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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| July 06, 2015 01:20PM | |
Registered: 9 years ago Posts: 7 |
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
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)
Editing sub-brick 0
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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)
Editing sub-brick 0
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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
| Subject | Author | Posted |
|---|---|---|
|
lindsle6 | July 06, 2015 12:22PM |
|
Peter Molfese | July 06, 2015 12:38PM |
|
lindsle6 | July 06, 2015 01:20PM |
|
Peter Molfese | July 06, 2015 01:29PM |
|
rick reynolds | July 06, 2015 02:25PM |
|
Isaac Schwabacher | July 13, 2015 02:38PM |
|
rick reynolds | July 13, 2015 04:20PM |
|
Isaac Schwabacher | July 13, 2015 05:00PM |
|
rick reynolds | July 13, 2015 08:37PM |
