay_off' is used. # # Jan, 2017c: # + better centering of slices. # # Jan, 2017d: # + better slice selection/centering. # + adjust for different orders of orientation # #set version = "1.6"; set rev_dat = "Feb 6, 2017" # + olay quotes # #set version = "2.1"; set rev_dat = "Feb 27, 2017" # + can have IJK labels -> DWImager # #set version = "2.2"; set rev_dat = "Mar 29, 2017" # + xvfb-run introduced: should work better/more generally # on biowulf? [thanks D. Godlove for suggesting this fix] #set version = "2.3"; set rev_dat = "May 3, 2017" # + xvfb-run: new option to set colordepth to 24, so opacity works # in the AFNI commands # #set version = "2.4"; set rev_dat = "May 20, 2017" # + more unique naming of tempdir; safer for cluster runs # #set version = "2.5"; set rev_dat = "June 1, 2017" # + back to regular xvfb and Bob's search # #set version = "2.6"; set rev_dat = "June 1, 2017" # + default interpolation to NN, but add in option to set # #set version = "2.7"; set rev_dat = "June 20, 2017" # + new opts, for SET_SUBBRICKS # #set version = "2.8"; set rev_dat = "Aug 17, 2017" # + new opt, allow SET_XYZ # #set version = "2.9"; set rev_dat = "Sep 04, 2017" # + remove '-outdir ...' and have path set by '-prefix ...', # like most other AFNI programs # + set default zoom to NN, so no smoothing # via -> AFNI_IMAGE_ZOOM_NN # #set version = "3.0"; set rev_dat = "Nov 24, 2017" # + start helpifying # #set version = "3.1"; set rev_dat = "Nov 27, 2017" # + improve/correct slice-width selection (thanks, J. Lee!) # #set version = "3.2"; set rev_dat = "Feb 21, 2018" # + add in p-to-stat capability for thresholding, via # "-thr_olay_p2stat .." opt # #set version = "3.3"; set rev_dat = "May 29, 2018" # + add in cropping ability, via '-crop_*' options # #set version = "3.4"; set rev_dat = "July 11, 2018" # + start adding in the 4D options: -mode_4D # #set version = "3.4"; set rev_dat = "July 12, 2018" # + mode_4d opts seem to be working now, at least some... # #set version = "3.5"; set rev_dat = "July 13, 2018" # + need to require sidedness of test for -thr_olay_p2stat! # + also switch to use p2dsetstat internally for getting that # threshold # #set version = "3.6"; set rev_dat = "July 20, 2018" # + in 4D mode, want percentage values to be consistent across all # slice montages. this will be done by calculating a table for # each of the reassembled volumes (= glued together slices from # across time for a each plane), and then combining these # percentile tables by taking the max at each percentile. # #set version = "3.7"; set rev_dat = "July 23, 2018" # + revising ulay percentiles-- of *whole* object, not just of # non-zero values as before. This should better match AFNI GUI # behavior, and lead masks to not have a range [1,1] # + now including the new drivability with: SET_ULAY_RANGE # (Thanks, Emperor Zhark!) # #set version = "3.8"; set rev_dat = "July 23, 2018" # + updating olays for 4d and thresholding # + no longer using pre-calc'ed tables # #set version = "3.9"; set rev_dat = "July 25, 2018" # + several small updates; renamed my_slicer, changed some help, # + default ulay now 0-98% in vol. # set version = "4.0"; set rev_dat = "July 27, 2018" # + deal with percentile values if user entered 4D olay/ulay for # non-4Dmode, but including subbrick selectors # # ===================================================================== # For more info about opts/fields, see: # # https://afni.nimh.nih.gov/pub/dist/doc/program_help/AFNI.afnirc.html # # https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html # ----------------- default/initialized environments -------------- # GUI settings for simplicity setenv AFNI_NOSPLASH YES setenv AFNI_SPLASH_MELT NO setenv AFNI_ENVIRON_WARNINGS NO setenv AFNI_COMPRESSOR NONE setenv AFNI_IMAGE_GLOBALRANGE VOLUME setenv AFNI_IMAGE_LABEL_IJK NO # thanks, Bob! setenv AFNI_IMAGE_ZOOM_NN YES # [PT: Sep 04, 2017] # ------------------------------------------------------------------- # ------------------- default/initialized variables ----------------- set ulay = "" # inp underlay set olay = "" # inp overlay set see_olay = "+" # turn *off* olay disp set ftype = PNG # output file format set impref = "image_file" # prefix of output; other things added set odir = "." # default output directory is "here" set my_cbar = "Plasma" # colorbar, if necessary set bufac = "2" # blowup factor set frange = "0" # either this (autorange), or user puts in set USER_FRANGE = 0 # internal toggle only set thrnew = "0." # threshold value (zero default) set p_thr_val = "" # for p-to-stat capability in thr set p_thr_side = "" # for p-to-stat capability in thr set thrflag = "*" # threshold flags set crossh = "OFF" # crosshairs OFF by default set opac = 6 # opacity of overlay set mx = 3 # 'x' dim of montage set my = 3 # 'y' dim of montage set delsag = -1 # (int) slice space in sag orient set delaxi = -1 # (int) slice space in axi orient set delcor = -1 # (int) slice space in cor orient set USER_COORS = 0 # switch to let user pick IJK set coors = ( 0 0 0 ) set gapord = ( 0 0 0 ) set coor_type = "SET_IJK" # default, can switch to SET_XYZ # for SET_PBAR_ALL set pbar_sign = "-" # + is pos. only, - is both (switch for both) set ncolors = "99" # default number of colors set topval = 1 # upper scale value in colorbar set func_resam = "NN" # def. no resample; opt: {NN|Li|Cu|Bk} set acropx = ( 0 0 ) # [PT: May 29, 2018] set acropy = ( 0 0 ) # can crop in axi, sag, cor; x- and y-axes set scropx = ( 0 0 ) set scropy = ( 0 0 ) set ccropx = ( 0 0 ) set ccropy = ( 0 0 ) set MODE_4D = 0 set spre4d = "sli4d" set opre4d = "" set upre4d = "" set Nreps = 1 # default: for if we *don't* have -mode_4D # this order matches how stuff comes out in MODE_4D set ppord = ( "sagittal" "coronal" "axial" ) set pord = ( "sag" "cor" "axi" ) set subbb = ( -1 -1 -1 ) # for SET_FUNC_ALPHA set alpha_par = "Off" # set alpha_floor = "" # set alpha_edgize_no = 0 # =1 -> SETENV AFNI_EDGIZE_OVERLAY NO set do_quit = "QUITT" # quick-quit; not subject to change # tmp dir, in case under- and overlays are in separate dirs set tmp_code = `3dnewid -fun11` # should be essentially unique hash set tmp_dir = "__tmp_chauf_${tmp_code}" set DO_CLEAN = 0 set my_clean = "-no_clean" set read_dir = "" set read_ulay = tmp_ulay.nii set USER_ULAY_RANGE = 0 # def: user doesn't enter ulay range set ulay_nz = "" # [PT: Jul 23, 2018] new ulay def: NOT non-0 set olay_nz = "-non-zero" # [PT: Jul 23, 2018] same olay def: non-0 set com_ulay_str = "DO_NOTHING" # [PT: Jul 23, 2018] so we can drive values set umax_scale = 1 set umax_magic = "98" set BIGNEG = -100000001 @ BIGNEGp1 = $BIGNEG + 1 # ------------------------------------------------------------------- # ----------------------------- ugh --------------------------------- # needed to deal with orientation permutability : AIL, LAI, PSR, etc. set listori = ( 'R' 'L' 'A' 'P' 'I' 'S' ) set listind = ( 1 1 2 2 3 3 ) # ------------------------------------------------------------------- # ------------------- process options, a la rr ---------------------- if ( $#argv == 0 ) goto SHOW_HELP set ac = 1 while ( $ac <= $#argv ) # terminal options if ( ("$argv[$ac]" == "-h" ) || ("$argv[$ac]" == "-help" )) then goto SHOW_HELP endif if ( "$argv[$ac]" == "-ver" ) then goto SHOW_VERSION endif # required if ( "$argv[$ac]" == "-ulay" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set ulay = "$argv[$ac]" else if ( "$argv[$ac]" == "-olay" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set olay = "$argv[$ac]" else if ( "$argv[$ac]" == "-olay_off" ) then set see_olay = "-" # [PT: July 11, 2018] Do some reslicing of dsets and glue # together; will require at least one of ulay and olay to be 4D else if ( "$argv[$ac]" == "-mode_4D" ) then set MODE_4D = 1 # [PT: Sep 04, 2017] Change behavior to get output dir from just # the prefix. Duh. else if ( "$argv[$ac]" == "-prefix" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 #set impref = "$argv[$ac]" set impref = `basename "$argv[$ac]"` set odir = `dirname "$argv[$ac]"` else if ( "$argv[$ac]" == "-cbar" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set my_cbar = "$argv[$ac]" else if ( "$argv[$ac]" == "-blowup" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set bufac = "$argv[$ac]" else if ( "$argv[$ac]" == "-set_xhairs" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set crossh = "$argv[$ac]" else if ( "$argv[$ac]" == "-opacity" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set opac = "$argv[$ac]" else if ( "$argv[$ac]" == "-delta_slices" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 @ gapord[1] = "$argv[$ac]" @ ac += 1 @ gapord[2] = "$argv[$ac]" @ ac += 1 @ gapord[3] = "$argv[$ac]" else if ( "$argv[$ac]" == "-thr_olay" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set thrnew = "$argv[$ac]" # [PT: Feb 21, 2018] else if ( "$argv[$ac]" == "-thr_olay_p2stat" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set p_thr_val = "$argv[$ac]" # [PT: July 13, 2018] anything allowed by p2dsetstat else if ( "$argv[$ac]" == "-thr_olay_pside" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set p_thr_side = "$argv[$ac]" else if ( "$argv[$ac]" == "-thrflag" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set thrflag = "$argv[$ac]" # [PT: June 20, 2017]: SET_SUBBRICKS i j k else if ( "$argv[$ac]" == "-set_subbricks" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set subbb[1] = "$argv[$ac]" @ ac += 1 set subbb[2] = "$argv[$ac]" @ ac += 1 set subbb[3] = "$argv[$ac]" # refers to olay else if ( "$argv[$ac]" == "-func_range" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set frange = "$argv[$ac]" set USER_FRANGE = 1 # SET_FUNC_RESAM [c.]{NN|Li|Cu|Bk}[.{NN|Li|Cu|Bk}] else if ( "$argv[$ac]" == "-func_resam" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set func_resam = "$argv[$ac]" if ( ( "$func_resam" != "NN" ) || \ ( "$func_resam" != "Li" ) || \ ( "$func_resam" != "Cu" ) || \ ( "$func_resam" != "Bk" ) ) then echo "** Error! '-func_resam ...' input" echo " needs to be one of {NN|Li|Cu|Bk}." goto BAD_EXIT endif # refers to olay else if ( "$argv[$ac]" == "-func_range_perc" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set frange_perc = "$argv[$ac]" set olay_nz = "" set USER_FRANGE = 2 # refers to olay else if ( "$argv[$ac]" == "-func_range_perc_nz" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set frange_perc = "$argv[$ac]" set olay_nz = "-non-zero" set USER_FRANGE = 2 else if ( "$argv[$ac]" == "-pbar_posonly" ) then set pbar_sign = "+" else if ( "$argv[$ac]" == "-cbar_ncolors" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set ncolors = "$argv[$ac]" else if ( "$argv[$ac]" == "-cbar_topval" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set topval = "$argv[$ac]" # SAVE_ALLJPEG [c].imagewindowname filename # SAVE_ALLPNG [c].imagewindowname filename # SAVE_MPEG [c].imagewindowname filename # SAVE_AGIF [c].imagewindowname filename # SAVE_JPEG [c.]windowname filename # SAVE_PNG [c.]windowname filename else if ( "$argv[$ac]" == "-save_ftype" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set ftype = "$argv[$ac]" # takes 3 numbers else if ( "$argv[$ac]" == "-set_ijk" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set coors[1] = "$argv[$ac]" @ ac += 1 set coors[2] = "$argv[$ac]" @ ac += 1 set coors[3] = "$argv[$ac]" set USER_COORS = 1 # [PT: Aug 17, 2017] takes 3 numbers else if ( "$argv[$ac]" == "-set_dicom_xyz" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set coor_type = "SET_DICOM_XYZ" set coors[1] = "$argv[$ac]" @ ac += 1 set coors[2] = "$argv[$ac]" @ ac += 1 set coors[3] = "$argv[$ac]" set USER_COORS = 1 else if ( "$argv[$ac]" == "-montx" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set mx = "$argv[$ac]" else if ( "$argv[$ac]" == "-monty" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set my = "$argv[$ac]" else if ( "$argv[$ac]" == "-crop_axi_x" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set acropx[1] = "$argv[$ac]" @ ac += 1 set acropx[2] = "$argv[$ac]" else if ( "$argv[$ac]" == "-crop_axi_y" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set acropy[1] = "$argv[$ac]" @ ac += 1 set acropy[2] = "$argv[$ac]" else if ( "$argv[$ac]" == "-crop_sag_x" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set scropx[1] = "$argv[$ac]" @ ac += 1 set scropx[2] = "$argv[$ac]" else if ( "$argv[$ac]" == "-crop_sag_y" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set scropy[1] = "$argv[$ac]" @ ac += 1 set scropy[2] = "$argv[$ac]" else if ( "$argv[$ac]" == "-crop_cor_x" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set ccropx[1] = "$argv[$ac]" @ ac += 1 set ccropx[2] = "$argv[$ac]" else if ( "$argv[$ac]" == "-crop_cor_y" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set ccropy[1] = "$argv[$ac]" @ ac += 1 set ccropy[2] = "$argv[$ac]" else if ( "$argv[$ac]" == "-alpha_par" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set alpha_par = "$argv[$ac]" else if ( "$argv[$ac]" == "-alpha_floor" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set alpha_floor = "$argv[$ac]" else if ( "$argv[$ac]" == "-alpha_edgize_no" ) then setenv AFNI_EDGIZE_OVERLAY NO else if ( "$argv[$ac]" == "-image_zoom_nn_no" ) then setenv AFNI_IMAGE_ZOOM_NN NO else if ( "$argv[$ac]" == "-zerocolor" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_ZEROCOLOR "$argv[$ac]" # AFNI_IMAGE_LABEL_MODE = 1 // draw labels in UL of Image windows # AFNI_IMAGE_LABEL_SIZE = 3 // size of labels in Image windows # AFNI_IMAGE_LABEL_COLOR = white // color of labels in Image windows # AFNI_IMAGE_LABEL_SETBACK = 0.01 // distance from edges for labels else if ( "$argv[$ac]" == "-label_mode" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_LABEL_MODE "$argv[$ac]" else if ( "$argv[$ac]" == "-label_size" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_LABEL_SIZE "$argv[$ac]" else if ( "$argv[$ac]" == "-label_color" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_LABEL_COLOR "$argv[$ac]" else if ( "$argv[$ac]" == "-label_setback" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_LABEL_SETBACK "$argv[$ac]" # [PT: Aug 17, 2017] probably need quotes... else if ( "$argv[$ac]" == "-label_string" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_LABEL_STRING "$argv[$ac]" # Feb, 2017: useful when each slice is a from a sep vol, i.e., for # @djunct*imager else if ( "$argv[$ac]" == "-image_label_ijk" ) then setenv AFNI_IMAGE_LABEL_IJK YES # default = VOLUME else if ( "$argv[$ac]" == "-globalrange" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 setenv AFNI_IMAGE_GLOBALRANGE "$argv[$ac]" set USER_ULAY_RANGE = 1 # also use this here else if ( "$argv[$ac]" == "-ulay_range" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set umin = "$argv[$ac]" @ ac += 1 set umax = "$argv[$ac]" set USER_ULAY_RANGE = 1 else if ( "$argv[$ac]" == "-ulay_range_nz" ) then if ( $ac >= $#argv ) goto FAIL_MISSING_ARG @ ac += 1 set umin = "$argv[$ac]" @ ac += 1 set umax = "$argv[$ac]" set ulay_nz = "-non-zero" set USER_ULAY_RANGE = 1 else if ( "$argv[$ac]" == "-do_clean" ) then set DO_CLEAN = 1 set my_clean = "-pass" # for @djunct_4d_slices* else echo "** unexpected option #$ac = '$argv[$ac]'" exit 2 endif @ ac += 1 end # ------------------------------------------------------------------- # similar defaults to AFNI GUI, though GUI is slicewise, not # volumewise if ( $USER_ULAY_RANGE != 1 ) then set umin = "0%" set umax = "98%" set ulay_nz = "" set USER_ULAY_RANGE = 1 endif # ------------------------------------------------------------------- echo "++ My command:" echo " @chauffeur_afni $argv" # ------------------------------------------------------------------- # ------------------ check about auxiliary progs -------------------- # from Bob's @snapshot* progs set nerr = 0 set errm = "** ERROR:" # (Ubuntu hassle ->) not using: pamcomp set plist = ( Xvfb djpeg cjpeg pnmcat pbmtext \ pamstretch pbmtopgm ) foreach pppp ( $plist ) set wwww = `which $pppp` if( $status != 0 )then @ nerr++ set errm = "$errm $pppp" endif end if( $nerr > 0 )then echo "$errm -- not found in path -- program fails" goto BAD_EXIT endif # ------------------------------------------------------------------- # -------------------------- check INPUTS --------------------------- echo "\n------------------ start of optionizing ------------------\n" # need more cowbell if ( ("$ulay" == "") ) then echo "** ERROR: need to have an underlay, at least!" goto BAD_EXIT endif # need more cowbell, but will proceed anyways if (( "$olay" == "" ) && ( "$see_olay" == "+" )) then echo "+* Noting: you did NOT provide an overlay, and yet" echo " you did NOT turn off the overlay with '-olay_off'" echo " --> so I assume you just want to view the underlay." set see_olay = "-" endif # check blowup factor set check_list = ( `seq 1 1 4` ) set innit = 0 foreach i ( $check_list ) if ( $bufac == ${check_list[${i}]} ) then echo "++ Using blowup factor: $bufac" set innit = 1 break endif end if ( $innit == 0 ) then echo "+* BAD blowup factor: $bufac!" echo " ---> needs to be (exactly) one of: $check_list\n\n" goto BAD_EXIT endif # check opacity set check_list = ( `seq 1 1 9` ) set innit = 0 foreach i ( $check_list ) if ( $opac == ${check_list[${i}]} ) then echo "++ Using opacity: $opac" set innit = 1 break endif end if ( $innit == 0 ) then echo "+* BAD opacity: $opac!" echo " ---> needs to be (exactly) one of: $check_list\n\n" goto BAD_EXIT endif # -------------------- make temp working dir # in so many cases we need a tmp working directory set read_dir = "$odir/$tmp_dir" if ( ! -e $read_dir ) then echo "++ Making temporary work directory to copy vis files: $read_dir" mkdir $read_dir endif # -------------------- 4D mode reslicing+assembling if necessary if ( $MODE_4D == 1 ) then set upre4d = "$read_dir/${spre4d}_u" # full one also has "_{1,2,3}" # -------- deal with having/not having olay set opre4d = "" set m4d_olay = ( "-pass" "-pass" ) if ( "$olay" != "" ) then set m4d_olay = ( -olay "$olay" ) set opre4d = "$read_dir/${spre4d}_o" # full one also has "_{1,2,3}" endif # ------------- translate what coor: need to reset values in other # ------------- part below.... set m4d_loc = ( "-pass" "-pass" "-pass" "-pass" ) if ( $USER_COORS == 1 ) then if ( "$coor_type" == "SET_IJK" ) then echo "++ Will have user's chosen: $coor_type $coors" set m4d_loc = ( -set_ijk $coors ) else if ( "$coor_type" == "SET_DICOM_XYZ" ) then echo "++ Will have user's chosen: $coor_type $coors" set m4d_loc = ( -set_dicom_xyz $coors ) else echo "** ERROR: unknown coor_type somehow?: $coor_type" goto BAD_EXIT endif else echo "+* Warning: No coordinates selected (?)." echo " Will then just be something near central in vols." endif echo "++ Start slicing ..." @djunct_4d_slices_to_3d_vol \ -ulay "$ulay" \ "$m4d_olay[1]" "$m4d_olay[2]" \ -prefix "$read_dir/$spre4d" \ "$my_clean" \ "$m4d_loc[1]" "$m4d_loc[2]" \ "$m4d_loc[3]" "$m4d_loc[4]" echo "++ ... End slicing." set Nreps = 3 else # p-to-stat calc *cannot* be done for MODE_4D, because the # conversion might not be constant across slices! # --------------------- p-to-stat thr capability ----------------- set statthr = "0" if ( "${p_thr_val}" != "" && "${p_thr_side}" == "" ) then echo "** ERROR!" echo " You specified a p-value to convert, but not the sidedness!" echo " Select the sidedness and enter it with '-thr_olay_pside ..'" goto BAD_EXIT endif # Get info stored in header about: what kind of stat is stored, # what params are known about it (e.g., degrees of freedom), and # use that to calculate a value corresponding to user's selected # p-value. This involves "reading attributes" from the header # with 3dAttribute. To learn more about these numbers, see: # https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html # Need 3 conditions here: a pval entered, **a type of sidedness**, # and a subbrick index for the thr dset specified # [PT: July 27, 2018] More proper check on $subbb[3] if ( "${p_thr_val}" != "" && "${p_thr_side}" != "" \ && `echo " $subbb[3] >= 0 " | bc ` ) then echo "++ Will calc threshold based on stat in [${subbb[3]}] brick" set thrnew = `p2dsetstat \ -inset "$olay""[$subbb[3]]" \ -pval "${p_thr_val}" \ -"${p_thr_side}" \ -quiet` echo "++ Converted p=${p_thr_val} with ${p_thr_side} testing" echo " to stat value: ${thrnew}" endif endif # ================== now get serious ============================ # will have 3 loops if in MODE_4D; otherwise, just one foreach rrr ( `seq 1 1 $Nreps` ) ### the BIG loop starts if ( $MODE_4D ) then set ulay = ${upre4d}_${rrr}.nii.gz if ( "$opre4d" != "" ) then set olay = ${opre4d}_${rrr}.nii.gz endif # this calc pad was calc'ed earlier and passed along with each # input dset, using @djunct_calc_mont_dims.py set calc_pad = "${upre4d}_${rrr}.dat" set padpars = `grep -v "#" $calc_pad` set Nsli = $padpars[1] set Npad = $padpars[2] set Ncol = $padpars[3] set Nrow = $padpars[4] # override settings user migth set, for specific 4D case if ( ( "$ftype" == "AGIF" ) || ( "$ftype" == "MPEG" ) ) then set mx = 1 set my = 1 set coors = ( 0 0 0 ) else set mx = $Ncol set my = $Nrow set coors = ( 0 0 0 ) set mrow = `echo " ( $Nrow / 2 ) " | bc` set mcol = `echo " ( $Ncol / 2 ) " | bc` set midsli = `echo " ( $Ncol * $mrow ) + $mcol " | bc` set coors[$rrr] = $midsli endif set gapord = ( 1 1 1 ) set USER_COORS = 1 set coor_type = "SET_IJK" endif # ---------------------------------------------------------------- # for scaling ulay uniformly with reasonable values when brightness # range is the same across the volume set urange = `echo $AFNI_IMAGE_GLOBALRANGE` if ( ( $urange == "VOLUME" ) || ( $urange == "DSET" ) \ || ( $urange == "YES" ) ) then if ( $USER_ULAY_RANGE ) then echo "++ Copy ulay to visualize (volumetric) within user's range:" # will be 0 if no percent; otherwise, >0 if percent set is_umin_perc = `echo ${umin} | awk '{print index ( $0,"%" ) }'` set is_umax_perc = `echo ${umax} | awk '{print index ( $0,"%" ) }'` if ( ($is_umin_perc > 0) && ($is_umax_perc > 0) ) then # percentages! set pmin = "$umin" # this silliness allows for percentiles > 100, which # means that a valid ${umax_magic}%ile value is scaled # up. set pmax_orig = "$umax" # remove "%" set umax = `echo "$umax" | \ awk '{print substr($0,1,length($0)-1)}'` if ( `echo " $umax > 100 " | bc` ) then set umax_scale = `echo "scale=5; \ $umax / ${umax_magic} " | bc` set umax = "$umax_magic" echo "++ Ulay range calc for >100%ile ulay max:" echo " calculating ${umax}%ile value, and then" echo " multiplying it by a scale factor = $umax_scale," echo " in order to produce the ${umax}%ile value" endif set pmax = "$umax" if ( $MODE_4D ) then # utilized perc val is max of the 3 sep volumes at # that perc set amax = "$BIGNEG" foreach jjj ( `seq 1 1 3` ) set vvv = `3dBrickStat $olay_nz \ -percentile ${pmax} 1 ${pmax} \ "${upre4d}_${jjj}.nii.gz"` if ( `echo " $vvv[2] > $amax " | bc` ) then set amax = "$vvv[2]" endif end # and check if ( `echo " $BIGNEGp1 > $amax " | bc` ) then echo "** ERROR! Badness in make 4D percentile table!" echo " Does ulay have very large, negative values?" goto BAD_EXIT endif # same for min set amin = $amax foreach jjj ( `seq 1 1 3` ) set vvv = `3dBrickStat $olay_nz \ -percentile ${pmin} 1 ${pmin} \ "${upre4d}_${jjj}.nii.gz"` if ( `echo " $vvv[2] < $amin " | bc` ) then set amin = "$vvv[2]" endif end # and check if ( `echo " $amin > $amax " | bc` ) then echo "** ERROR! Badness in make 4D percentile table!" echo " ulay min > ulay max??" goto BAD_EXIT endif set umin = $amin set umax = `echo " $amax * $umax_scale " | bc` else # [PT: July 27, 2018] need to use subbb[1] brick # selector for olay percentile if user has entered # it!! if ( `echo " ${subbb[1]} > -1 " | bc` ) then set amin = `3dBrickStat $ulay_nz \ -percentile ${pmin} 1 ${pmin} \ "${ulay}[${subbb[1]}]"` set amax = `3dBrickStat $ulay_nz \ -percentile ${pmax} 1 ${pmax} \ "${ulay}[${subbb[1]}]"` else set amin = `3dBrickStat $ulay_nz \ -percentile ${pmin} 1 ${pmin} \ "$ulay"` set amax = `3dBrickStat $ulay_nz \ -percentile ${pmax} 1 ${pmax} \ "$ulay"` endif set umin = $amin[2] set umax = `echo " $amax[2] * $umax_scale " | bc` endif echo "++ Ulay to be visualized within user range:" echo " [${pmin}, ${pmax_orig}] -> [${umin}, ${umax}]" else echo "++ Ulay to be visualized within user range:" echo " [${umin}, ${umax}]" endif # need to unset this variable for this drive command to be # effective unsetenv AFNI_IMAGE_GLOBALRANGE set com_ulay_str = "SET_ULAY_RANGE A.all $umin $umax" endif # Special behavior if ulay max %ile is > 100; copy over # *ceilinged* version to temporary read dir if ( $umax_scale != 1 ) then 3dcalc \ -overwrite \ -a "$ulay" \ -expr "a*within(a,${umin},${amax[2]}) \ + ${umin}*step($umin-a) \ + ${amax[2]}*step(a-${amax[2]})" \ -prefix $read_dir/$read_ulay else # copy over dset temporary read dir; with new SET_ULAY_RANGE, # don't need to threshold artificially. 3dcalc \ -overwrite \ -a "$ulay" \ -expr "a" \ -prefix $read_dir/$read_ulay endif else if ( `3dinfo -datum "$ulay"` == "rgb" ) then # not sure why 3dcalc won't preserve rgb-ness... 3dcopy \ -overwrite \ "$ulay" $read_dir/$read_ulay else echo "++ For ulay, AFNI_IMAGE_GLOBALRANGE is set to be: $urange" # just copy over *original* version to temporary read dir 3dcalc \ -overwrite \ -a "$ulay" \ -expr "a" \ -prefix $read_dir/$read_ulay endif endif # always determine dim from ulay, because that's how montaging works! set Dim = `3dinfo -n4 "$ulay"` # IF we don't want to see the olay, then set it to be the ulay, for # later simplicity with the automontaging if ( "$see_olay" == "-" ) then echo "++ No overlay viewing" set olay = "" # don't need to copy anything, just set this for scripty purposes, # doesn't affect visualization. set read_olay = $read_ulay set Dim = `3dinfo -n4 "$ulay"` else set read_olay = tmp_olay.nii 3dcalc \ -a "$olay" \ -expr 'a' \ -prefix $read_dir/$read_olay \ -overwrite if ( $USER_FRANGE == 1 ) then # just a number, no translation necessary even in MODE_4D case echo "++ User-entered function range value value (${frange})" else # set frange, if user hasn't, based on data: if ( $USER_FRANGE == 0 ) then # match more with GUI behavior, if user enters nothing set frange_perc = 100 else # in this case, just check that the user-entered value # is in an OK range if ( ( `echo " $frange_perc < 0 " | bc` ) || \ ( `echo " $frange_perc > 100 " | bc` ) ) then echo "**ERROR! bad olay percentile: $frange_perc." echo " Must be [0, 100]." goto BAD_EXIT endif endif if ( $MODE_4D ) then # utilized perc val is max of the 3 sep volumes at # that perc set frange = "$BIGNEG" foreach jjj ( `seq 1 1 3` ) set vvv = `3dBrickStat $olay_nz \ -percentile ${frange_perc} 1 ${frange_perc} \ "${opre4d}_${jjj}.nii.gz"` if ( `echo " $vvv[2] > $frange " | bc` ) then set frange = "$vvv[2]" endif end # and check if ( `echo " $BIGNEGp1 > $frange " | bc` ) then echo "** ERROR! Badness in make 4D percentile table!" echo " Does olay have very large, negative values?" goto BAD_EXIT endif else # match more with GUI behavior, if user enters nothing # [PT: July 27, 2018] need to use subbb[2] brick # selector for olay percentile if user has entered # it!! if ( `echo " ${subbb[2]} > -1 " | bc` ) then set vvv = `3dBrickStat $olay_nz \ -percentile ${frange_perc} 1 ${frange_perc} \ "$read_dir/${read_olay}[${subbb[2]}]"` else set vvv = `3dBrickStat $olay_nz \ -percentile ${frange_perc} 1 ${frange_perc} \ $read_dir/$read_olay` endif set frange = "$vvv[2]" endif echo "++ For olay, the ${frange_perc}%ile value leads to" echo " --> upper range value: $frange" endif endif # Calculate numbers of slices in each direction, if not given by user. # Take number of mont wins plus a couple to calculate. @ Nwin = $mx * $my # silly stuff to deal with orientation set ori = `3dinfo -orient "$ulay"` set ori0 = `echo $ori | awk '{print substr($0,1,1)}'` set ori1 = `echo $ori | awk '{print substr($0,2,1)}'` set ori2 = `echo $ori | awk '{print substr($0,3,1)}'` set all_ori = ( $ori0 $ori1 $ori2 ) set order = () foreach oo ( $all_ori ) foreach i ( `seq 1 1 ${#listori}` ) if ( $oo == "$listori[${i}]" ) then set order = ( $order ${listind[$i]} ) break endif end end echo "++ Cryptic info: $ori -> $all_ori -> $order" echo "++ Dimensions (xyzt): $Dim" foreach i ( `seq 1 1 3` ) if( $gapord[$order[$i]] <= 0 ) then @ gapord[$order[$i]] = $Dim[$i] / ( $Nwin ) if( $gapord[$order[$i]] <= 0 ) then @ gapord[$order[$i]] = 1 endif endif end echo "++ Slice spacing ordered (x,y,z) is: $gapord" # get ceilings of 'montage number + 1', in each direction set xo2 = `echo "scale=2; ( $mx + 1 ) / 2." | bc` set cmx = `echo $xo2 | perl -nl -MPOSIX -e 'print ceil($_);'` set yo2 = `echo "scale=2; ( $my + 1 ) / 2." | bc` set cmy = `echo $yo2 | perl -nl -MPOSIX -e 'print ceil($_);'` @ tot = $mx * $my @ hpan = ( ( $cmy - 1 ) * $mx ) + $cmx #echo "$cmx $cmy $tot $hpan" set pfrac = `echo "scale=5; ( $hpan / ( $tot + 1 ) ) " | bc` # ???? echo "++ pfrac = $pfrac" # These need to reflect the order of the original. Ugh, annoying # conditions. if ( $USER_COORS == 1 ) then if ( "$coor_type" == "SET_IJK" ) then echo "++ Will have user's chosen: $coor_type $coors" else if ( "$coor_type" == "SET_DICOM_XYZ" ) then echo "++ Will have user's chosen: $coor_type $coors" else echo "** ERROR: unknown coor_type somehow?: $coor_type" goto BAD_EXIT endif else foreach i ( `seq 1 1 3` ) set qfrac = `echo "scale=5; ( $pfrac ) " | bc` # frac to center set qsh = ""#+ 1" # 0-base count offset if ( ( $all_ori[$i] == 'R' ) || ( $all_ori[$i] == 'P' ) \ || ( $all_ori[$i] == 'S' ) ) then #echo "++ Coor calc: $all_ori[$i] for $order[$i]" set qfrac = `echo "scale=5; ( 1 - $pfrac ) " | bc` #else # echo "++ Coor value: $all_ori[$i] for $order[$i]" endif set nn = `echo "scale=0; ( ( $Dim[$i] * $qfrac ) $qsh )" | bc` set coors[$i] = `echo $nn | perl -nl -MPOSIX -e 'print floor($_);'` end echo "++ Will have: $coor_type $coors" endif echo "\n------------------- end of optionizing -------------------\n" # ------------------------------------------------------------------- # ------------------------- Make virtual frame ---------------------- # start the X virtual frame buffer on display #xdisplay, a la bob if ( $rrr == 1 ) then ### only need to start once, i.e., if in MODE_4D set ranval = `count -dig 1 1 999999 R1` if ( $?xdisplay == 0 ) then set killX = 1 set ntry = 1 set Xnotfound = 1 while( $Xnotfound ) set xdisplay = `count -dig 1 3 999 R1` if( -e /tmp/.X${xdisplay}-lock ) continue echo " -- trying to start Xvfb :${xdisplay}" Xvfb :${xdisplay} -screen 0 1024x768x24 & sleep 1 jobs > zzerm.$ranval.txt grep -q Xvfb zzerm.$ranval.txt set Xnotfound = $status \rm -f zzerm.$ranval.txt if ( $Xnotfound == 0 ) break ; @ ntry++ if ( $ntry > 99 ) then echo "** ERROR: can't start Xvfb -- exiting" goto BAD_EXIT endif end endif setenv DISPLAY :${xdisplay} set OW = "OPEN_WINDOW" endif # ------------------------------------------------------------------- # ---------------- The actual, driven command! ---------------------- if ( $MODE_4D ) then afni -noplugins -no_detach -echo_edu \ -com "SWITCH_UNDERLAY ${read_ulay}" \ -com "SWITCH_OVERLAY ${read_olay}" \ -com "SEE_OVERLAY ${see_olay}" \ -com "SET_PBAR_ALL ${pbar_sign}${ncolors} $topval $my_cbar" \ -com "SET_SUBBRICKS ${subbb}" \ -com "$com_ulay_str" \ -com "SET_FUNC_RANGE ${frange}" \ -com "SET_THRESHNEW $thrnew $thrflag" \ -com "SET_FUNC_ALPHA $alpha_par $alpha_floor" \ -com "SET_FUNC_RESAM ${func_resam}.${func_resam}" \ -com "SET_XHAIRS ${crossh}" \ -com "$OW ${ppord[$rrr]}image opacity=${opac} \ mont=${mx}x${my}:${gapord[3]} \ crop=${acropx[1]}:${acropx[2]},${acropy[1]}:${acropy[2]}" \ -com "$coor_type $coors" \ -com "SAVE_${ftype} ${ppord[$rrr]}image \ ${odir}/${impref}.${pord[$rrr]} \ blowup=${bufac}" \ -com "${do_quit}" \ "${read_dir}" else # "$com_ulay_str" \ #xvfb-run -d --server-args="-screen 0 1024x768x24" -w 0 \ afni -noplugins -no_detach -echo_edu \ -com "SWITCH_UNDERLAY ${read_ulay}" \ -com "SWITCH_OVERLAY ${read_olay}" \ -com "SEE_OVERLAY ${see_olay}" \ -com "SET_PBAR_ALL ${pbar_sign}${ncolors} $topval $my_cbar" \ -com "SET_SUBBRICKS ${subbb}" \ -com "$com_ulay_str" \ -com "SET_FUNC_RANGE ${frange}" \ -com "SET_THRESHNEW $thrnew $thrflag" \ -com "SET_FUNC_ALPHA $alpha_par $alpha_floor" \ -com "SET_FUNC_RESAM ${func_resam}.${func_resam}" \ -com "SET_XHAIRS ${crossh}" \ -com "$OW sagittalimage opacity=${opac} \ mont=${mx}x${my}:${gapord[1]} \ crop=${scropx[1]}:${scropx[2]},${scropy[1]}:${scropy[2]}" \ -com "$OW coronalimage opacity=${opac} \ mont=${mx}x${my}:${gapord[2]} \ crop=${ccropx[1]}:${ccropx[2]},${ccropy[1]}:${ccropy[2]}" \ -com "$OW axialimage opacity=${opac} \ mont=${mx}x${my}:${gapord[3]} \ crop=${acropx[1]}:${acropx[2]},${acropy[1]}:${acropy[2]}" \ -com "$coor_type $coors" \ -com "SAVE_${ftype} sagittalimage ${odir}/${impref}.sag \ blowup=${bufac}" \ -com "SAVE_${ftype} coronalimage ${odir}/${impref}.cor \ blowup=${bufac}" \ -com "SAVE_${ftype} axialimage ${odir}/${impref}.axi \ blowup=${bufac}" \ -com "${do_quit}" \ "${read_dir}" endif end ### ... of BIG loop # A la bob: stop Xvfb if we started it ourselves if( $?killX ) kill %1 if ( $DO_CLEAN ) then echo "\n+* Removing temporary image directory '$odir/$tmp_dir'.\n" # AKA $read_dir, at present \rm $odir/$tmp_dir/* \rmdir $odir/$tmp_dir else echo "\n++ NOT removing temporary directory '$odir/$tmp_dir'.\n" endif goto GOOD_EXIT # =========================================================================== # various FAIL condition labels follow SHOW_VERSION: echo "\n\n++ Version: $version\n\n" goto GOOD_EXIT # ---------------------------------- SHOW_HELP: cat < because different stats in a volume might have different conversions) + when using this opt, at least on of UUU and OOO *must* have >1 volumes. + if one of the ulay/olay volumes has only one brick, it will be viewed in the same way across the entire montage (i.e., as if it were a constant volume throughout 'time'). -olay_off :explicitly state you are not using olay (opt); if not used and no olay is given, then the user just gets prompted to be sure they haven't forgotten the olay dset. -prefix PPP :prefix for output files (required). -ulay_range UMIN UMAX :specify min and max range values of ulay dset; if a "%" is on both numbers, then treat the numerical part of UMIN and UMAX as percentiles from which to calculate actual values; otherwise, treat UMIN and UMAX as values directly. (def: UMIN=0% and UMAX=98%). (See DR: SET_ULAY_RANGE) Also, see "Special Ulay Range" and "Combining %ile values..." in NOTES, below. -ulay_range_nz UMIN UMAX :same as the preceding opt, but when "%" is on both numbers, here the percentiles are only calculated over the *non-zero* voxels. The above one is more in line with the AFNI GUI default behavior for percentile calcs (though GUI by default works slicewise). If %ile values are not given, then both this and the above option produce identical results for the same UMIN and UMAX values. (See DR: SET_ULAY_RANGE) "Special Ulay Range" and "Combining %ile values..." in NOTES, below. -globalrange GR :specify how lookup range for matching ulay values is done (def: VOLUME); (see ENV: AFNI_IMAGE_GLOBALRANGE) Ignored if '-ulay_range* ..' is set. Note for '-mode_4D': this setting applies to the resliced volume (i.e., the one made of one slice of each subbrick). See "Combining %ile values..." in NOTES, below. -func_range FR :specify upper value FR of the olay dset to be matched to top of colorbar (def: calc 98%ile non-zero value of dset and use that). -func_range_perc_nz FRP :alternative to "-func_range ..."; specify a percentile value FRP to use to make the upper value of the olay dset to be matched to the top of the colorbar (def: calc 98%ile non-zero value of dset and use that). NB: this percentile range is always among *non-zero* voxel values with this option; see below. -func_range_perc FRP :same as above option, but this is a percentile among *all* voxel values, not just those with non-zero values. -func_resam RES :set the resampling mode for dsets; valid values are: NN Li Cu Bk (def: NN; hey, voxels are voxels!). (See DR: SET_FUNC_RESAM) -thr_olay THR :threshold the olay dset at THR (def: 0, or unthreshold). If you are thresholding a statistic brick, then you should see the "-thr_olay_p2stat ..." option, below. (See DR: SET_THRESHNEW) -thrflag 'fff' :further control of how the THR value is interpreted (def: "*"). (See DR: SET_THRESHNEW) -thr_olay_p2stat PP :an alternative way to specify a voxelwise threshold (i.e., instead of "-thr_olay ..."), when thresholding based on a statistic; you can specify the p-value you want, and using internal header information, the appropriate value for whatever statistic is in the statistic brick will be calculated and applied; you likely need to use "-set_subbricks i j k" with this, where 'k' would be the index of the statistic brick (and likely 'j' would be the index of the associated coefficient/beta brick; 'i' would be the brick of the underlay volume, and if there is only a single volume there, it could just be either '0' or '-1'). And see next option '-thr_olay_pside', below. -thr_olay_pside SS :(required if using '-thr_olay_p2stat ..') specify the sidedness of the testing for the conversion of p-to-stat. Valid values for SS at present include: bisided 2sided 1sided -cbar CCC :specify a new colorbar, where CCC can be any of the cbars in the standard AFNI list (def: $my_cbar). -pbar_posonly :for color range specification, default is to use both positive and negative values; enter this flag to use only the positive range. (See DR: SET_PBAR_ALL) -cbar_ncolors NC :set colorscale mode (def: 99) (See DR: SET_PBAR_ALL, the 2nd usage case, description about '99'). -cbar_topval TOPV :set colorscale mode (def: 1) (See DR: SET_PBAR_ALL, the 2nd usage case, description about 'topval'). -opacity OO :enter an "opacity factor" for the olay, where OO is an integer in the interval [0, 9], with the 9 being opaque (see DR). -blowup BB :enter a "blowup factor", where BB is an integer in the interval [1, 8]. Increases spatial resolution in the output by a factor of BB (see DR; def: 2). -set_xhairs XX :specify type and/or existence of crosshairs in the image (see DR: SET_XHAIRS). -delta_slices DS DC DA :when montaging, (DS, DC, DA) is the integer number of slices to use as spacing between views along the (sag, cor, axi) axes, respectively (def: automatically calculate to ~evenly fit the number of selected montage slices along this axis). (See DR: "mont=PxQ:R"; basically, each D? is the 'R' value along the given axis). Users can specify a delta_slice value along *some* axis and leave other(s) to be chosen automatically, by specifying a D? value >0 for their own value, and given any other D? value -1. For example: -delta_slices 40 -1 -1 would specify every 40th slice along the sag axis, while the cor and axi spacing would be automatically calculated. -set_subbricks i j k :for 3D image viewing, specify subbricks being viewed in the ulay, olay and threshold dsets (def: "-1 -1 -1", which means ignore these values). This is the way to specify different overlay and threshold subbricks for displaying, such as using the "beta" or "coefficient" for color and the "statistic" as the threshold level. (See DR: SET_SUBBRICKS) -save_ftype FTYPE :type of file as which to save images; key types are listed in the Driver description (def: PNG) (See DR: SAVE_ALLJPEG, SAVE_ALLPNG, SAVE_MPEG, SAVE_AGIF, SAVE_JPEG, SAVE_PNG; for which the user would enter just the non-"SAVE_" part, just as "PNG", "MPEG", etc.) -set_ijk II JJ KK :Set the controller coordinates to the given triple, which are integer index selectors along the three spatial axes. This essentially specifies the middle image in the montage (def: for each coordinate, choose middle slice along axis). -set_dicom_xyz XX YY ZZ :Set the controller coordinates to the given triple, which are the (x, y, z) coordinates in AFNI's favorite RAI DICOM notation. (def: for each coordinate, choose middle slice along axis). -montx MX :in creating montage, the number of image panels in a row, i.e., the number of columns (def: 3); the total number of panels per axis is: MX*MY (see below "-monty ..."). (See DR: "mont=PxQ:R"; basically, MX is the 'P' value). -monty MY :in creating montage, the number of image panels in a column, i.e., the number of rows (def: 3); the total number of panels per axis is: MX*MY (see above "-montx ..."). (See DR: "mont=PxQ:R"; basically, MY is the 'Q' value). -alpha_par ALPHP :In addition to representing olay values as colors with a threshold, one also apply opacity information to 'soften' the effect of thresholding; see DR: SET_FUNC_ALPHA for a description of this behavior (def: "Off", which is just standard thresholding stuff). -alpha_floor ALPHF :second parameter for more complicated olay thresholding behavior. Too complicated for simple me to explain-- see DR: SET_FUNC_ALPHA (def: ""; this empty string means use default value, which at time of writing is 0) -alpha_edgize_no :even *more* control over fancy alpha-based thresholding; for this, see ENV: AFNI_EDGIZE_OVERLAY, whose default value is "YES". Using this option changes that value to 'NO' internally. -image_zoom_nn_no :the default zoom is set to NN mode, so no smoothing occurs (see ENV: AFNI_IMAGE_ZOOM_NN). This option changes behavior internally to set this variable to have the value "NO". -crop_axi_x CAX1 CAX2, -crop_axi_y CAY1 CAY2 :crop axial image(s) to be between voxels CAX1 and CAX2 along the x-axis (inclusive) and CAY1 and CAY2 along the y-axis. These values are integer row and column numbers. (See DR: "crop=x1:x2,y1:y2"; CAX1 is x1, etc.; def: no cropping -- CAX1=0, CAX2=0, etc.) -crop_sag_x CSX1 CSX2, -crop_sag_y CSY1 CSY2 :same as other '-crop_*' above, but for sagittal images. -crop_cor_x CCX1 CCX2, -crop_cor_y CCY1 CCY2 :same as other '-crop_*' above, but for coronal images. -zerocolor ZC :Change the default 'background' ulay color of zero values (def: "Black"); ZC can be set to any allowed AFNI value (see ENV: AFNI_IMAGE_ZEROCOLOR). This option is mainly for G. Chen, who flaunts convention whenever possible. -label_mode LM :control labels, ON/OFF and location (def: 1); (see ENV: AFNI_IMAGE_LABEL_MODE) -label_size LS :control labels, size (def: 3); (see ENV: AFNI_IMAGE_LABEL_SIZE) -label_color LC :control labels, color (def: white); (see ENV: AFNI_IMAGE_LABEL_COLOR) -label_setback LB :control labels, offset from edge (def: 0.01); (see ENV: AFNI_IMAGE_LABEL_SETBACK) -label_string LSTR :control labels, string automatically appended to the slice (def: ""); (see ENV: AFNI_IMAGE_LABEL_STRING) -image_label_ijk :If this option is used, then the image label will be based on the slice index rather than the spatial (mm) coordinate; thanks, Bob! (see ENV: AFNI_IMAGE_LABEL_IJK) -do_clean :by default, the temporary directory of copying files and such is not removed; using this option means that that working directory *is* removed. # ======================================================================== NOTES ~1~ + Description of "4D mode" ~2~ In this case the assumption/requirement is that you have at least one 4D data set to look at; for each viewing plane, one slice is selected across time for viewing. For each viewing plane, the slices across time are spatially concatenated to form a single, temporary 3D dset (a "planar" or "slicewise" volume), which is what is actually put into AFNI to generate images in that relevant plane. How percentile values are calculated is discussed in the next "NOTE", below. When both an overlay and underlay are used, the usual resampling rules of the AFNI GUI apply (and user can specify the resampling option with "-func_resam .."). If one volume is 4D and one is 3D (e.g., for checking alignment across time), then the relevant single slice of the 3D volume is basically just repeated in a given plane. + Combining %ile values "-mode_4D" for olay and/or ulay ~2~ When using a percentile to set a range in 4D mode for either ulay (e.g., "-ulay_range* ..") or olay (e.g., "-func_range_perc_nz* .."), that percentile is calculated for each of the three "planar" or "slicewise" volumes, and then the *max* of those three numbers is applied with the colorbar. If one of your ulay or olay in 4D mode is just a 3D volume and you want a percentile related to the whole thing, you can calculate any of those values beforehand using "3dBrickStat -percentile ..", and then apply those. + Special Ulay Range ~2~ If UMAX is a percentile >100%, then what happens is this: the ${umax_magic}%ile value in the dset is calculated, and the result is multiplied by (UMAX/${umax_magic}); the ulay dataset is 'ceilinged' at the ${umax_magic}%ile value, and its upper range is set to UMAX/${umax_magic}. The purpose of this madness? To give a nice, controllably darkened ulay (esp. when that is an anatomical). My suspicion is that having a darker-than-usual ulay is nice to allow the overlay colors to show up better. I am currently of the opinion that a UMAX of around ~150-190% is a nice value (and UMIN can be set to 0%) # ======================================================================== EXAMPLES ~1~ A) Basic vanilla: make a 3x5 montage of just a ulay; there will be 15 slices shown, evenly spaced along each axis, with some labels on the corners. @chauffeur_afni \ -ulay MY_ULAY.nii.gz \ -prefix PRETTY_PICTURE \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 3 \ -do_clean B) Make a 3x5 montage of an overlayed data set that has an ROI map, so we want it to be colored-by-integer. Put the images into a pre-existing directory, SUBDIR/. @chauffeur_afni \ -ulay MY_ULAY.nii.gz \ -olay MY_OLAY.nii.gz \ -pbar_posonly \ -cbar "ROI_i256" \ -func_range 256 \ -opacity 4 \ -prefix SUBDIR/PRETTY_PICTURE2 \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 3 \ -do_clean C) Make a 3x5 montage of an overlayed data set that shows the beta coefficients stored in brick [1] while thresholding the associated statistic stored in brick [2] at voxelwise p=0.001, overlayed on the anatomical volume. @chauffeur_afni \ -ulay anat.nii.gz \ -olay stats.nii.gz \ -cbar Plasma \ -func_range 3 \ -thr_olay_p2stat 0.001 \ -thr_olay_pside bisided \ -set_subbricks -1 1 2 \ -opacity 4 \ -prefix STAT_MAP \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 3 \ -do_clean # ------------------------------------------------------------------- EOF goto GOOD_EXIT # ---------------------------------- FAIL_MISSING_ARG: echo "** missing parameter for option $argv[$ac]" goto BAD_EXIT # ---------------------------------- BAD_EXIT: exit 1 # ---------------------------------- GOOD_EXIT: exit 0