afni_ci_test_data/AFNI_data6/FT_analysis/s17.proc.FT.rest.11

#!/bin/tcsh -xef

echo "auto-generated by afni_proc.py, Mon Feb 25 16:50:45 2019"
echo "(version 6.32, February 22, 2019)"
echo "execution started: `date`"

# to execute via tcsh: 
#   tcsh -xef proc.FT.rest.11 |& tee output.proc.FT.rest.11
# to execute via bash: 
#   tcsh -xef proc.FT.rest.11 2>&1 | tee output.proc.FT.rest.11

# =========================== auto block: setup ============================
# script setup

# take note of the AFNI version
afni -ver

# check that the current AFNI version is recent enough
afni_history -check_date 17 Jan 2019
if ( $status ) then
    echo "** this script requires newer AFNI binaries (than 17 Jan 2019)"
    echo "   (consider: @update.afni.binaries -defaults)"
    exit
endif

# the user may specify a single subject to run with
if ( $#argv > 0 ) then
    set subj = $argv[1]
else
    set subj = FT.rest.11
endif

# assign output directory name
set output_dir = $subj.results

# verify that the results directory does not yet exist
if ( -d $output_dir ) then
    echo output dir "$subj.results" already exists
    exit
endif

# set list of runs
set runs = (`count -digits 2 1 3`)

# create results and stimuli directories
mkdir $output_dir
mkdir $output_dir/stimuli

# copy anatomy to results dir
3dcopy FT/FT_anat+orig $output_dir/FT_anat

# copy anatomical follower datasets into the results dir
3dcopy FT/SUMA/aparc.a2009s+aseg.nii $output_dir/copy_af_aaseg
3dcopy FT/SUMA/aparc.a2009s+aseg.nii $output_dir/copy_af_aeseg
3dcopy FT/SUMA/FT_vent.nii $output_dir/copy_af_FSvent
3dcopy FT/SUMA/FT_white.nii $output_dir/copy_af_FSWe

# ============================ auto block: tcat ============================
# apply 3dTcat to copy input dsets to results dir,
# while removing the first 2 TRs
3dTcat -prefix $output_dir/pb00.$subj.r01.tcat FT/FT_epi_r1+orig'[2..$]'
3dTcat -prefix $output_dir/pb00.$subj.r02.tcat FT/FT_epi_r2+orig'[2..$]'
3dTcat -prefix $output_dir/pb00.$subj.r03.tcat FT/FT_epi_r3+orig'[2..$]'

# and make note of repetitions (TRs) per run
set tr_counts = ( 150 150 150 )

# -------------------------------------------------------
# enter the results directory (can begin processing data)
cd $output_dir


# ========================== auto block: outcount ==========================
# data check: compute outlier fraction for each volume
touch out.pre_ss_warn.txt
foreach run ( $runs )
    3dToutcount -automask -fraction -polort 3 -legendre                     \
                pb00.$subj.r$run.tcat+orig > outcount.r$run.1D

    # censor outlier TRs per run, ignoring the first 0 TRs
    # - censor when more than 0.1 of automask voxels are outliers
    # - step() defines which TRs to remove via censoring
    1deval -a outcount.r$run.1D -expr "1-step(a-0.1)" > rm.out.cen.r$run.1D

    # outliers at TR 0 might suggest pre-steady state TRs
    if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
        echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \
            >> out.pre_ss_warn.txt
    endif
end

# catenate outlier counts into a single time series
cat outcount.r*.1D > outcount_rall.1D

# catenate outlier censor files into a single time series
cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D

# get run number and TR index for minimum outlier volume
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
set ovals = ( `1d_tool.py -set_run_lengths $tr_counts                       \
                          -index_to_run_tr $minindex` )
# save run and TR indices for extraction of vr_base_min_outlier
set minoutrun = $ovals[1]
set minouttr  = $ovals[2]
echo "min outlier: run $minoutrun, TR $minouttr" | tee out.min_outlier.txt

# ================================ despike =================================
# apply 3dDespike to each run
foreach run ( $runs )
    3dDespike -NEW -nomask -prefix pb01.$subj.r$run.despike \
        pb00.$subj.r$run.tcat+orig
end

# ================================= tshift =================================
# time shift data so all slice timing is the same 
foreach run ( $runs )
    3dTshift -tzero 0 -quintic -prefix pb02.$subj.r$run.tshift \
             pb01.$subj.r$run.despike+orig
end

# --------------------------------
# extract volreg registration base
3dbucket -prefix vr_base_min_outlier                           \
    pb02.$subj.r$minoutrun.tshift+orig"[$minouttr]"

# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, FT_anat_ns+orig)
align_epi_anat.py -anat2epi -anat FT_anat+orig   \
       -save_skullstrip -suffix _al_junk         \
       -epi vr_base_min_outlier+orig -epi_base 0 \
       -epi_strip 3dAutomask                     \
       -volreg off -tshift off

# ================================== tlrc ==================================
# warp anatomy to standard space (non-linear warp)
auto_warp.py -base MNI_caez_N27+tlrc -input FT_anat_ns+orig \
             -skull_strip_input no

# move results up out of the awpy directory
# - NL-warped anat, affine warp, NL warp
# - use typical standard space name for anat
# - wildcard is a cheap way to go after any .gz
# - be sure NIFTI sform_code=2 means standard space
3dbucket -DAFNI_NIFTI_VIEW=tlrc                             \
         -prefix FT_anat_ns awpy/FT_anat_ns.aw.nii*
mv awpy/anat.un.aff.Xat.1D .
mv awpy/anat.un.aff.qw_WARP.nii .

# ================================= volreg =================================
# align each dset to base volume, to anat, warp to tlrc space

# verify that we have a +tlrc warp dataset
if ( ! -f FT_anat_ns+tlrc.HEAD ) then
    echo "** missing +tlrc warp dataset: FT_anat_ns+tlrc.HEAD" 
    exit
endif

# register and warp
foreach run ( $runs )
    # register each volume to the base image
    3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig                  \
             -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run               \
             -cubic                                                           \
             -1Dmatrix_save mat.r$run.vr.aff12.1D                             \
             pb02.$subj.r$run.tshift+orig

    # create an all-1 dataset to mask the extents of the warp
    3dcalc -overwrite -a pb02.$subj.r$run.tshift+orig -expr 1                 \
           -prefix rm.epi.all1

    # catenate volreg/epi2anat/tlrc xforms
    cat_matvec -ONELINE                                                       \
               anat.un.aff.Xat.1D                                             \
               FT_anat_al_junk_mat.aff12.1D -I                                \
               mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D

    # apply catenated xform: volreg/epi2anat/tlrc/NLtlrc
    # then apply non-linear standard-space warp
    3dNwarpApply -master FT_anat_ns+tlrc -dxyz 2.5                            \
                 -source pb02.$subj.r$run.tshift+orig                         \
                 -nwarp "anat.un.aff.qw_WARP.nii mat.r$run.warp.aff12.1D"     \
                 -prefix rm.epi.nomask.r$run

    # warp the all-1 dataset for extents masking 
    3dNwarpApply -master FT_anat_ns+tlrc -dxyz 2.5                            \
                 -source rm.epi.all1+orig                                     \
                 -nwarp "anat.un.aff.qw_WARP.nii mat.r$run.warp.aff12.1D"     \
                 -interp cubic                                                \
                 -ainterp NN -quiet                                           \
                 -prefix rm.epi.1.r$run

    # make an extents intersection mask of this run
    3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc
end

# make a single file of registration params
cat dfile.r*.1D > dfile_rall.1D

# ----------------------------------------
# create the extents mask: mask_epi_extents+tlrc
# (this is a mask of voxels that have valid data at every TR)
3dMean -datum short -prefix rm.epi.mean rm.epi.min.r*.HEAD 
3dcalc -a rm.epi.mean+tlrc -expr 'step(a-0.999)' -prefix mask_epi_extents

# and apply the extents mask to the EPI data 
# (delete any time series with missing data)
foreach run ( $runs )
    3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc               \
           -expr 'a*b' -prefix pb03.$subj.r$run.volreg
end

# warp the volreg base EPI dataset to make a final version
cat_matvec -ONELINE                                                           \
           anat.un.aff.Xat.1D                                                 \
           FT_anat_al_junk_mat.aff12.1D -I  > mat.basewarp.aff12.1D

3dNwarpApply -master FT_anat_ns+tlrc -dxyz 2.5                                \
             -source vr_base_min_outlier+orig                                 \
             -nwarp "anat.un.aff.qw_WARP.nii mat.basewarp.aff12.1D"           \
             -prefix final_epi_vr_base_min_outlier

# create an anat_final dataset, aligned with stats
3dcopy FT_anat_ns+tlrc anat_final.$subj

# record final registration costs
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX                \
            -input anat_final.$subj+tlrc |& tee out.allcostX.txt

# -----------------------------------------
# warp anat follower datasets (non-linear)
3dNwarpApply -source copy_af_aaseg+orig                                       \
             -master anat_final.$subj+tlrc                                    \
             -ainterp NN -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D    \
             -prefix follow_ROI_aaseg
3dNwarpApply -source copy_af_aeseg+orig                                       \
             -master pb03.$subj.r01.volreg+tlrc                               \
             -ainterp NN -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D    \
             -prefix follow_ROI_aeseg
3dNwarpApply -source copy_af_FSvent+orig                                      \
             -master pb03.$subj.r01.volreg+tlrc                               \
             -ainterp NN -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D    \
             -prefix follow_ROI_FSvent
3dNwarpApply -source copy_af_FSWe+orig                                        \
             -master pb03.$subj.r01.volreg+tlrc                               \
             -ainterp NN -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D    \
             -prefix follow_ROI_FSWe
3dNwarpApply -source FT_anat+orig                                             \
             -master anat_final.$subj+tlrc                                    \
             -ainterp wsinc5 -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D\
             -prefix anat_w_skull_warped

# ================================== blur ==================================
# blur each volume of each run
foreach run ( $runs )
    3dmerge -1blur_fwhm 4.0 -doall -prefix rm.pb04.$subj.r$run.blur  \
            pb03.$subj.r$run.volreg+tlrc

    # and apply extents mask, since no scale block
    3dcalc -a rm.pb04.$subj.r$run.blur+tlrc -b mask_epi_extents+tlrc \
           -expr 'a*b' -prefix pb04.$subj.r$run.blur
end

# ================================== mask ==================================
# create 'full_mask' dataset (union mask)
foreach run ( $runs )
    3dAutomask -prefix rm.mask_r$run pb04.$subj.r$run.blur+tlrc
end

# create union of inputs, output type is byte
3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj

# ---- create subject anatomy mask, mask_anat.$subj+tlrc ----
#      (resampled from tlrc anat)
3dresample -master full_mask.$subj+tlrc -input FT_anat_ns+tlrc        \
           -prefix rm.resam.anat

# convert to binary anat mask; fill gaps and holes
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc  \
            -prefix mask_anat.$subj

# compute tighter EPI mask by intersecting with anat mask
3dmask_tool -input full_mask.$subj+tlrc mask_anat.$subj+tlrc          \
            -inter -prefix mask_epi_anat.$subj

# compute overlaps between anat and EPI masks
3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc    \
            |& tee out.mask_ae_overlap.txt

# note Dice coefficient of masks, as well
3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc               \
      |& tee out.mask_ae_dice.txt

# ---- create group anatomy mask, mask_group+tlrc ----
#      (resampled from tlrc base anat, MNI_caez_N27+tlrc)
3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group      \
           -input /home/rickr/abin/MNI_caez_N27+tlrc

# convert to binary group mask; fill gaps and holes
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \
            -prefix mask_group

# ================================ regress =================================

# compute de-meaned motion parameters (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_nruns 3                            \
           -demean -write motion_demean.1D

# compute motion parameter derivatives (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_nruns 3                            \
           -derivative -demean -write motion_deriv.1D

# convert motion parameters for per-run regression
1d_tool.py -infile motion_demean.1D -set_nruns 3                         \
           -split_into_pad_runs mot_demean

1d_tool.py -infile motion_deriv.1D -set_nruns 3                          \
           -split_into_pad_runs mot_deriv

# create censor file motion_${subj}_censor.1D, for censoring motion 
1d_tool.py -infile dfile_rall.1D -set_nruns 3                            \
    -show_censor_count -censor_prev_TR                                   \
    -censor_motion 0.2 motion_${subj}

# combine multiple censor files
1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D         \
       -expr "a*b" > censor_${subj}_combined_2.1D

# create ROI regressor: FSWe
# (get each ROI average time series and remove resulting mean)
foreach run ( $runs )
    3dmaskave -quiet -mask follow_ROI_FSWe+tlrc                          \
              pb03.$subj.r$run.volreg+tlrc                               \
            | 1d_tool.py -infile - -demean -write rm.ROI.FSWe.r$run.1D
end
# and catenate the demeaned ROI averages across runs
cat rm.ROI.FSWe.r*.1D > ROI.FSWe_rall.1D

# note TRs that were not censored
set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D              \
                       -show_trs_uncensored encoded`

# ------------------------------
# create ROI PC ort sets: FSvent

# create a time series dataset to run 3dpc on...

# detrend, so principal components are not affected
foreach run ( $runs )
    # to censor, create per-run censor files
    1d_tool.py -set_run_lengths $tr_counts -select_runs $run             \
               -infile censor_${subj}_combined_2.1D -write rm.censor.r$run.1D

    # do not let censored time points affect detrending
    3dTproject -polort 3 -prefix rm.det_pcin_r$run                       \
               -censor rm.censor.r$run.1D -cenmode KILL                  \
               -input pb03.$subj.r$run.volreg+tlrc
end

# catenate runs, prepare to censor TRs
3dTcat -prefix rm.det_pcin_rall rm.det_pcin_r*+tlrc.HEAD

# make ROI PCs : FSvent
3dpc -mask follow_ROI_FSvent+tlrc -pcsave 3                              \
     -prefix rm.ROIPC.FSvent rm.det_pcin_rall+tlrc

# zero pad censored TRs
1d_tool.py -censor_fill_parent censor_${subj}_combined_2.1D              \
    -infile rm.ROIPC.FSvent_vec.1D                                       \
    -write ROIPC.FSvent.1D

# ------------------------------
# run the regression analysis
3dDeconvolve -input pb04.$subj.r*.blur+tlrc.HEAD                         \
    -censor censor_${subj}_combined_2.1D                                 \
    -ortvec ROI.FSWe_rall.1D ROI.FSWe                                    \
    -ortvec ROIPC.FSvent.1D ROIPC.FSvent                                 \
    -ortvec mot_demean.r01.1D mot_demean_r01                             \
    -ortvec mot_demean.r02.1D mot_demean_r02                             \
    -ortvec mot_demean.r03.1D mot_demean_r03                             \
    -ortvec mot_deriv.r01.1D mot_deriv_r01                               \
    -ortvec mot_deriv.r02.1D mot_deriv_r02                               \
    -ortvec mot_deriv.r03.1D mot_deriv_r03                               \
    -polort 3                                                            \
    -num_stimts 0                                                        \
    -fout -tout -x1D X.xmat.1D -xjpeg X.jpg                              \
    -x1D_uncensored X.nocensor.xmat.1D                                   \
    -fitts fitts.$subj                                                   \
    -errts errts.${subj}                                                 \
    -x1D_stop                                                            \
    -bucket stats.$subj

# -- use 3dTproject to project out regression matrix --
3dTproject -polort 0 -input pb04.$subj.r*.blur+tlrc.HEAD                 \
           -censor censor_${subj}_combined_2.1D -cenmode ZERO            \
           -ort X.nocensor.xmat.1D -prefix errts.${subj}.tproject



# if 3dDeconvolve fails, terminate the script
if ( $status != 0 ) then
    echo '---------------------------------------'
    echo '** 3dDeconvolve error, failing...'
    echo '   (consider the file 3dDeconvolve.err)'
    exit
endif


# display any large pairwise correlations from the X-matrix
1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt

# display degrees of freedom info from X-matrix
1d_tool.py -show_df_info -infile X.xmat.1D |& tee out.df_info.txt

# create an all_runs dataset to match the fitts, errts, etc.
3dTcat -prefix all_runs.$subj pb04.$subj.r*.blur+tlrc.HEAD

# --------------------------------------------------
# generate fast ANATICOR result: errts.$subj.fanaticor+tlrc

# --------------------------------------------------
# fast ANATICOR: generate local FSWe time series averages
# create catenated volreg dataset
3dTcat -prefix rm.all_runs.volreg pb03.$subj.r*.volreg+tlrc.HEAD

# mask white matter before blurring
3dcalc -a rm.all_runs.volreg+tlrc -b follow_ROI_FSWe+tlrc                \
       -expr "a*bool(b)" -datum float -prefix rm.all_runs.volreg.mask

# generate ANATICOR voxelwise regressors via blur
3dmerge -1blur_fwhm 30 -doall -prefix Local_FSWe_rall                    \
    rm.all_runs.volreg.mask+tlrc

# -- use 3dTproject to project out regression matrix --
3dTproject -polort 0 -input pb04.$subj.r*.blur+tlrc.HEAD                 \
           -censor censor_${subj}_combined_2.1D -cenmode ZERO            \
           -dsort Local_FSWe_rall+tlrc                                   \
           -ort X.nocensor.xmat.1D -prefix errts.$subj.fanaticor

# --------------------------------------------------
# create a temporal signal to noise ratio dataset 
#    signal: if 'scale' block, mean should be 100
#    noise : compute standard deviation of errts
3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]"
3dTstat -stdev -prefix rm.noise.all errts.$subj.fanaticor+tlrc"[$ktrs]"
3dcalc -a rm.signal.all+tlrc                                             \
       -b rm.noise.all+tlrc                                              \
       -c mask_epi_anat.$subj+tlrc                                       \
       -expr 'c*a/b' -prefix TSNR.$subj 

# ---------------------------------------------------
# compute and store GCOR (global correlation average)
# (sum of squares of global mean of unit errts)
3dTnorm -norm2 -prefix rm.errts.unit errts.$subj.fanaticor+tlrc
3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc           \
          > gmean.errts.unit.1D
3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D
echo "-- GCOR = `cat out.gcor.1D`"

# ---------------------------------------------------
# compute correlation volume
# (per voxel: average correlation across masked brain)
# (now just dot product with average unit time series)
3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP
3dTstat -sum -prefix corr_brain rm.DP+tlrc

# compute 2 requested correlation volume(s)
# create correlation volume corr_af_aeseg
3dcalc -a follow_ROI_aeseg+tlrc -b full_mask.$subj+tlrc -expr 'a*b'      \
       -prefix rm.fm.aeseg
3dmaskave -q -mask rm.fm.aeseg+tlrc rm.errts.unit+tlrc > mean.unit.aeseg.1D
3dcalc -a rm.errts.unit+tlrc -b mean.unit.aeseg.1D                       \
       -expr 'a*b' -prefix rm.DP.aeseg
3dTstat -sum -prefix corr_af_aeseg rm.DP.aeseg+tlrc

# create correlation volume corr_af_FSvent
3dcalc -a follow_ROI_FSvent+tlrc -b full_mask.$subj+tlrc -expr 'a*b'     \
       -prefix rm.fm.FSvent
3dmaskave -q -mask rm.fm.FSvent+tlrc rm.errts.unit+tlrc > mean.unit.FSvent.1D
3dcalc -a rm.errts.unit+tlrc -b mean.unit.FSvent.1D                      \
       -expr 'a*b' -prefix rm.DP.FSvent
3dTstat -sum -prefix corr_af_FSvent rm.DP.FSvent+tlrc

# --------------------------------------------------------
# compute sum of non-baseline regressors from the X-matrix
# (use 1d_tool.py to get list of regressor colums)
set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest`
3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]"

# also, create a stimulus-only X-matrix, for easy review
1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D

# ============================ blur estimation =============================
# compute blur estimates
touch blur_est.$subj.1D   # start with empty file

# create directory for ACF curve files
mkdir files_ACF

# -- estimate blur for each run in epits --
touch blur.epits.1D

# restrict to uncensored TRs, per run
foreach run ( $runs )
    set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \
                          -show_trs_run $run`
    if ( $trs == "" ) continue
    3dFWHMx -detrend -mask mask_epi_anat.$subj+tlrc                      \
            -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D                \
            all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D
end

# compute average FWHM blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` )
echo average epits FWHM blurs: $blurs
echo "$blurs   # epits FWHM blur estimates" >> blur_est.$subj.1D

# compute average ACF blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` )
echo average epits ACF blurs: $blurs
echo "$blurs   # epits ACF blur estimates" >> blur_est.$subj.1D

# -- estimate blur for each run in errts --
touch blur.errts.1D

# restrict to uncensored TRs, per run
foreach run ( $runs )
    set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \
                          -show_trs_run $run`
    if ( $trs == "" ) continue
    3dFWHMx -detrend -mask mask_epi_anat.$subj+tlrc                      \
            -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D                \
            errts.$subj.fanaticor+tlrc"[$trs]" >> blur.errts.1D
end

# compute average FWHM blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` )
echo average errts FWHM blurs: $blurs
echo "$blurs   # errts FWHM blur estimates" >> blur_est.$subj.1D

# compute average ACF blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` )
echo average errts ACF blurs: $blurs
echo "$blurs   # errts ACF blur estimates" >> blur_est.$subj.1D


# ================== auto block: generate review scripts ===================

# generate a review script for the unprocessed EPI data
gen_epi_review.py -script @epi_review.$subj            \
    -dsets pb00.$subj.r*.tcat+orig.HEAD

# generate scripts to review single subject results
# (try with defaults, but do not allow bad exit status)
gen_ss_review_scripts.py -mot_limit 0.2 -out_limit 0.1 \
    -errts_dset errts.$subj.fanaticor+tlrc.HEAD -exit0 \
    -ss_review_dset out.ss_review.$subj.txt            \
    -write_uvars_json out.ss_review_uvars.json

# ========================== auto block: finalize ==========================

# remove temporary files
\rm -fr rm.* awpy

# if the basic subject review script is here, run it
# (want this to be the last text output)
if ( -e @ss_review_basic ) then
    ./@ss_review_basic |& tee out.ss_review.$subj.txt

    # generate html ss review pages
    # (akin to static images from running @ss_review_driver)
    apqc_make_tcsh.py -review_style basic -subj_dir . \
        -uvar_json out.ss_review_uvars.json
    tcsh @ss_review_html
    apqc_make_html.py -qc_dir QC_$subj

    echo "\nconsider running: \n\n    afni_open -b $subj.results/QC_$subj/index.html\n"
endif

# return to parent directory (just in case...)
cd ..

echo "execution finished: `date`"




# ==========================================================================
# script generated by the command:
#
# afni_proc.py -subj_id FT.rest.11 -script proc.FT.rest.11 -scr_overwrite   \
#     -blocks despike tshift align tlrc volreg blur mask regress -copy_anat \
#     FT/FT_anat+orig -anat_follower_ROI aaseg anat                         \
#     FT/SUMA/aparc.a2009s+aseg.nii -anat_follower_ROI aeseg epi            \
#     FT/SUMA/aparc.a2009s+aseg.nii -anat_follower_ROI FSvent epi           \
#     FT/SUMA/FT_vent.nii -anat_follower_ROI FSWe epi FT/SUMA/FT_white.nii  \
#     -dsets FT/FT_epi_r1+orig.HEAD FT/FT_epi_r2+orig.HEAD                  \
#     FT/FT_epi_r3+orig.HEAD -tcat_remove_first_trs 2 -tlrc_base            \
#     MNI_caez_N27+tlrc -tlrc_NL_warp -volreg_align_to MIN_OUTLIER          \
#     -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 -mask_epi_anat yes \
#     -regress_ROI_PC FSvent 3 -regress_ROI FSWe -regress_make_corr_vols    \
#     aeseg FSvent -regress_anaticor_fast -regress_anaticor_label FSWe      \
#     -regress_motion_per_run -regress_censor_motion 0.2                    \
#     -regress_censor_outliers 0.1 -regress_apply_mot_types demean deriv    \
#     -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no