AFNI Message Board

Dear AFNI users-

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

History of AFNI updates  

|
October 23, 2019 01:41PM
Whenever I have an oblique warning, the obliquity is about 1 degree or even less, and I want to ask if I need to bother with deobliquing in this case? I attach screenshots of raw EPI data superimposed on raw anatomical data, and if you can make a suggestion, that would be nice.

The EPI voxel size is 3x3x4mm, and since I don't know why you mean by "afni_proc.py command", I attach my script below.

#!/bin/tcsh -xef

echo "auto-generated by afni_proc.py, Tue Oct 15 15:34:29 2019"
echo "(version 6.32, February 22, 2019)"
echo "execution started: `date`"

# to execute via tcsh:
# tcsh -xef proc.265001 |& tee output.proc.265001
# to execute via bash:
# tcsh -xef proc.265001.s1 2>&1 | tee output.proc.265001.s1

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

# take note of the AFNI version
afni -ver

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

# the user may specify a single subject to run with
if ( $#argv > 0 ) then
set subj = $argv[1]
else
set subj = 265001
endif

set sNUM = 1

# assign output directory name
set output_dir = ${subj}.s$sNUM.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 6`)

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

# copy stim files into stimulus directory
cp /home/sungjin/fMRI/CGE/CGE_Raw_Data/Timing_CGE.txt $output_dir/stimuli

# copy anatomy to results dir
3dcopy CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/anatSS.SSW.nii \
$output_dir/anatSS.SSW

# copy external -tlrc_NL_warped_dsets datasets
3dcopy CGE_Raw_Data/Session$sNUM/${subj}_S$sNUM/subject_raw/anatQQ.SSW.nii \
$output_dir/anatQQ.SSW
3dcopy CGE_Raw_Data/Session$sNUM/${subj}_S$sNUM/subject_raw/anatQQ.SSW.aff12.1D \
$output_dir/anatQQ.SSW.aff12.1D
3dcopy CGE_Raw_Data/Session$sNUM/${subj}_S$sNUM/subject_raw/anatQQ.SSW_WARP.nii \
$output_dir/anatQQ.SSW_WARP.nii

# ============================ 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 \
CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/deob.rest1.s1+orig'[0..$]'
3dTcat -prefix $output_dir/pb00.$subj.r02.tcat \
CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/deob.pv.s1+orig'[0..$]'
3dTcat -prefix $output_dir/pb00.$subj.r03.tcat \
CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/deob.14p.s1+orig'[0..$]'
3dTcat -prefix $output_dir/pb00.$subj.r04.tcat \
CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/deob.6p.s1+orig'[0..$]'
3dTcat -prefix $output_dir/pb00.$subj.r05.tcat \
CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/deob.flk.s1+orig'[0..$]'
3dTcat -prefix $output_dir/pb00.$subj.r06.tcat \
CGE_Raw_Data/Session1/${subj}_S$sNUM/subject_raw/deob.rest2.s1+orig'[0..$]'

# and make note of repetitions (TRs) per run
set tr_counts = ( 180 150 150 150 150 180 )

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


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

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

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

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

# ================================= 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

# ================================ despike =================================
# apply 3dDespike to each run
foreach run ( $runs )
3dDespike -NEW -nomask -prefix pb02.$subj.r$run.despike \
pb01.$subj.r$run.tshift+orig
end

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

# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be current anatSS.SSW+orig)
align_epi_anat.py -anat2epi -anat anatSS.SSW+orig \
-suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-anat_has_skull no \
-cost lpc+ZZ \
-volreg off -tshift off

# ================================== tlrc ==================================

# nothing to do: have external -tlrc_NL_warped_dsets

# warped anat : anatQQ.SSW+tlrc
# affine xform : anatQQ.SSW.aff12.1D
# non-linear warp : anatQQ.SSW_WARP.nii

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

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

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

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

# catenate volreg/epi2anat/tlrc xforms
cat_matvec -ONELINE \
anatQQ.SSW.aff12.1D \
anatSS.SSW_al_junk_mat.aff12.1D -I \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D

# apply catenated xform: volreg/epi2anat/tlrc/NLtlrc
# then apply non-linear standard-space warp
3dNwarpApply -master anatQQ.SSW+tlrc -dxyz 1 \
-source pb02.$subj.r$run.despike+orig \
-nwarp "anatQQ.SSW_WARP.nii mat.r$run.warp.aff12.1D" \
-prefix rm.epi.nomask.r$run

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

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

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

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

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

# warp the volreg base EPI dataset to make a final version
cat_matvec -ONELINE \
anatQQ.SSW.aff12.1D \
anatSS.SSW_al_junk_mat.aff12.1D -I > mat.basewarp.aff12.1D

3dNwarpApply -master anatQQ.SSW+tlrc -dxyz 1 \
-source vr_base_min_outlier+orig \
-nwarp "anatQQ.SSW_WARP.nii mat.basewarp.aff12.1D" \
-prefix final_epi_vr_base_min_outlier

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

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

# ================================== blur ==================================
# blur each volume of each run
foreach run ( $runs )
3dmerge -1blur_fwhm 6.0 -doall -prefix pb04.$subj.r$run.blur \
pb03.$subj.r$run.volreg+tlrc
end

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

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

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

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

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

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

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

# ---- create group anatomy mask, mask_group+tlrc ----
# (resampled from tlrc base anat, MNI152_2009_template_SSW.nii.gz)
3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \
-input /home/sungjin/abin/MNI152_2009_template_SSW.nii.gz

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

# ================================= 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 pb04.$subj.r$run.blur+tlrc
3dcalc -a pb04.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \
-c mask_epi_extents+tlrc \
-expr 'c * min(200, a/b*100)*step(a)*step(b)' \
-prefix pb05.$subj.r$run.scale
end

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

# compute de-meaned motion parameters (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_run_lengths 180 150 150 150 150 180 \
-demean -write motion_demean.1D

# compute motion parameter derivatives (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_run_lengths 180 150 150 150 150 180 \
-derivative -demean -write motion_deriv.1D

# convert motion parameters for per-run regression
1d_tool.py -infile motion_demean.1D -set_run_lengths 180 150 150 150 150 180 \
-split_into_pad_runs mot_demean

1d_tool.py -infile motion_deriv.1D -set_run_lengths 180 150 150 150 150 180 \
-split_into_pad_runs mot_deriv

# create censor file motion_${subj}_censor.1D, for censoring motion
1d_tool.py -infile dfile_rall.1D -set_run_lengths 180 150 150 150 150 180 \
-show_censor_count -censor_prev_TR \
-censor_motion 0.5 motion_${subj}

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

# ------------------------------
# run the regression analysis
3dDeconvolve -input pb05.$subj.r*.scale+tlrc.HEAD \
-censor motion_${subj}_censor.1D \
-ortvec mot_demean.r01.1D mot_demean_r01 \
-ortvec mot_demean.r02.1D mot_demean_r02 \
-ortvec mot_demean.r03.1D mot_demean_r03 \
-ortvec mot_demean.r04.1D mot_demean_r04 \
-ortvec mot_demean.r05.1D mot_demean_r05 \
-ortvec mot_demean.r06.1D mot_demean_r06 \
-ortvec mot_deriv.r01.1D mot_deriv_r01 \
-ortvec mot_deriv.r02.1D mot_deriv_r02 \
-ortvec mot_deriv.r03.1D mot_deriv_r03 \
-ortvec mot_deriv.r04.1D mot_deriv_r04 \
-ortvec mot_deriv.r05.1D mot_deriv_r05 \
-ortvec mot_deriv.r06.1D mot_deriv_r06 \
-polort 3 \
-num_stimts 1 \
-stim_times 1 stimuli/Timing_CGE.txt 'GAM' \
-stim_label 1 Timing_CGE.txt \
-jobs 4 \
-GOFORIT 5 \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-errts errts.${subj} \
-bucket stats.$subj


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


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

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

# -- execute the 3dREMLfit script, written by 3dDeconvolve --
tcsh -x stats.REML_cmd

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


# create an all_runs dataset to match the fitts, errts, etc.
3dTcat -prefix all_runs.$subj pb05.$subj.r*.scale+tlrc.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.$subj+tlrc"[$ktrs]"
3dTstat -stdev -prefix rm.noise.all errts.${subj}_REML+tlrc"[$ktrs]"
3dcalc -a rm.signal.all+tlrc \
-b rm.noise.all+tlrc \
-c full_mask.$subj+tlrc \
-expr 'c*a/b' -prefix TSNR.$subj

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

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

# create fitts dataset from all_runs and errts
3dcalc -a all_runs.$subj+tlrc -b errts.${subj}+tlrc -expr a-b \
-prefix fitts.$subj
# create fitts from REML errts
3dcalc -a all_runs.$subj+tlrc -b errts.${subj}_REML+tlrc -expr a-b \
-prefix fitts.$subj\_REML

# create ideal files for fixed response stim types
1dcat X.nocensor.xmat.1D'[24]' > ideal_Timing_CGE.txt.1D

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

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

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

# create directory for ACF curve files
mkdir files_ACF

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

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

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

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

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

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

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

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

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

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

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

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


# add 3dClustSim results as attributes to any stats dset
mkdir files_ClustSim

# run Monte Carlo simulations using method 'ACF'
set params = ( `grep ACF blur_est.$subj.1D | tail -n 1` )
3dClustSim -both -mask full_mask.$subj+tlrc -acf $params[1-3] \
-cmd 3dClustSim.ACF.cmd -prefix files_ClustSim/ClustSim.ACF

# run 3drefit to attach 3dClustSim results to stats
set cmd = ( `cat 3dClustSim.ACF.cmd` )
$cmd stats.$subj+tlrc stats.${subj}_REML+tlrc


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

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

# generate scripts to review single subject results
# (try with defaults, but do not allow bad exit status)
gen_ss_review_scripts.py -mot_limit 0.5 -exit0 \
-ss_review_dset out.ss_review.$subj.txt \
-write_uvars_json out.ss_review_uvars.json

# ========================== 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 ) then
./@ss_review_basic |& tee out.ss_review.$subj.txt

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

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

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

echo "execution finished: `date`"




# ==========================================================================
# script generated by the command:
#
# afni_proc.py -subj_id 265001 -script proc.265001 -scr_overwrite -blocks \
# tshift despike align tlrc volreg blur mask scale regress -copy_anat \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatSS.SSW.nii \
# -anat_has_skull no -dsets \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.rest1.s1+orig.HEAD \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.pv.s1+orig.HEAD \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.14p.s1+orig.HEAD \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.6p.s1+orig.HEAD \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.flk.s1+orig.HEAD \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.rest2.s1+orig.HEAD \
# -tcat_remove_first_trs 0 -align_opts_aea -cost lpc+ZZ -volreg_align_to \
# MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -tlrc_base \
# MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.nii \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.aff12.1D \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW_WARP.nii \
# -blur_size 6.0 -regress_stim_times \
# /home/sungjin/fMRI/CGE/CGE_Raw_Data/Timing_CGE.txt -regress_stim_labels \
# Timing_CGE.txt -regress_basis 'BLOCK(6,1)' -regress_censor_motion 0.5 \
# -regress_apply_mot_types demean deriv -regress_motion_per_run \
# -regress_opts_3dD -jobs 4 -GOFORIT 5 -regress_reml_exec \
# -regress_compute_fitts -regress_make_ideal_sum sum_ideal.1D \
# -regress_est_blur_epits -regress_est_blur_errts
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Subject Author Posted

current memory mallocated error

cooldesert October 21, 2019 02:34PM

Re: current memory mallocated error

ptaylor October 21, 2019 05:04PM

Re: current memory mallocated error

cooldesert October 23, 2019 11:57AM

Re: current memory mallocated error

ptaylor October 23, 2019 12:37PM

Re: current memory mallocated error

cooldesert October 23, 2019 12:53PM

Re: current memory mallocated error

ptaylor October 23, 2019 01:00PM

Re: current memory mallocated error Attachments

cooldesert October 23, 2019 01:41PM

Re: current memory mallocated error

ptaylor October 23, 2019 03:22PM

Re: current memory mallocated error

rick reynolds October 23, 2019 03:24PM

Re: current memory mallocated error

cooldesert October 24, 2019 01:34PM

Re: current memory mallocated error

cooldesert October 26, 2019 05:11PM

Re: current memory mallocated error

rick reynolds October 28, 2019 09:57AM

Re: current memory mallocated error

cooldesert October 31, 2019 03:29PM

Re: current memory mallocated error

rick reynolds October 31, 2019 05:08PM

Re: current memory mallocated error Attachments

cooldesert November 01, 2019 04:35PM

Re: current memory mallocated error

rick reynolds November 14, 2019 09:48AM