Hi Peter,
I tried removing the commented out lines, and I still am getting the same error. I've pasted both the script generated by proc.py and the output of proc.py
=====================================================================
This is the script generated by proc.py
=====================================================================
#!/bin/tcsh -xef
echo "auto-generated by afni_proc.py, Mon Jul 6 12:11:56 2015"
echo "(version 4.32, March 2, 2015)"
echo "execution started: `date`"
# execute via :
# tcsh -xef /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery/sub11_imagery_proc_script |& tee output./media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery/sub11_imagery_proc_script
# =========================== 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 9 Feb 2014
if ( $status ) then
echo "** this script requires newer AFNI binaries (than 9 Feb 2014)"
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 = sub11
endif
# assign output directory name
set output_dir = /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.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 2`)
# create results and stimuli directories
mkdir $output_dir
mkdir $output_dir/stimuli
# copy anatomy to results dir
3dcopy \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig \
$output_dir/sub11.PTSD_Conditioning.spgr
# ============================ auto block: tcat ============================
# apply 3dTcat to copy input dsets to results dir, while
# removing the first 0 TRs
3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Neutral+orig'[0..$]'
3dTcat -prefix $output_dir/pb00.$subj.r02.tcat \
/media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Trauma+orig'[0..$]'
# and make note of repetitions (TRs) per run
set tr_counts = ( 273 273 )
# -------------------------------------------------------
# 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 ( $runs )
3dToutcount -automask -fraction -polort 4 -legendre \
pb00.$subj.r$run.tcat+orig > outcount.r$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
# ================================= tshift =================================
# time shift data so all slice timing is the same
foreach run ( $runs )
3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \
pb00.$subj.r$run.tcat+orig
end
# ================================= volreg =================================
# align each dset to base volume
foreach run ( $runs )
# register each volume to the base
3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' \
-1Dfile dfile.r$run.1D -prefix pb02.$subj.r$run.volreg \
-cubic \
pb01.$subj.r$run.tshift+orig
end
# make a single file of registration params
cat dfile.r*.1D > dfile_rall.1D
# compute motion magnitude time series: the Euclidean norm
# (sqrt(sum squares)) of the motion parameter derivatives
1d_tool.py -infile dfile_rall.1D -set_nruns 2 \
-derivative -collapse_cols euclidean_norm \
-write motion_${subj}_enorm.1D
# create an anat_final dataset, aligned with stats
3dcopy sub11.PTSD_Conditioning.spgr+orig anat_final.$subj
# ================================== blur ==================================
# blur each volume of each run
foreach run ( $runs )
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur \
pb02.$subj.r$run.volreg+orig
end
# ================================== mask ==================================
# create 'full_mask' dataset (union mask)
foreach run ( $runs )
3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+orig
end
# create union of inputs, output type is byte
3dmask_tool -inputs rm.mask_r*+orig.HEAD -union -prefix full_mask.$subj
# ================================= scale ==================================
# scale each voxel time series to have a mean of 100
# (be sure no negatives creep in)
# (subject to a range of [0,200])
foreach run ( $runs )
3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+orig
3dcalc -a pb03.$subj.r$run.blur+orig -b rm.mean_r$run+orig \
-expr 'min(200, a/b*100)*step(a)*step(b)' \
-prefix pb04.$subj.r$run.scale
end
# ================================ regress =================================
# compute de-meaned motion parameters (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_nruns 2 \
-demean -write motion_demean.1D
# compute motion parameter derivatives (just to have)
1d_tool.py -infile dfile_rall.1D -set_nruns 2 \
-derivative -demean -write motion_deriv.1D
# run the regression analysis
3dDeconvolve -input pb04.$subj.r*.scale+orig.HEAD \
-polort 4 \
-num_stimts 6 \
-stim_file 1 motion_demean.1D'[0]' -stim_base 1 -stim_label 1 roll \
-stim_file 2 motion_demean.1D'[1]' -stim_base 2 -stim_label 2 pitch \
-stim_file 3 motion_demean.1D'[2]' -stim_base 3 -stim_label 3 yaw \
-stim_file 4 motion_demean.1D'[3]' -stim_base 4 -stim_label 4 dS \
-stim_file 5 motion_demean.1D'[4]' -stim_base 5 -stim_label 5 dL \
-stim_file 6 motion_demean.1D'[5]' -stim_base 6 -stim_label 6 dP \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-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*.scale+orig.HEAD \
-ort X.xmat.1D -prefix errts.${subj}.tproject
# if 3dDeconvolve fails, terminate the script
if ( $status != 0 ) then
echo '---------------------------------------'
echo '** 3dDeconvolve error, failing...'
echo ' (consider the file 3dDeconvolve.err)'
exit
endif
# display any large pariwise correlations from the X-matrix
1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt
# create an all_runs dataset to match the fitts, errts, etc.
3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+orig.HEAD
# --------------------------------------------------
# create a temporal signal to noise ratio dataset
# signal: if 'scale' block, mean should be 100
# noise : compute standard deviation of errts
3dTstat -mean -prefix rm.signal.all all_runs.$subj+orig
3dTstat -stdev -prefix rm.noise.all errts.${subj}.tproject+orig
3dcalc -a rm.signal.all+orig \
-b rm.noise.all+orig \
-c full_mask.$subj+orig \
-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}.tproject+orig
3dmaskave -quiet -mask full_mask.$subj+orig rm.errts.unit+orig > \
gmean.errts.unit.1D
3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D
echo "-- GCOR = `cat out.gcor.1D`"
# ---------------------------------------------------
# compute correlation volume
# (per voxel: average correlation across masked brain)
# (now just dot product with average unit time series)
3dcalc -a rm.errts.unit+orig -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP
3dTstat -sum -prefix corr_brain rm.DP+orig
# --------------------------------------------------------
# compute sum of non-baseline regressors from the X-matrix
# (use 1d_tool.py to get list of regressor colums)
set reg_cols = `1d_tool.py -infile X.xmat.1D -show_indices_interest`
3dTstat -sum -prefix sum_ideal.1D X.xmat.1D"[$reg_cols]"
# also, create a stimulus-only X-matrix, for easy review
1dcat X.xmat.1D"[$reg_cols]" > X.stim.xmat.1D
# ================== auto block: generate review scripts ===================
# generate a review script for the unprocessed EPI data
gen_epi_review.py -script @epi_review.$subj \
-dsets pb00.$subj.r*.tcat+orig.HEAD
# generate scripts to review single subject results
# (try with defaults, but do not allow bad exit status)
gen_ss_review_scripts.py -exit0
# ========================== auto block: finalize ==========================
# remove temporary files
\rm -f rm.*
# if the basic subject review script is here, run it
# (want this to be the last text output)
if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt
# return to parent directory
cd ..
echo "execution finished: `date`"
# ==========================================================================
# script generated by the command:
#
# afni_proc.py -subj_id sub11 -script \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery/sub11_imagery_proc_script \
# -out_dir \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results \
# -dsets \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Neutral+orig.HEAD \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Trauma+orig.HEAD \
# -copy_anat \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig
=====================================================================
This is the output of proc.py
=====================================================================
echo auto-generated by afni_proc.py, Mon Jul 6 12:11:56 2015
auto-generated by afni_proc.py, Mon Jul 6 12:11:56 2015
echo (version 4.32, March 2, 2015)
(version 4.32, March 2, 2015)
echo execution started: `date`
date
execution started: Mon Jul 6 12:11:56 CDT 2015
afni -ver
Precompiled binary linux_openmp_64: Mar 2 2015 (Version AFNI_2011_12_21_1014)
afni_history -check_date 9 Feb 2014
-- is current: afni_history as new as: 09 Feb 2014
most recent entry is: 02 Mar 2015
if ( 0 ) then
if ( 0 > 0 ) then
set subj = sub11
endif
set output_dir = /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results
if ( -d /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results ) then
set runs = ( `count -digits 2 1 2` )
count -digits 2 1 2
mkdir /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results
mkdir /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results/stimuli
3dcopy /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results/sub11.PTSD_Conditioning.spgr
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
3dTcat -prefix /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results/pb00.sub11.r01.tcat /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Neutral+orig[0..$]
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
3dTcat -prefix /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results/pb00.sub11.r02.tcat /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Trauma+orig[0..$]
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
set tr_counts = ( 273 273 )
cd /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 )
3dToutcount -automask -fraction -polort 4 -legendre pb00.sub11.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ 30408 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
echo ** TR #0 outliers: possible pre-steady state TRs in run 01
endif
end
3dToutcount -automask -fraction -polort 4 -legendre pb00.sub11.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ 30436 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
echo ** TR #0 outliers: possible pre-steady state TRs in run 02
endif
end
cat outcount.r01.1D outcount.r02.1D
foreach run ( 01 02 )
3dTshift -tzero 0 -quintic -prefix pb01.sub11.r01.tshift pb00.sub11.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
end
3dTshift -tzero 0 -quintic -prefix pb01.sub11.r02.tshift pb00.sub11.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
end
foreach run ( 01 02 )
3dvolreg -verbose -zpad 1 -base pb01.sub11.r01.tshift+orig[2] -1Dfile dfile.r01.1D -prefix pb02.sub11.r01.volreg -cubic pb01.sub11.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./pb01.sub11.r01.tshift+orig.BRIK
++ Reading input dataset ./pb01.sub11.r01.tshift+orig.BRIK
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 33252 voxels
+ 5188 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 273 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.284 pitch=-0.383 yaw=-0.260 dS=-0.970 dL=-0.214 dP=-0.189
++ Mean: roll=+0.000 pitch=-0.164 yaw=-0.055 dS=+0.462 dL=-0.013 dP=+0.078
++ Max : roll=+0.200 pitch=+0.164 yaw=+0.106 dS=+1.026 dL=+0.220 dP=+0.175
++ Max displacements (mm) for each sub-brick:
1.10 1.21 0.00 0.06 0.14 0.24 0.17 0.17 0.28 0.12 0.14 0.19 0.13 0.19 0.18 0.20 0.24 0.22 0.21 0.19 0.21 0.20 0.19 0.22 0.19 0.22 0.20 0.22 0.23 0.24 0.26 0.23 0.26 0.28 0.29 0.28 0.27 0.28 0.24 0.29 0.30 0.26 0.30 0.31 0.32 0.29 0.30 0.34 0.31 0.35 0.34 0.32 0.31 0.29 0.26 0.25 0.30 0.23 0.26 0.23 0.24 0.24 0.25 0.27 0.32 0.12 0.47 0.44 0.39 0.44 0.42 0.48 0.44 0.52 0.43 0.50 0.53 0.55 0.58 0.55 0.60 0.54 0.58 0.46 0.45 0.72 0.69 0.75 0.75 0.80 0.77 0.73 0.74 0.70 0.76 0.72 0.75 0.74 0.73 0.75 0.70 0.75 0.72 0.76 0.77 0.71 0.74 0.73 0.77 0.74 0.71 0.71 0.69 0.71 0.77 0.85 0.81 0.80 0.81 0.77 0.84 0.80 0.86 0.84 0.84 0.81 0.85 0.90 0.92 0.93 0.93 0.93 0.90 0.96 0.90 0.90 0.92 1.00 0.95 1.01 0.95 0.99 0.99 1.01 1.04 1.00 1.07 1.00 1.04 1.03 0.89 0.79 0.86 0.88 0.88 0.95 0.89 0.94 0.89 0.94 0.97 0.98 0.98 0.92 0.99 0.88 0.73 0.81 0.87 0.88 0.83 0.88 0.78 0.80 0.74 0.68 0.68 0.67 0.54 0.57 0.56 0.60 0.66 0.63 0.68 0.61 0.67 0.62 0.63 0.64 0.65 0.68 0.64 0.69 0.64 0.71 0.52 0.29 0.55 0.54 0.63 0.65 0.66 0.73 0.65 0.71 0.68 0.72 0.70 0.75 0.74 0.70 0.51 0.63 0.74 0.69 0.73 0.76 0.82 0.81 0.90 0.91 0.93 0.87 0.97 1.03 1.11 1.10 1.15 1.18 1.18 1.23 1.21 1.33 1.29 1.32 1.33 1.36 1.36 1.32 1.37 1.36 1.41 1.36 1.40 1.44 1.20 0.91 1.14 1.18 1.23 1.32 1.32 1.39 1.37 1.41 1.42 1.51 1.53 1.49 1.53 1.52 1.50 1.24 1.38 1.39 1.37 1.43 1.46 1.40 1.16 1.41 1.45
++ Max displacement in automask = 1.53 (mm) at sub-brick 258
++ Wrote dataset to disk in ./pb02.sub11.r01.volreg+orig.BRIK
end
3dvolreg -verbose -zpad 1 -base pb01.sub11.r01.tshift+orig[2] -1Dfile dfile.r02.1D -prefix pb02.sub11.r02.volreg -cubic pb01.sub11.r02.tshift+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./pb01.sub11.r01.tshift+orig.BRIK
++ Reading input dataset ./pb01.sub11.r02.tshift+orig.BRIK
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 33554 voxels
+ 5285 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 273 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=+0.122 pitch=-2.153 yaw=-1.308 dS=-1.027 dL=-0.741 dP=+0.118
++ Mean: roll=+0.503 pitch=-1.219 yaw=-0.731 dS=+0.431 dL=+0.164 dP=+0.596
++ Max : roll=+0.907 pitch=-0.098 yaw=-0.382 dS=+1.159 dL=+0.497 dP=+0.921
++ Max displacements (mm) for each sub-brick:
2.11 1.78 1.53 1.50 1.51 1.63 1.62 1.67 1.67 1.69 1.69 1.67 1.69 1.69 1.70 1.66 1.68 1.64 1.68 1.64 1.64 1.62 1.61 1.65 1.62 1.61 1.57 1.57 1.56 1.58 1.56 1.57 1.57 1.59 1.59 1.58 1.60 1.58 1.60 1.56 1.56 1.46 1.45 1.67 1.69 1.69 1.72 1.71 1.73 1.68 1.75 1.84 1.89 1.91 1.89 1.96 1.97 2.05 2.05 2.09 2.16 2.18 2.27 2.29 2.36 2.43 2.48 2.40 2.40 2.52 2.57 2.61 2.61 2.62 2.68 2.70 2.75 2.74 2.79 2.85 2.87 2.90 2.92 2.96 2.92 2.99 3.00 3.03 3.05 3.07 3.08 3.06 3.12 3.07 3.10 3.08 2.73 2.74 2.90 2.90 3.04 3.04 3.07 3.05 3.03 3.13 3.14 3.19 3.15 3.07 3.04 3.04 2.90 2.87 2.94 2.96 2.99 2.90 2.89 2.55 2.65 2.76 2.75 2.83 2.85 2.80 2.76 2.70 2.68 2.76 2.75 2.79 2.86 2.92 2.97 2.99 3.00 3.03 3.07 3.15 3.24 3.35 3.39 3.42 3.48 3.58 3.69 3.84 3.93 4.04 4.04 4.00 3.91 3.92 3.96 3.94 3.91 3.85 3.98 4.09 4.22 4.28 4.26 4.38 4.45 4.40 4.31 4.31 4.37 4.27 4.24 4.21 4.25 4.32 4.23 4.27 4.23 4.25 4.29 4.28 4.35 4.26 4.29 4.29 4.34 4.32 3.95 3.47 3.61 3.66 3.62 3.61 3.54 3.59 3.61 3.56 3.64 3.54 3.51 3.60 3.55 3.59 3.62 3.58 3.60 3.51 3.55 3.50 3.52 3.52 3.52 3.52 3.51 3.51 3.47 3.22 3.16 3.15 3.14 3.20 3.30 3.59 3.69 3.64 3.60 3.64 3.65 3.85 3.81 3.89 3.96 3.84 3.92 4.00 4.05 3.94 3.79 3.93 3.86 3.73 3.63 3.61 3.61 3.55 3.62 3.55 3.23 2.79 2.59 2.19 2.54 2.74 2.75 2.80 2.81 2.67 2.73 2.93 2.98 3.05 2.97 2.99 3.07 3.02 3.25 3.32 3.29 3.32 3.38 3.29 3.18 3.28 3.19
++ Max displacement in automask = 4.45 (mm) at sub-brick 164
++ Wrote dataset to disk in ./pb02.sub11.r02.volreg+orig.BRIK
end
cat dfile.r01.1D dfile.r02.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 2 -derivative -collapse_cols euclidean_norm -write motion_sub11_enorm.1D
3dcopy sub11.PTSD_Conditioning.spgr+orig anat_final.sub11
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
foreach run ( 01 02 )
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.sub11.r01.blur pb02.sub11.r01.volreg+orig
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
Program 3dmerge
++ default -1dindex = 0
++ default -1tindex = 1
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (87.4 MB)
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Edit-- Wrote edited dataset: ./pb03.sub11.r01.blur+orig.BRIK
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end
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.sub11.r02.blur pb02.sub11.r02.volreg+orig
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
Program 3dmerge
++ default -1dindex = 0
++ default -1tindex = 1
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (87.4 MB)
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Edit-- Wrote edited dataset: ./pb03.sub11.r02.blur+orig.BRIK
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end
foreach run ( 01 02 )
3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub11.r01.blur+orig
++ 3dAutomask: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.sub11.r01.blur+orig
++ Forming automask
+ Fixed clip level = 1489.626221
+ Used gradual clip level = 960.365417 .. 1693.108276
+ Number voxels above clip level = 31851
+ Clustering voxels ...
+ Largest cluster has 31207 voxels
+ Clustering voxels ...
+ Largest cluster has 30902 voxels
+ Filled 136 voxels in small holes; now have 31038 voxels
+ Clustering voxels ...
+ Largest cluster has 31036 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 136888 voxels
+ Mask now has 31048 voxels
++ Dilating automask
+ Clustering voxels ...
+ Largest cluster has 131204 voxels
++ 36732 voxels in the mask [out of 167936: 21.87%]
++ first 13 x-planes are zero [from A]
++ last 2 x-planes are zero [from P]
++ first 11 y-planes are zero [from S]
++ last 12 y-planes are zero [from I]
++ first 0 z-planes are zero [from L]
++ last 0 z-planes are zero [from R]
++ Output dataset ./rm.mask_r01+orig.BRIK
++ CPU time = 0.000000 sec
end
3dAutomask -dilate 1 -prefix rm.mask_r02 pb03.sub11.r02.blur+orig
++ 3dAutomask: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.sub11.r02.blur+orig
++ Forming automask
+ Fixed clip level = 1480.503296
+ Used gradual clip level = 952.407410 .. 1689.523071
+ Number voxels above clip level = 32021
+ Clustering voxels ...
+ Largest cluster has 31313 voxels
+ Clustering voxels ...
+ Largest cluster has 31053 voxels
+ Filled 133 voxels in small holes; now have 31186 voxels
+ Clustering voxels ...
+ Largest cluster has 31181 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 136743 voxels
+ Mask now has 31193 voxels
++ Dilating automask
+ Clustering voxels ...
+ Largest cluster has 131042 voxels
++ 36894 voxels in the mask [out of 167936: 21.97%]
++ first 13 x-planes are zero [from A]
++ last 2 x-planes are zero [from P]
++ first 11 y-planes are zero [from S]
++ last 12 y-planes are zero [from I]
++ first 0 z-planes are zero [from L]
++ last 0 z-planes are zero [from R]
++ Output dataset ./rm.mask_r02+orig.BRIK
++ CPU time = 0.000000 sec
end
3dmask_tool -inputs rm.mask_r01+orig.HEAD rm.mask_r02+orig.HEAD -union -prefix full_mask.sub11
++ processing 2 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 2 volumes gives min count 0
++ voxel limits: 0 clipped, 36948 survived, 130988 were zero
++ writing result full_mask.sub11...
++ Output dataset ./full_mask.sub11+orig.BRIK
foreach run ( 01 02 )
3dTstat -prefix rm.mean_r01 pb03.sub11.r01.blur+orig
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r01+orig.BRIK
3dcalc -a pb03.sub11.r01.blur+orig -b rm.mean_r01+orig -expr min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub11.r01.scale
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.sub11.r01.scale+orig.BRIK
end
3dTstat -prefix rm.mean_r02 pb03.sub11.r02.blur+orig
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r02+orig.BRIK
3dcalc -a pb03.sub11.r02.blur+orig -b rm.mean_r02+orig -expr min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub11.r02.scale
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.sub11.r02.scale+orig.BRIK
end
1d_tool.py -infile dfile_rall.1D -set_nruns 2 -demean -write motion_demean.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 2 -derivative -demean -write motion_deriv.1D
3dDeconvolve -input pb04.sub11.r01.scale+orig.HEAD pb04.sub11.r02.scale+orig.HEAD -polort 4 -num_stimts 6 -stim_file 1 motion_demean.1D[0] -stim_base 1 -stim_label 1 roll -stim_file 2 motion_demean.1D[1] -stim_base 2 -stim_label 2 pitch -stim_file 3 motion_demean.1D[2] -stim_base 3 -stim_label 3 yaw -stim_file 4 motion_demean.1D[3] -stim_base 4 -stim_label 4 dS -stim_file 5 motion_demean.1D[4] -stim_base 5 -stim_label 5 dL -stim_file 6 motion_demean.1D[5] -stim_base 6 -stim_label 6 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -fitts fitts.sub11 -errts errts.sub11 -x1D_stop -bucket stats.sub11
++ 3dDeconvolve: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ Auto-catenated input datasets treated as multiple imaging runs
++ Auto-catenated datasets start at: 0 273
++ STAT automask has 167936 voxels (out of 167936 = 100.0%)
++ Skipping check for initial transients
++ Input polort=4; Longest run=546.0 s; Recommended minimum polort=4 ++ OK ++
++ Number of time points: 546 (no censoring)
+ Number of parameters: 16 [16 baseline ; 0 signal]
++ Memory required for output bricks = 734,216,192 bytes (about 734 million [mega])
++ Wrote matrix image to file X.jpg
++ Wrote matrix values to file X.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:
3dREMLfit -matrix X.xmat.1D \
-input "pb04.sub11.r01.scale+orig.HEAD pb04.sub11.r02.scale+orig.HEAD" \
-fout -tout -Rbuck stats.sub11_REML -Rvar stats.sub11_REMLvar \
-Rfitts fitts.sub11_REML -Rerrts errts.sub11_REML -verb
++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ ----- Signal+Baseline matrix condition [X] (546x16): 3.93414 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (546x16): 3.93414 ++ VERY GOOD ++
++ ----- stim_base-only matrix condition [X] (546x6): 2.53257 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (546x10): 1.01224 ++ VERY GOOD ++
++ 3dDeconvolve exits: -x1D_stop option was invoked
3dTproject -polort 0 -input pb04.sub11.r01.scale+orig.HEAD pb04.sub11.r02.scale+orig.HEAD -ort X.xmat.1D -prefix errts.sub11.tproject
++ have 2 input dataset names
++ Auto-catenated dataset has 2 runs
++ 3dTproject: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ Setting up regressors
+ 2 Blocks * 1 polynomials -- 2 polort regressors
+ -- 16 other fixed ort regressors
++ 546 retained time points MINUS 18 regressors ==> 528 D.O.F. left
++ no -mask option ==> processing all 167936 voxels in dataset
++ Compute pseudo-inverse of fixed orts
++ Loading dataset
++ Starting project-orization
++ Convert results to output dataset
++ Output dataset ./errts.sub11.tproject+orig.BRIK
++ ===== clock time = 6s 548ms
if ( 0 != 0 ) then
tee out.cormat_warn.txt
1d_tool.py -show_cormat_warnings -infile X.xmat.1D
-- no warnings for correlation matrix (cut = 0.400) --
3dTcat -prefix all_runs.sub11 pb04.sub11.r01.scale+orig.HEAD pb04.sub11.r02.scale+orig.HEAD
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
3dTstat -mean -prefix rm.signal.all all_runs.sub11+orig
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.signal.all+orig.BRIK
3dTstat -stdev -prefix rm.noise.all errts.sub11.tproject+orig
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.noise.all+orig.BRIK
3dcalc -a rm.signal.all+orig -b rm.noise.all+orig -c full_mask.sub11+orig -expr c*a/b -prefix TSNR.sub11
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./TSNR.sub11+orig.BRIK
3dTnorm -norm2 -prefix rm.errts.unit errts.sub11.tproject+orig
++ 3dTnorm: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: RW Cox
++ Output dataset ./rm.errts.unit+orig.BRIK
3dmaskave -quiet -mask full_mask.sub11+orig rm.errts.unit+orig
++ 3dmaskave: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
+++ 36948 voxels survive the mask
3dTstat -sos -prefix - gmean.errts.unit.1D'
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo -- GCOR = `cat out.gcor.1D`
cat out.gcor.1D
-- GCOR = 0.799206
3dcalc -a rm.errts.unit+orig -b gmean.errts.unit.1D -expr a*b -prefix rm.DP
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./rm.DP+orig.BRIK
3dTstat -sum -prefix corr_brain rm.DP+orig
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./corr_brain+orig.BRIK
set reg_cols = `1d_tool.py -infile X.xmat.1D -show_indices_interest`
1d_tool.py -infile X.xmat.1D -show_indices_interest
3dTstat -sum -prefix sum_ideal.1D X.xmat.1D[0..$]
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Mar 2 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
++ Output dataset ./sum_ideal.1D
1dcat X.xmat.1D[0..$]
gen_epi_review.py -script @epi_review.sub11 -dsets pb00.sub11.r01.tcat+orig.HEAD pb00.sub11.r02.tcat+orig.HEAD
gen_ss_review_scripts.py -exit0
** failed to guess at any stats dset, resting state?
(else X-matrix file "X.xmat.1D" may not apply)
** failed to guess align_anat (continuing)
++ writing ss review basic: @ss_review_basic
** no stats_dset dset, cannot drive view_stats, skipping...
++ writing ss review driver: @ss_review_driver
++ writing ss review drive commands: @ss_review_driver_commands
rm -f rm.DP+orig.BRIK rm.DP+orig.HEAD rm.errts.unit+orig.BRIK rm.errts.unit+orig.HEAD rm.mask_r01+orig.BRIK rm.mask_r01+orig.HEAD rm.mask_r02+orig.BRIK rm.mask_r02+orig.HEAD rm.mean_r01+orig.BRIK rm.mean_r01+orig.HEAD rm.mean_r02+orig.BRIK rm.mean_r02+orig.HEAD rm.noise.all+orig.BRIK rm.noise.all+orig.HEAD rm.signal.all+orig.BRIK rm.signal.all+orig.HEAD
if ( -e @ss_review_basic ) ./@ss_review_basic
tee out.ss_review.sub11.txt
./@ss_review_basic