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common_processing.tcsh
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#!/bin/tcsh -xef
echo "auto-generated by afni_proc.py, Tue Nov 29 09:27:30 2022"
echo "(version 7.12, April 14, 2020)"
echo "execution started: `date`"
# to execute via tcsh:
# tcsh -xef XXX.tcsh |& tee output.XXX
# to execute via bash:
# tcsh -xef XXX.tcsh 2>&1 | tee output.XXX
set dataFolder = XXX/quantitativ_fMRI/data
# assign output directory name
set subjects = ('Sujet2' 'Sujet3' 'Sujet4' 'Sujet5' 'Sujet6' 'Sujet7' 'Sujet8' 'Sujet9' 'Sujet10' 'Sujet11' 'Sujet13' )
set subjects = ('Sujet7' 'Sujet8' 'Sujet9' 'Sujet10' 'Sujet11' 'Sujet13' )
set output_directory = common_processing
# =========================== 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 27 Jun 2019
if ( $status ) then
echo "** this script requires newer AFNI binaries (than 27 Jun 2019)"
echo " (consider: @update.afni.binaries -defaults)"
exit
endif
cd $dataFolder
set home = $PWD
set template = XXX/abin/MNI152_T1_2009c+tlrc
# ============= SUBJECT loop =====================
# the user may specify a single subject to run with
foreach subj ( $subjects )
set output_dir = $dataFolder/$subj/Analysis/$output_directory
cd $subj
# verify that the results directory does not yet exist
if ( -d $output_dir ) then
echo output dir "$output_dir" already exists
exit
endif
if (! -d $output_dir/stimuli) mkdir -p $output_dir/stimuli
# set list of runs
if ( -d ./tapping ) then
set runs = (`count -digits 2 1 3`)
set runsMotReg = (`count -digits 2 2 3`)
else
set runs = (`count -digits 2 1 2`)
set runsMotReg = (`count -digits 2 2 2`)
endif
# note 4 echoes and registration echo index
set echo_list = (`count -digits 2 1 4`)
set echo_times = ( 9.1 25.0 39.6 54.3 )
set fave_echo = '01'
# create results and stimuli directories
# copy anatomy to results dir
3dcopy anat/anat.nii $output_dir/tmpanat
# copying respiratory data
if ( -f "gating/respData_r01.1D" ) then
cp gating/respData_r01.1D $output_dir/stimuli/
endif
if ( -f "gating/respData_r02.1D" ) then
cp gating/respData_r02.1D $output_dir/stimuli/
endif
if ( -f "gating/respData_r03.1D" ) then
cp gating/respData_r03.1D $output_dir/stimuli/
endif
# ============================ auto block: tcat ============================
# apply 3dTcat to copy input dsets to results dir,
# while removing the first 10 TRs
set FILE = 'breathhold/deobECHO1.nii'
if ( ! -f "$FILE" ) then
3dWarp -deoblique -prefix breathhold/deobECHO1.nii breathhold/ECHO1.nii
3dWarp -deoblique -prefix breathhold/deobECHO2.nii breathhold/ECHO2.nii
3dWarp -deoblique -prefix breathhold/deobECHO3.nii breathhold/ECHO3.nii
3dWarp -deoblique -prefix breathhold/deobECHO4.nii breathhold/ECHO4.nii
3dWarp -deoblique -prefix hick/deobECHO1.nii hick/ECHO1.nii
3dWarp -deoblique -prefix hick/deobECHO2.nii hick/ECHO2.nii
3dWarp -deoblique -prefix hick/deobECHO3.nii hick/ECHO3.nii
3dWarp -deoblique -prefix hick/deobECHO4.nii hick/ECHO4.nii
if ( -d ./tapping ) then
3dWarp -deoblique -prefix tapping/deobECHO1.nii tapping/ECHO1.nii
3dWarp -deoblique -prefix tapping/deobECHO2.nii tapping/ECHO2.nii
3dWarp -deoblique -prefix tapping/deobECHO3.nii tapping/ECHO3.nii
3dWarp -deoblique -prefix tapping/deobECHO4.nii tapping/ECHO4.nii
endif
endif
3dWarp -deoblique -prefix $output_dir/anat $output_dir/tmpanat+orig
# EPI runs for echo 1 (fave_echo = registration driver)
3dTcat -prefix $output_dir/pb00.$subj.r01.e01.tcat breathhold/deobECHO1.nii
3dTcat -prefix $output_dir/pb00.$subj.r02.e01.tcat hick/deobECHO1.nii
# EPI runs for echo 2 (registration follower)
3dTcat -prefix $output_dir/pb00.$subj.r01.e02.tcat breathhold/deobECHO2.nii
3dTcat -prefix $output_dir/pb00.$subj.r02.e02.tcat hick/deobECHO2.nii
# EPI runs for echo 3 (registration follower)
3dTcat -prefix $output_dir/pb00.$subj.r01.e03.tcat breathhold/deobECHO3.nii
3dTcat -prefix $output_dir/pb00.$subj.r02.e03.tcat hick/deobECHO3.nii
# EPI runs for echo 4 (registration follower)
3dTcat -prefix $output_dir/pb00.$subj.r01.e04.tcat breathhold/deobECHO4.nii
3dTcat -prefix $output_dir/pb00.$subj.r02.e04.tcat hick/deobECHO4.nii
if ( -d ./tapping ) then
3dTcat -prefix $output_dir/pb00.$subj.r03.e01.tcat tapping/deobECHO1.nii
3dTcat -prefix $output_dir/pb00.$subj.r03.e02.tcat tapping/deobECHO2.nii
3dTcat -prefix $output_dir/pb00.$subj.r03.e03.tcat tapping/deobECHO3.nii
3dTcat -prefix $output_dir/pb00.$subj.r03.e04.tcat tapping/deobECHO4.nii
endif
# -------------------------------------------------------
# enter the results directory (can begin processing data)
cd $output_dir
set TR1 = "`3dinfo -nt pb00.$subj.r01.e01.tcat+orig.HEAD`"
set TR2 = "`3dinfo -nt pb00.$subj.r02.e01.tcat+orig.HEAD`"
if ( -d ../../tapping ) then
set TR3 = "`3dinfo -nt pb00.$subj.r03.e01.tcat+orig.HEAD`"
set tr_counts=("$TR1" "$TR2" "$TR3")
else
set tr_counts=("$TR1" "$TR2")
endif
#set TR1end = "`expr $TR1 - 1`"
# and make note of repetitions (TRs) per run
# ========================== auto block: outcount ==========================
# data check: compute outlier fraction for each volume
touch out.pre_ss_warn.txt
foreach run ( $runs )
3dToutcount -automask -fraction -polort 7 -legendre \
pb00.$subj.r$run.e$fave_echo.tcat+orig > outcount.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
# 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 )
foreach eind ( $echo_list )
3dDespike -NEW -nomask -prefix rm.pb01.$subj.r$run.e$eind.despike \
pb00.$subj.r$run.e$eind.tcat+orig
end
end
# ======================== respiratory correction ==========================
# apply retricor to each run
foreach eind ( $echo_list )
mv rm.pb01.$subj.r01.e$eind.despike+orig.BRIK pb01.$subj.r01.e$eind.despike+orig.BRIK
mv rm.pb01.$subj.r01.e$eind.despike+orig.HEAD pb01.$subj.r01.e$eind.despike+orig.HEAD
end
foreach run ( $runsMotReg )
set FILE = stimuli/respData_r${run}.1D
if ( -f "$FILE" ) then
foreach eind ( $echo_list )
3dretroicor -prefix pb01.$subj.r$run.e$eind.despike \
-resp stimuli/respData_r$run.1D -respphase stimuli/respPhase_r$run.1D \
rm.pb01.$subj.r$run.e$eind.despike+orig
end
else
foreach eind ( $echo_list )
mv rm.pb01.$subj.r$run.e$eind.despike+orig.BRIK pb01.$subj.r$run.e$eind.despike+orig.BRIK
mv rm.pb01.$subj.r$run.e$eind.despike+orig.HEAD pb01.$subj.r$run.e$eind.despike+orig.HEAD
end
endif
end
# ================================= tshift =================================
# time shift data so all slice timing is the same
foreach run ( $runs )
foreach eind ( $echo_list )
3dTshift -tzero 0 -quintic -prefix pb02.$subj.r$run.e$eind.tshift \
pb01.$subj.r$run.e$eind.despike+orig
end
end
# --------------------------------
# extract volreg registration base
3dbucket -prefix vr_base_min_outlier \
pb02.$subj.r$minoutrun.e$fave_echo.tshift+orig"[$minouttr]"
# ================================= align ==================================
# a2e: align anatomy to EPI registration base
# (new anat will be aligned and stripped, anat_al_keep+orig)
align_epi_anat.py -anat2epi -anat anat+orig \
-suffix _al_keep \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dSkullStrip \
-giant_move -cmass cmass+a \
-volreg off -tshift off
# ================================== tlrc ==================================
# warp anatomy to standard space
@auto_tlrc -base $template -input anat_al_keep+orig -no_ss -init_xform AUTO_CENTER
# store forward transformation matrix in a text file
cat_matvec anat_al_keep+tlrc::WARP_DATA -I > warp.anat.Xat.1D
# ================================= volreg =================================
# align each dset to base volume, warp to tlrc space
# verify that we have a +tlrc warp dataset
if ( ! -f anat_al_keep+tlrc.HEAD ) then
echo "** missing +tlrc warp dataset: anat_al_keep+tlrc.HEAD"
exit
endif
# register and warp
foreach run ( $runs )
# register each volume to the base image
# (registration is driven by $fave_echo)
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig \
-1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run.e$fave_echo \
-cubic \
-1Dmatrix_save mat.r$run.vr.aff12.1D \
pb02.$subj.r$run.e$fave_echo.tshift+orig
# create an all-1 dataset to mask the extents of the warp
3dcalc -overwrite -a pb02.$subj.r$run.e$fave_echo.tshift+orig -expr 1 \
-prefix rm.epi.all1
# catenate volreg/tlrc xforms
cat_matvec -ONELINE \
anat_al_keep+tlrc::WARP_DATA -I \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D
# apply catenated xform: volreg/tlrc
# (apply warps per echo - warps are fixed, per run)
foreach eind ( $echo_list )
3dAllineate -base anat_al_keep+tlrc \
-input pb02.$subj.r$run.e$eind.tshift+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 3 \
-prefix rm.epi.nomask.r$run.e$eind
end
# warp the all-1 dataset for extents masking
3dAllineate -base anat_al_keep+tlrc \
-input rm.epi.all1+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 3 -final 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
# compute motion magnitude time series: the Euclidean norm
# (sqrt(sum squares)) of the motion parameter derivatives
1d_tool.py -infile dfile_rall.1D \
-set_run_lengths $tr_counts \
-derivative -collapse_cols euclidean_norm \
-write motion_${subj}_enorm.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 )
foreach eind ( $echo_list )
3dcalc -a rm.epi.nomask.r$run.e$eind+tlrc -b mask_epi_extents+tlrc \
-expr 'a*b' -prefix pb03.$subj.r$run.e$eind.volreg
end
end
# warp the volreg base EPI dataset to make a final version
cat_matvec -ONELINE anat_al_keep+tlrc::WARP_DATA -I > mat.basewarp.aff12.1D
3dAllineate -base anat_al_keep+tlrc \
-input vr_base_min_outlier+orig \
-1Dmatrix_apply mat.basewarp.aff12.1D \
-mast_dxyz 3 \
-prefix final_epi_vr_base_min_outlier
# create an anat_final dataset, aligned with stats
3dcopy anat_al_keep+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 (affine)
# catenate all transformations
cat_matvec -ONELINE \
warp.anat.Xat.1D \
anat_al_keep_mat.aff12.1D > warp.all.anat.aff12.1D
3dAllineate -source anat+orig \
-master anat_final.$subj+tlrc \
-final wsinc5 -1Dmatrix_apply warp.all.anat.aff12.1D \
-prefix anat_w_skull_warped
# ================================== mask ==================================
# create 'full_mask' dataset (union mask)
foreach run ( $runs )
3dAutomask -prefix rm.mask_r$run pb03.$subj.r$run.e$fave_echo.volreg+tlrc
end
# create union of inputs, output type is byte
3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj
# ---- create subject anatomy mask, mask_anat.$subj+tlrc ----
# (resampled from tlrc anat)
3dresample -master full_mask.$subj+tlrc -input anat_al_keep+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, MNI152_T1_2009c+tlrc)
3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \
-input $template
# convert to binary group mask; fill gaps and holes
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \
-prefix mask_group
# note Dice coefficient of anat and template masks
3ddot -dodice mask_anat.$subj+tlrc mask_group+tlrc \
|& tee out.mask_at_dice.txt
# ---- segment anatomy into classes CSF/GM/WM ----
3dSeg -anat anat_final.$subj+tlrc -mask AUTO -classes 'CSF ; GM ; WM'
# copy resulting Classes dataset to current directory
3dcopy Segsy/Classes+tlrc .
# make individual ROI masks for regression (CSF GM WM and CSFe GMe WMe)
foreach class ( CSF GM WM )
# unitize and resample individual class mask from composite
3dmask_tool -input Segsy/Classes+tlrc"<$class>" \
-prefix rm.mask_${class}
3dresample -master pb03.$subj.r01.e$eind.volreg+tlrc -rmode NN \
-input rm.mask_${class}+tlrc -prefix mask_${class}_resam
# also, generate eroded masks
3dmask_tool -input Segsy/Classes+tlrc"<$class>" -dilate_input -1 \
-prefix rm.mask_${class}e
3dresample -master pb03.$subj.r01.e$eind.volreg+tlrc -rmode NN \
-input rm.mask_${class}e+tlrc -prefix mask_${class}e_resam
end
# ================================ combine =================================
# combine multi-echo data per run, using m_tedana_OC (tedana from MEICA group)
# ----- method m_tedana_OC : generate tedana (MEICA group) results -----
# (get MEICA tedana OC result, desc-optcomDenoised_bold.nii.gz)
# first run tedana commands, to see if they all succeed
foreach run ( $runs )
tedana -d pb03.$subj.r$run.e*.volreg+tlrc.HEAD \
-e $echo_times \
--mask mask_epi_anat.$subj+tlrc.HEAD \
--out-dir tedana_r$run
end
# now get the tedana results
foreach run ( $runs )
# copy result back here
3dcopy tedana_r$run/desc-optcomDenoised_bold.nii.gz pb04.$subj.r$run.combine+tlrc
# for some reason, tedana combination brings the data of orig status to TLRC
3drefit -space tlrc pb04.$subj.r$run.combine+tlrc
end
# ================================== Perfusion Weights datasets creation ==================================
# 4 different datasets : filtering at 0.009 Hz, Suround Substraction, MEICA, and meaning
# blur each volume of each run
foreach run ( $runs )
foreach e (1 2 3 4)
# Running Surround Substraction
3dcalc \
-a pb03.$subj.r$run.e0$e.volreg+tlrc \
-b 'a[0,0,0,1]*d' \
-c 'a[0,0,0,-1]*d' \
-d mask_epi_anat.${subj}+tlrc \
-expr '(a*d-0.5*(b+c))*(-1)**(l+1)' \
-prefix pb04.$subj.r$run.e0$e.SuroundSubstr
# Low pass filtering for MEICA algorithme.
3dTproject -polort -1 -input pb03.$subj.r$run.e0$e.volreg+tlrc -prefix BOLD_ECHO${e}.r$run.nii -stopband 0.09 9999 -mask mask_epi_anat.${subj}+tlrc.HEAD
end
3dAFNItoNIFTI mask_epi_anat.${subj}+tlrc.HEAD
# MEICA
if (! -d ./MEICAtoBEerased) mkdir ./MEICAtoBEerased
# isolating BOLd and artefacts components
tedana -d BOLD_ECHO*.r$run.nii -e 9.1 25 39.6 54.3 --fittype loglin --out-dir ./MEICAtoBEerased --mask mask_epi_anat.${subj}+tlrc.HEAD --seed 69
# extracting PW data with MEICA technique
3dTproject -input pb03.$subj.r$run.e01.volreg+tlrc -prefix rm.MEICA_PW_ECHO1.r$run.nii -dsort ./MEICAtoBEerased/desc-optcomRejected_bold.nii* -dsort ./MEICAtoBEerased/desc-optcomAccepted_bold.nii* -mask mask_epi_anat.${subj}+tlrc.HEAD
3dTproject -input rm.MEICA_PW_ECHO1.r$run.nii -prefix rm.highPassedEcho1.r$run -polort -1 -stopband 0 0.09
1deval -expr 'cos(PI*(t+1))' -num $tr_counts[$run] > cos.1D
3dcalc -a rm.highPassedEcho1.r$run+tlrc.BRIK -b cos.1D -prefix pb04.$subj.r$run.e01.MEICA -expr 'a*b'
# MEAN dataset
foreach e (1 2 3 4)
3dAFNItoNIFTI -prefix ECHO$e.VolregTemp.nii pb03.$subj.r$run.e0$e.volreg+tlrc
3dcalc -a mask_epi_anat.${subj}+tlrc.HEAD -b ECHO$e.VolregTemp.nii -expr "a*b" -prefix SSECHO$e.VolregTemp.nii
3dTproject -input SSECHO$e.VolregTemp.nii -prefix highPassed.r$run.e0$e.nii -polort -1 -stopband 0 0.09
rm *ECHO$e.VolregTemp.nii
1deval -expr 'cos(PI*(t+1))' -num $tr_counts[$run] > cos.1D
3dcalc -a highPassed.r$run.e0$e.nii -b cos.1D -prefix pb04.$subj.r$run.e0$e.Filt009 -expr 'a*b' #verified through matlab
end
3dcalc -a pb04.$subj.r$run.e01.Filt009+tlrc \
-b pb04.$subj.r$run.e02.Filt009+tlrc \
-c pb04.$subj.r$run.e03.Filt009+tlrc \
-d pb04.$subj.r$run.e04.Filt009+tlrc \
-expr '(a+b+c+d)/4' -prefix pb04.$subj.r$run.eMEAN.Filt009
rm -R ./MEICAtoBEerased
end
#rm rm.*
rm BOLD_ECHO*
# ================================== blur ==================================
# blur each volume of each run
foreach run ( $runs )
3dmerge -1blur_fwhm 4.5 -doall -prefix rm.pb05.$subj.r$run.blur \
pb04.$subj.r$run.combine+tlrc
3dmerge -1blur_fwhm 4.5 -doall -prefix rm.pb05.$subj.r$run.e01.PW.blur \
pb04.$subj.r$run.e01.Filt009+tlrc
3dmerge -1blur_fwhm 4.5 -doall -prefix rm.pb05.$subj.r$run.eMEAN.blur \
pb04.$subj.r$run.eMEAN.Filt009+tlrc
3dmerge -1blur_fwhm 4.5 -doall -prefix rm.pb05.$subj.r$run.e01.SurSub.blur \
pb04.$subj.r$run.e01.SuroundSubstr+tlrc
3dmerge -1blur_fwhm 4.5 -doall -prefix rm.pb05.$subj.r$run.e01.MEICA.blur \
pb04.$subj.r$run.e01.MEICA+tlrc
# copying 2nd echo as BOLD signal
3dmerge -1blur_fwhm 4.5 -doall -prefix rm.pb05.$subj.r$run.e02.blur \
pb03.$subj.r$run.e02.volreg+tlrc.HEAD
# and apply extents mask, since no scale block
3dcalc -a rm.pb05.$subj.r$run.blur+tlrc -b mask_epi_anat.${subj}+tlrc.HEAD \
-expr 'a*b' -prefix pb05.$subj.r$run.blur
3dcalc -a rm.pb05.$subj.r$run.e01.PW.blur+tlrc -b mask_epi_anat.${subj}+tlrc.HEAD \
-expr 'a*b' -prefix pb05.$subj.r$run.e01.PW.blur
3dcalc -a rm.pb05.$subj.r$run.eMEAN.blur+tlrc -b mask_epi_anat.${subj}+tlrc.HEAD \
-expr 'a*b' -prefix pb05.$subj.r$run.eMEAN.blur
3dcalc -a rm.pb05.$subj.r$run.e01.SurSub.blur+tlrc -b mask_epi_anat.${subj}+tlrc.HEAD \
-expr 'a*b' -prefix pb05.$subj.r$run.e01.SurSub.blur
3dcalc -a rm.pb05.$subj.r$run.e01.MEICA.blur+tlrc -b mask_epi_anat.${subj}+tlrc.HEAD \
-expr 'a*b' -prefix pb05.$subj.r$run.e01.MEICA.blur
3dcalc -a rm.pb05.$subj.r$run.e02.blur+tlrc -b mask_epi_anat.${subj}+tlrc.HEAD \
-expr 'a*b' -prefix pb05.$subj.r$run.e02.blur
end
mkdir -p "$dataFolder/$subj/Analysis/Images"
@snapshot_volreg \
"$dataFolder/$subj/Analysis/$output_directory/anat_final.${subj}+tlrc.BRIK" \
"$dataFolder/$subj/Analysis/$output_directory/pb04.${subj}.r01.combine+tlrc" \
"$dataFolder/$subj/Analysis/Images/alignment_anat_to_epi_${subj}+tlrc"
@snapshot_volreg \
"$dataFolder/$subj/Analysis/$output_directory/anat_final.${subj}+tlrc.BRIK" \
$template \
"$dataFolder/$subj/Analysis/Images/alignment_anat_to_template_${subj}+tlrc"
# remove temporary files
\rm -fr rm.* Segsy
cd $dataFolder/$subj/Analysis/$output_directory
mkdir ../temp$output_directory
foreach run ( $runs )
cp motion_${subj}_enorm.1D ../temp${output_directory}/motion_${subj}_censor.1D
cp pb04.$subj.r01.combine+tlrc.HEAD ../temp${output_directory}/pb02.$subj.r01.volreg+tlrc.HEAD
cp pb04.$subj.r01.combine+tlrc.BRIK ../temp${output_directory}/pb02.$subj.r01.volreg+tlrc.BRIK
cp pb05.$subj.r$run.e01.MEICA.blur+tlrc.* \
pb05.$subj.r$run.e01.SurSub.blur+tlrc.* \
pb05.$subj.r$run.eMEAN.blur+tlrc.* \
pb05.$subj.r$run.e01.PW.blur+tlrc.* \
pb05.$subj.r$run.e02.blur+tlrc.* \
pb05.$subj.r$run.blur+tlrc.* \
pb04.$subj.r01.combine+tlrc.* \
anat_final.${subj}+tlrc.* \
anat+orig.* \
anat_al_keep+orig* \
anat_final.${subj}+tlrc.HEAD \
dfile* \
*mask* \
*warp* \
*.1D \
*.jpg \
*.txt \
pb00.${subj}.r01.e01.tcat+orig.HEAD \
outcount_rall.1D \
motion_${subj}_enorm.1D \
dfile_rall.1D \
../temp$output_directory
end
rm $dataFolder/$subj/Analysis/$output_directory/*.*
cp ../temp$output_directory/* ../$output_directory
rm -R ../temp$output_directory
cd $home
end
# ========================== auto block: finalize ==========================
# if the basic subject review script is here, run it
# (want this to be the last text output)
if ( -e @ss_review_basic ) then
./@ss_review_basic |& tee out.ss_review.$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 |& tee out.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 ${subj} -blocks despike tshift align tlrc volreg mask \
# combine blur regress -copy_anat anat.nii.gz -echo_times 9.1 25 39.6 \
# 54.3 -blur_size 4.5 -reg_echo 1 -dsets_me_run hick/ECHO1.nii.gz \
# hick/ECHO2.nii.gz hick/ECHO3.nii.gz hick/ECHO4.nii.gz \
# -regress_motion_per_run -dsets_me_run breathhold/ECHO1.nii.gz \
# breathhold/ECHO2.nii.gz breathhold/ECHO3.nii.gz breathhold/ECHO4.nii.gz \
# -tlrc_base MNI152_T1_2009c+tlrc -tcat_remove_first_trs 10 \
# -volreg_align_to MIN_OUTLIER -volreg_tlrc_warp -regress_reml_exec \
# -regress_compute_tsnr yes -align_epi_strip_method 3dSkullStrip \
# -align_opts_aea -giant_move -cmass cmass+a -combine_method m_tedana_OC \
# -mask_segment_anat yes -mask_segment_erode yes -regress_stim_times \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-10TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-11TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-12TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-2TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-3TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-4TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-5TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-6TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-7TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-8TR.1D \
# XXX/quantitativ_fMRI/data/regressors/BH_regressor_2runs_${subj}_-9TR.1D \
# XXX/quantitativ_fMRI/data/regressors/thirdScanHickregressor_cond1_ofst10_2runs_${subj}.1D \
# XXX/quantitativ_fMRI/data/regressors/thirdScanHickregressor_cond2_ofst10_2runs_${subj}.1D \
# XXX/quantitativ_fMRI/data/regressors/thirdScanHickregressor_cond4_ofst10_2runs_${subj}.1D \
# -regress_stim_labels 0TR m1TR m2TR 8TR 7TR 6TR 5TR 4TR 3TR 2TR 1TR \
# cond1 cond2 cond3 -mask_epi_anat yes