From 88d5d600127617ba84759ccc831a9188cc5bee22 Mon Sep 17 00:00:00 2001 From: RuthPauli Date: Thu, 7 Apr 2016 12:47:16 +0100 Subject: [PATCH] AFNI single-subject t-test without the additional motion regressors --- afni_no_motion_regressors/README.md | 11 + afni_no_motion_regressors/batch.sh | 1 + afni_no_motion_regressors/cmd.ap.sub_001 | 37 ++ afni_no_motion_regressors/proc.sub_001 | 416 ++++++++++++++++++ .../sub_001.results/3dClustSim.cmd | 1 + .../sub_001.results/3dDeconvolve.err | 1 + .../sub_001.results/@epi_review.sub_001 | 78 ++++ .../sub_001.results/@ss_review_basic | 330 ++++++++++++++ .../sub_001.results/@ss_review_driver | 199 +++++++++ .../@ss_review_driver_commands | 28 ++ .../sub_001.results/ClustSim.NN1_1sided.1D | 37 ++ .../sub_001.results/ClustSim.NN1_1sided.niml | 45 ++ .../sub_001.results/ClustSim.NN1_2sided.1D | 37 ++ .../sub_001.results/ClustSim.NN1_2sided.niml | 45 ++ .../sub_001.results/ClustSim.NN1_bisided.1D | 37 ++ .../sub_001.results/ClustSim.NN1_bisided.niml | 45 ++ .../sub_001.results/ClustSim.NN2_1sided.1D | 37 ++ .../sub_001.results/ClustSim.NN2_1sided.niml | 45 ++ .../sub_001.results/ClustSim.NN2_2sided.1D | 37 ++ .../sub_001.results/ClustSim.NN2_2sided.niml | 45 ++ .../sub_001.results/ClustSim.NN2_bisided.1D | 37 ++ .../sub_001.results/ClustSim.NN2_bisided.niml | 45 ++ .../sub_001.results/ClustSim.NN3_1sided.1D | 37 ++ .../sub_001.results/ClustSim.NN3_1sided.niml | 45 ++ .../sub_001.results/ClustSim.NN3_2sided.1D | 37 ++ .../sub_001.results/ClustSim.NN3_2sided.niml | 45 ++ .../sub_001.results/ClustSim.NN3_bisided.1D | 37 ++ .../sub_001.results/ClustSim.NN3_bisided.niml | 45 ++ .../sub_001.results/ClustSim.mask | 56 +++ .../sub_001.results/Clust_mask+tlrc.BRIK.gz | 3 + .../sub_001.results/Clust_mask+tlrc.HEAD | 3 + .../sub_001.results/TSNR.sub_001+tlrc.BRIK | 3 + .../sub_001.results/TSNR.sub_001+tlrc.HEAD | 3 + .../sub_001.results/X.jpg | 3 + .../sub_001.results/X.nocensor.xmat.1D | 130 ++++++ .../sub_001.results/X.stim.xmat.1D | 104 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afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xat.1D create mode 100644 afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns_WarpDrive.log create mode 100644 afni_no_motion_regressors/sub_001.results/sum_ideal.1D create mode 100644 afni_no_motion_regressors/sub_001.results/warp.anat.Xat.1D diff --git a/afni_no_motion_regressors/README.md b/afni_no_motion_regressors/README.md new file mode 100644 index 0000000..080b8b9 --- /dev/null +++ b/afni_no_motion_regressors/README.md @@ -0,0 +1,11 @@ +AFNI single subject t-test results from subject 01, tone counting task, taken from OpenfMRI (BIDS) DS000011 classification learning and tone counting experiment. + +The six motion regressors (for rotations and shifts) have been removed from the model. + +Contrast used: +tone counting vs. baseline + +For a description of the task, see: + +https://openfmri.org/dataset/ds000011/ + diff --git a/afni_no_motion_regressors/batch.sh b/afni_no_motion_regressors/batch.sh new file mode 100644 index 0000000..591b7e6 --- /dev/null +++ b/afni_no_motion_regressors/batch.sh @@ -0,0 +1 @@ +3dclust -1Dformat -nosum -1dindex 2 -1tindex 2 -2thresh -3.406 3.406 -inmask -dxyz=1 -savemask Clust_mask 1.01 2 ./afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.HEAD \ No newline at end of file diff --git a/afni_no_motion_regressors/cmd.ap.sub_001 b/afni_no_motion_regressors/cmd.ap.sub_001 new file mode 100755 index 0000000..f9b715d --- /dev/null +++ b/afni_no_motion_regressors/cmd.ap.sub_001 @@ -0,0 +1,37 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.37 (April 14, 2015) +# creation date: Wed Mar 2 09:54:17 2016 + +# set data directories +set top_dir = ./afni_no_motion_regressors + +# set subject and group identifiers +set subj = sub_001 +set group_id = DS0011 + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $top_dir/sub-01_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $top_dir/sub-01_task-tonecounting_bold.nii.gz \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 4.0 \ + -regress_stim_times \ + $top_dir/tone_counting_onset_times.txt \ + $top_dir/tone_counting_probe_duration.txt \ + -regress_stim_labels \ + tone_counting probe \ + -regress_basis_multi \ + 'BLOCK(4)' 'dmBLOCK' \ + -regress_stim_types \ + times AM1 \ + -regress_censor_motion 0.3 \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts + diff --git a/afni_no_motion_regressors/proc.sub_001 b/afni_no_motion_regressors/proc.sub_001 new file mode 100755 index 0000000..702a8fa --- /dev/null +++ b/afni_no_motion_regressors/proc.sub_001 @@ -0,0 +1,416 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Apr 7 12:17:12 2016" +echo "(version 4.57, December 7, 2015)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_001 |& tee output.proc.sub_001 + +# =========================== 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 28 Oct 2015 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 28 Oct 2015)" + 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 = sub_001 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + ./afni_no_motion_regressors/tone_counting_onset_times.txt \ + ./afni_no_motion_regressors/tone_counting_probe_duration.txt \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w + +# ============================ 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 \ + sub-01_task-tonecounting_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 104 ) + +# ------------------------------------------------------- +# 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 ( $runs ) + 3dToutcount -automask -fraction -polort 2 -legendre \ + pb00.$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$run.tcat+orig +end + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-01_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-01_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi pb01.$subj.r01.tshift+orig -epi_base 2 \ + -epi_strip 3dAutomask \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-01_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-01_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg, epi2anat and tlrc transformations + cat_matvec -ONELINE \ + sub-01_T1w_ns+tlrc::WARP_DATA -I \ + sub-01_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform : volreg, epi2anat and tlrc + 3dAllineate -base sub-01_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 3 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-01_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 3 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc 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 pb02.$subj.r$run.volreg +end + +# create an anat_final dataset, aligned with stats +3dcopy sub-01_T1w_ns+tlrc anat_final.$subj + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-01_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== 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+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$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.$subj+tlrc -input sub-01_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute 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, TT_N27+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/u1591557/abin/TT_N27+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= 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+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (just to have) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 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 pb04.$subj.r*.scale+tlrc.HEAD \ + -censor motion_${subj}_censor.1D \ + -polort 2 \ + -num_stimts 2 \ + -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' \ + -stim_label 1 tone_counting \ + -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' \ + -stim_label 2 probe \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+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}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D +1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$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 + +# -- 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 \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average blur and append +set blurs = ( `cat blur.epits.1D` ) +echo average epits blurs: $blurs +echo "$blurs # epits 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 \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average blur and append +set blurs = ( `cat blur.errts.1D` ) +echo average errts blurs: $blurs +echo "$blurs # errts blur estimates" >> blur_est.$subj.1D + + +# add 3dClustSim results as attributes to any stats dset +set fxyz = ( `tail -1 blur_est.$subj.1D` ) +3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] \ + -prefix ClustSim +set cmd = ( `cat 3dClustSim.cmd` ) +$cmd stats.$subj+tlrc + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_001 -script proc.sub_001 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# ./afni_no_motion_regressors/sub-01_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# ./afni_no_motion_regressors/sub-01_task-tonecounting_bold.nii.gz \ +# -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size \ +# 4.0 -regress_stim_times \ +# ./afni_no_motion_regressors/tone_counting_onset_times.txt \ +# ./afni_no_motion_regressors/tone_counting_probe_duration.txt \ +# -regress_stim_labels tone_counting probe -regress_basis_multi \ +# 'BLOCK(4)' dmBLOCK -regress_stim_types times AM1 -regress_censor_motion \ +# 0.3 -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# -regress_est_blur_errts diff --git a/afni_no_motion_regressors/sub_001.results/3dClustSim.cmd b/afni_no_motion_regressors/sub_001.results/3dClustSim.cmd new file mode 100644 index 0000000..49188b8 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/3dClustSim.cmd @@ -0,0 +1 @@ +3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:ClustSim.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:ClustSim.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:ClustSim.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:ClustSim.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:ClustSim.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:ClustSim.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:ClustSim.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:ClustSim.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:ClustSim.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:ClustSim.NN3_bisided.niml diff --git a/afni_no_motion_regressors/sub_001.results/3dDeconvolve.err b/afni_no_motion_regressors/sub_001.results/3dDeconvolve.err new file mode 100644 index 0000000..5299d4f --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/3dDeconvolve.err @@ -0,0 +1 @@ +*+ WARNING: '-stim_times_AM1 2' (LOCAL) run#1 has 1 times outside range 0 .. 206 [PSFB syndrome] diff --git a/afni_no_motion_regressors/sub_001.results/@epi_review.sub_001 b/afni_no_motion_regressors/sub_001.results/@epi_review.sub_001 new file mode 100755 index 0000000..da79b80 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/@epi_review.sub_001 @@ -0,0 +1,78 @@ +#!/bin/tcsh + +# ------------------------------------------------------ +# review EPI data via 'afni' and 'plugout_drive' + +# note that when running this script, prompts to change +# datasets will appear in the terminal window + +# ------------------------------------------------------ +# set the list of datasets +set dsets = ( pb00.sub_001.r01.tcat ) + +# ------------------------------------------------------ +# verify that the input data exists +if ( ! -f $dsets[1]+orig.HEAD ) then + echo "** missing data to review (e.g. $dsets[1])" + exit +endif + +# ------------------------------------------------------ +# start afni is listening mode, and take a brief nap + +afni -yesplugouts & + +sleep 5 + +# ------------------------------------------------------ +# tell afni to load the first dataset and open windows + +plugout_drive \ + -com "SWITCH_UNDERLAY pb00.sub_001.r01.tcat" \ + -com "OPEN_WINDOW sagittalimage \ + geom=300x300+420+400" \ + -com "OPEN_WINDOW axialimage \ + geom=300x300+720+400" \ + -com "OPEN_WINDOW sagittalgraph \ + geom=400x300+0+400" \ + -quit + +sleep 2 # give afni time to open the windows + + +# ------------------------------------------------------ +# process each dataset using video mode + +foreach dset ( $dsets ) + plugout_drive \ + -com "SWITCH_UNDERLAY $dset" \ + -com "OPEN_WINDOW sagittalgraph \ + keypress=a \ + keypress=v" \ + -quit + + sleep 2 # wait for plugout_drive output + + echo "" + echo "++ now viewing $dset, hit enter to continue" + set ret = $< # wait for user to hit enter +end + + +# ------------------------------------------------------ +# stop video mode when the user is done + +plugout_drive -com "OPEN_WINDOW sagittalgraph keypress=s" -quit + + +sleep 2 # wait for plugout_drive output + +echo "" +echo "data review complete" + + +# ---------------------------------------------------------------- +# auto-generated by gen_epi_review.py, version 0.3, Sep 23, 2008 +# +# gen_epi_review.py -script @epi_review.sub_001 -dsets \ +# pb00.sub_001.r01.tcat+orig.HEAD diff --git a/afni_no_motion_regressors/sub_001.results/@ss_review_basic b/afni_no_motion_regressors/sub_001.results/@ss_review_basic new file mode 100755 index 0000000..7ab0bd0 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/@ss_review_basic @@ -0,0 +1,330 @@ +#!/bin/tcsh + +# ---------------------------------------------------------------------- +# output some basic details about this subjects input and results: +# - subject ID, TRs removed, num stim files, motion limit, outlier limit +# - num runs, TRs per run, total TRs +# - TRs censored, fraction, num regs of interest +# - per reg: num TRs applied, num TRs censored, fraction censored +# - num stim files found, TSNR average, max F-stat, blur estimates +# +# This script should be run from a '.results' directory, produced by an +# afni_proc.py processing script. +# +# NOTE: this script is not particularly meant to be easy to read and follow, +# but is more to just be executed. Yanking numbers from datasets is +# not such a common need. +# +# NOTE: this script creates one new file: X.stim.xmat.1D +# +# - an X-matrix containing only uncensored regressors of interest +# +# This new file is used to compute fractions of "response TRs" censored, +# per stimulus class of interest, where a "response TR" means the given +# regressor was non-zero at that TR. +# + +# ------------------------------------------------------------ +# try to avoid any oblique warnings throughout script +setenv AFNI_NO_OBLIQUE_WARNING YES + +# ---------------------------------------------------------------------- +# main variables regarding this single subject analysis +set subj = sub_001 +set rm_trs = 0 +set num_stim = 2 +set mot_limit = 0.3 +set out_limit = 0.1 +set final_view = tlrc +set was_censored = 1 + +set tcat_dset = pb00.sub_001.r01.tcat+orig.HEAD +set gcor_dset = out.gcor.1D +set mask_corr_dset = out.mask_ae_dice.txt +set enorm_dset = motion_sub_001_enorm.1D +set motion_dset = dfile_rall.1D +set outlier_dset = outcount_rall.1D +set xmat_regress = X.xmat.1D +set stats_dset = stats.sub_001+tlrc.HEAD +set errts_dset = errts.sub_001+tlrc.HEAD +set censor_dset = motion_sub_001_censor.1D +set xmat_uncensored = X.nocensor.xmat.1D +set final_anat = anat_final.sub_001+tlrc.HEAD +set mask_dset = full_mask.sub_001+tlrc.HEAD +set tsnr_dset = TSNR.sub_001+tlrc.HEAD + + +# ------------------------------------------------------------ +# some overview details +echo "" +echo "subject ID : $subj" + +if ( $?rm_trs ) then + set value = $rm_trs +else + set value = UNKNOWN +endif +echo "TRs removed (per run) : $value" + +echo "num stim classes provided : $num_stim" +echo "final anatomy dset : $final_anat" +echo "final stats dset : $stats_dset" +echo "final voxel resolution : `3dinfo -ad3 $stats_dset`" +echo "" + +# ------------------------------------------------------------ +# report motion limit, average motion and number of TRs exceeding limit + +echo "motion limit : $mot_limit" + +set mcount = `1deval -a $enorm_dset -expr "step(a-$mot_limit)" \ + | awk '$1 != 0 {print}' | wc -l` +echo "num TRs above mot limit : $mcount" + +set mmean = `3dTstat -prefix - -mean $enorm_dset\' | & tail -n 1` +echo "average motion (per TR) : $mmean" + +if ( $?motion_dset ) then + if ( $was_censored ) then + # compute average censored motion + 1deval -a $enorm_dset -b $censor_dset -expr 'a*b' > rm.ec.1D + set mmean = `3dTstat -prefix - -nzmean rm.ec.1D\' | & tail -n 1` + echo "average censored motion : $mmean" + \rm -f rm.ec.1D + endif + + # compute the maximum motion displacement over all TR pairs + set disp = `1d_tool.py -infile $motion_dset -show_max_displace -verb 0` + echo "max motion displacement : $disp" + + if ( $was_censored ) then + # compute the maximum motion displacement over all TR pairs + set disp = `1d_tool.py -infile $motion_dset -show_max_displace \ + -censor_infile $censor_dset -verb 0` + echo "max censored displacement : $disp" + endif +endif + +# ------------------------------------------------------------ +# report outlier limit, average and number of TRs exceeding limit + +echo "outlier limit : $out_limit" + +set mmean = `3dTstat -prefix - -mean $outlier_dset\' | & tail -n 1` +echo "average outlier frac (TR) : $mmean" + +set mcount = `1deval -a $outlier_dset -expr "step(a-$out_limit)" \ + | awk '$1 != 0 {print}' | wc -l` +echo "num TRs above out limit : $mcount" + + +echo "" + +# ------------------------------------------------------------ +# note number of runs, TRs per run, and possibly censored TRs per run +set nruns = ( `1d_tool.py -infile X.xmat.1D -show_num_runs` ) +set trs = ( `1d_tool.py -infile X.xmat.1D -show_tr_run_counts trs_no_cen` ) +echo "num runs found : $nruns" +echo "num TRs per run : $trs" + +if ( $was_censored ) then + set tra = ( `1d_tool.py -infile $xmat_regress -show_tr_run_counts trs`) + set trc = ( `1d_tool.py -infile $xmat_regress -show_tr_run_counts trs_cen`) + set trf = ( `1d_tool.py -infile $xmat_regress -show_tr_run_counts frac_cen`) + echo "num TRs per run (applied) : $tra" + echo "num TRs per run (censored): $trc" + echo "fraction censored per run : $trf" +endif + +# ------------------------------------------------------------ +# count total TRs (uncensored and censored) from X-matrix + +# note X-matrix dimensions +set rows_cols = ( `1d_tool.py -infile $xmat_regress -show_rows_cols -verb 0` ) +set num_trs = $rows_cols[1] +set total_trs = $num_trs # total might change if censoring + +if ( $?xmat_uncensored ) then + set xmat = $xmat_uncensored + set urc = ( `1d_tool.py -infile $xmat -show_rows_cols -verb 0` ) + set total_trs = $urc[1] + echo "TRs total (uncensored) : $total_trs" +endif + +echo "TRs total : $num_trs" + +@ dof_rem = $rows_cols[1] - $rows_cols[2] +echo "degrees of freedom used : $rows_cols[2]" +echo "degrees of freedom left : $dof_rem" +echo "" +# ------------------------------------------------------------ +# make non-basline X-matrix, if one is not already here +if ( $?xmat_uncensored ) then + set xmat = $xmat_uncensored +else + set xmat = $xmat_regress +endif + +set xstim = X.stim.xmat.1D +if ( ! -f $xstim ) then + set reg_cols = `1d_tool.py -infile $xmat -show_indices_interest` + 1d_tool.py -infile $xmat"[$reg_cols]" -overwrite -write $xstim +endif + +# ---------------------------------------------------------------------- +# report TR counts per stim, and possibly censor counts + +# note number of regressors of interest +set rc = ( `1d_tool.py -infile $xstim -show_rows_cols -verb 0` ) +set nint = $rc[2] +@ nm1 = $nint - 1 + +# if censoring, print main censor fraction +if ( $was_censored ) then + set ntr_censor = `cat $censor_dset | grep 0 | wc -l` + echo "TRs censored : $ntr_censor" + echo "censor fraction : `ccalc $ntr_censor/$total_trs`" +endif + +# print num regressors of interest +if ( $num_stim > 0 ) then + echo "num regs of interest : $nint" +else + echo "num regs of interest : $num_stim" +endif + + +# report per-stim censoring +if ( $was_censored && $num_stim > 0 ) then + # compute fractions of stimulus TRs censored in each + set stim_trs = () + set stim_trs_censor = () + set stim_frac_censor = () + foreach index ( `count -digits 1 0 $nm1` ) + # count response TRs, with and without censoring + # (their difference is the number of TRs lost to censoring) + set st = `1deval -a $xstim"[$index]" -expr 'bool(a)' | grep 1 | wc -l` + set sc = `1deval -a $xstim"[$index]" -b $censor_dset -expr 'bool(a*b)'\ + | grep 1 | wc -l` + set sc = `ccalc -i "$st-$sc"` # change to num censored + set ff = `ccalc -form '%.3f' "$sc/$st"` # and the fraction censored + + # keep lists of reponse TRs, # censored and fractions censored + # (across all stimulus regressors) + set stim_trs = ( $stim_trs $st ) + set stim_trs_censor = ( $stim_trs_censor $sc ) + set stim_frac_censor = ( $stim_frac_censor $ff ) + end + + echo "num TRs per stim (orig) : $stim_trs" + echo "num TRs censored per stim : $stim_trs_censor" + echo "fraction TRs censored : $stim_frac_censor" +else if ( $num_stim > 0 ) then + # no censoring - just compute num TRs per regressor + set stim_trs = () + foreach index ( `count -digits 1 0 $nm1` ) + set st = `1deval -a $xstim"[$index]" -expr 'bool(a)' | grep 1 | wc -l` + set stim_trs = ( $stim_trs $st ) + end + echo "num TRs per stim : $stim_trs" +endif + + +# ---------------------------------------------------------------------- +# compute average motion per stim response + +if ( $was_censored && $num_stim > 0 ) then + set sresp_mot = () + set sresp_mot_cen = () + foreach index ( `count -digits 1 0 $nm1` ) + set st = `1deval -a $xstim"[$index]" -expr 'bool(a)' | grep 1 | wc -l` + set snc = `1deval -a $xstim"[$index]" -b $censor_dset \ + -expr 'bool(a*b)' | grep 1 | wc -l` + set sm = `1deval -a $xstim"[$index]" -b $enorm_dset -expr 'bool(a)*b'\ + | 3dTstat -sum -prefix - 1D:stdin\' |& tail -n 1` + set smc = `1deval -a $xstim"[$index]" -b $enorm_dset -c $censor_dset \ + -expr 'bool(a)*b*c' | 3dTstat -sum -prefix - 1D:stdin\' \ + |& tail -n 1` + set sm = `ccalc $sm/$st` + set smc = `ccalc $smc/$snc` + + set sresp_mot = ( $sresp_mot $sm ) + set sresp_mot_cen = ( $sresp_mot_cen $smc ) + end + + echo "ave mot per sresp (orig) : $sresp_mot" + echo "ave mot per sresp (cens) : $sresp_mot_cen" + +else if ( $num_stim > 0 ) then + set sresp_mot = () + foreach index ( `count -digits 1 0 $nm1` ) + set st = `1deval -a $xstim"[$index]" -expr 'bool(a)' | grep 1 | wc -l` + set sm = `1deval -a $xstim"[$index]" -b $enorm_dset -expr 'bool(a)*b'\ + | 3dTstat -sum -prefix - 1D:stdin\' |& tail -n 1` + set sm = `ccalc $sm/$st` + set sresp_mot = ( $sresp_mot $sm ) + end + echo "ave mot per sresp : $sresp_mot" +endif + +echo "" + + +# ------------------------------------------------------------ +# get TSNR average +if ( -f $tsnr_dset && -f $mask_dset ) then + eval 'set tsnr_ave = `3dmaskave -quiet -mask $mask_dset $tsnr_dset`' >& /dev/null + echo "TSNR average : $tsnr_ave" +endif + +# ------------------------------------------------------------ +# get global correlation +if ( -f $gcor_dset ) then + set gcor_val = `cat $gcor_dset` + echo "global correlation (GCOR) : $gcor_val" +endif + +# ------------------------------------------------------------ +# get anat/EPI mask Dice coefficient +if ( -f $mask_corr_dset ) then + set val = `cat $mask_corr_dset` + echo "anat/EPI mask Dice coef : $val" +endif + +# ------------------------------------------------------------ +# note maximum masked F-stat +if ( -f "$stats_dset" && -f $mask_dset ) then + set fmax = `3dBrickStat -slow -max -mask $mask_dset $stats_dset"[Full_Fstat]"` + echo "maximum F-stat (masked) : $fmax" +endif + +# ------------------------------------------------------------' +# note blur estimates +set blur_file = blur_est.$subj.1D +if ( -f $blur_file ) then + set best = `awk '/errts/ {print $1, $2, $3}' $blur_file` + if ( $#best != 3 ) then + set best = `awk '/epits/ {print $1, $2, $3}' $blur_file` + endif + if ( $#best == 3 ) then + echo "blur estimates : $best" + endif +endif + +echo "" + +# ------------------------------------------------------------' +# if there happen to be pre-steady state warnings, show them +set pre_ss_warn = 'out.pre_ss_warn.txt' +if ( -f $pre_ss_warn ) then + cat $pre_ss_warn + echo "" +endif + + + +# ========================================================================== +# script generated by the command: +# +# gen_ss_review_scripts.py -mot_limit 0.3 -exit0 + diff --git a/afni_no_motion_regressors/sub_001.results/@ss_review_driver b/afni_no_motion_regressors/sub_001.results/@ss_review_driver new file mode 100755 index 0000000..d9eec0a --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/@ss_review_driver @@ -0,0 +1,199 @@ +#!/bin/tcsh + +# This script is meant to help review single subject results. +# +# It should be run from a '.results' directory, produced by an +# afni_proc.py processing script. +# +# It will not use variables, so that commands are very clear to users +# who read the script. Hopefully the only "ugly" things will be the +# prompt_user commands, which need to pass text to the prompt program. +# +# Some AFNI commands have extra options supplied to make them more +# clear when executing. Users need not bother with such worries when +# running similar commands on their own. +# +# at each step: +# - a "review" command is executed +# - a prompt explains to the user what to do or look at +# - when ready to proceed, the user clicks OK in the prompt window + +# ------------------------------------------------------------ +# try to avoid any oblique warnings throughout script +setenv AFNI_NO_OBLIQUE_WARNING YES + +# ------------------------------------------------------------ +# if the expected "basic" script is here, run it + +if ( -f @ss_review_basic ) then + echo ------------------- @ss_review_basic -------------------- + tcsh -f @ss_review_basic + echo --------------------------------------------------------- + + prompt_user -pause " \ + review output from @ss_review_basic \ + (in terminal window) for anything that \ + looks unreasonable \ + \ + --- click OK when finished --- \ + " + echo "" +else + echo "" + echo "*** missing @ss_review_basic script ***" + echo "" +endif + +# ------------------------------------------------------------ +# possibly consider running the @epi_review script here + + +echo ------------------- outliers and motion -------------------- + +1dplot -wintitle "motion, outliers" -ynames Mot OFrac \ + -censor_RGB green -censor motion_sub_001_censor.1D \ + -sepscl motion_sub_001_enorm.1D outcount_rall.1D & +1dplot -one -censor_RGB green -censor motion_sub_001_censor.1D \ + outcount_rall.1D "1D: 104@0.1" & +1dplot -one -censor_RGB green -censor motion_sub_001_censor.1D \ + motion_sub_001_enorm.1D "1D: 104@0.3" & + +prompt_user -pause " \ + review plots (colored TRs are censored): \ + - outliers and motion (plotted together) \ + - outliers with limit 0.1 \ + - motion with limit 0.3 \ + \ + --- close plots and click OK when finished --- \ + " +echo "" + + +echo ----------------- anat/EPI alignment check ----------------- + +# start afni with anat and volreg datasets only +afni anat_final.sub_001+tlrc.HEAD pb02.sub_001.r01.volreg+tlrc.HEAD & + + +prompt_user -pause " \ + review: check alignment between anat and EPI \ + - set underlay to anat \ + - set overlay to EPI \ + - look at gross alignment, maybe with thresholding \ + - turn off 'See Overlay' \ + - use 'u' key in image windows to toggle underlay \ + dataset between anat and EPI \ + - CSF should be dark in anat and bright in EPI \ + - follow ventricles and gyral patterns \ + \ + --- close afni and click OK when finished --- \ + " + + +echo -------------------- regession warnings -------------------- + +# if 3dDeconvolve made an error/warnings file, show it +if ( -f 3dDeconvolve.err ) then + echo ------------- 3dDeconvolve.err ------------- + cat 3dDeconvolve.err + echo -------------------------------------------- +else + echo --- no 3dDeconvolve.err warnings file --- +endif + +echo "" + +# show any timing_tool.py warnings about TENTs +if ( -f out.TENT_warn.txt ) then + echo ------------ out.TENT_warn.txt ------------- + cat out.TENT_warn.txt + echo -------------------------------------------- +else + echo --- no out.TENT_warn.txt warnings file --- +endif + +echo "" + +# show any pairwise correlation warnings from X-matrix +echo ----------- correlation warnings ----------- +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +echo -------------------------------------------- + +# if there are any pre-steady state warnings, show them +if ( -f out.pre_ss_warn.txt && ! -z out.pre_ss_warn.txt ) then + echo --------- pre-steady state warnings -------- + cat out.pre_ss_warn.txt + echo -------------------------------------------- +endif + + +prompt_user -pause " \ + review: check for regression warnings \ + - review any warnings from 3dDeconvolve \ + - review any TENT warnings from timing_tool.py \ + - review any X-matrix warnings from 1d_tool.py \ + \ + --- click OK when finished --- \ + " + + +echo ------------------------- X-matrix ------------------------- + +# plot X-matrix, but without baseline and motion +if ( -f X.stim.xmat.1D ) then + 1dplot -sepscl X.stim.xmat.1D & +else + echo --- no file X.stim.xmat.1D --- +endif + +# also plot the sum of those same regressors +if ( -f sum_ideal.1D ) then + 1dplot sum_ideal.1D & +else + echo --- no file sum_ideal.1D --- +endif + + +prompt_user -pause " \ + review: non-baseline regressors in X-matrix \ + - X.stim.xmat.1D shows non-baseline regressors \ + - sum_ideal.1D shows their sum \ + \ + --- close plots and click OK when finished --- \ + " + + +echo -------------------- view stats results -------------------- + +# get 90 percentile for thresholding in afni GUI +set pp = ( `3dBrickStat -slow -percentile 90 1 90 \ + -mask full_mask.sub_001+tlrc stats.sub_001+tlrc"[0]"` ) +set thresh = $pp[2] +echo -- thresholding F-stat at $thresh + +# locate peak coords of biggest masked cluster and jump there +3dcalc -a stats.sub_001+tlrc"[0]" -b full_mask.sub_001+tlrc -expr "a*b" \ + -overwrite -prefix .tmp.F +set maxcoords = ( `3dclust -1thresh $thresh -dxyz=1 1 2 .tmp.F+tlrc \ + | & awk '/^ / {print $14, $15, $16}' | head -n 1` ) +echo -- jumping to max coords: $maxcoords + +# start afni with stats thresholding at peak location +afni -com "OPEN_WINDOW A.axialimage" \ + -com "OPEN_WINDOW A.sagittalimage" \ + -com "SWITCH_UNDERLAY anat_final.sub_001" \ + -com "SWITCH_OVERLAY stats.sub_001" \ + -com "SET_SUBBRICKS A 0 0 0" \ + -com "SET_THRESHNEW A $thresh" \ + -com "SET_DICOM_XYZ A $maxcoords" + + +prompt_user -pause " \ + review: peruse statistical retsults \ + - thresholding Full-F at masked 90 percentile \ + (thresh = $thresh) \ + \ + --- close afni and click OK when finished --- \ + " + + diff --git a/afni_no_motion_regressors/sub_001.results/@ss_review_driver_commands b/afni_no_motion_regressors/sub_001.results/@ss_review_driver_commands new file mode 100755 index 0000000..1a0b5c4 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/@ss_review_driver_commands @@ -0,0 +1,28 @@ +tcsh -f @ss_review_basic +1dplot -wintitle "motion, outliers" -ynames Mot OFrac \ + -sepscl -censor_RGB green -censor motion_sub_001_censor.1D motion_sub_001_enorm.1D outcount_rall.1D & +1dplot -one -censor_RGB green -censor motion_sub_001_censor.1D outcount_rall.1D "1D: 104@0.1" & +1dplot -one -censor_RGB green -censor motion_sub_001_censor.1D motion_sub_001_enorm.1D "1D: 104@0.3" & +afni anat_final.sub_001+tlrc.HEAD pb02.sub_001.r01.volreg+tlrc.HEAD & +cat 3dDeconvolve.err +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +1dplot -sepscl X.stim.xmat.1D & +1dplot sum_ideal.1D & +set pp = ( `3dBrickStat -slow -percentile 90 1 90 \ + -mask full_mask.sub_001+tlrc stats.sub_001+tlrc"[0]"` ) +set thresh = $pp[2] +echo -- thresholding F-stat at $thresh +# locate peak coords of biggest masked cluster and jump there +3dcalc -a stats.sub_001+tlrc"[0]" -b full_mask.sub_001+tlrc -expr "a*b" \ + -overwrite -prefix .tmp.F +set maxcoords = ( `3dclust -1thresh $thresh -dxyz=1 1 2 .tmp.F+tlrc \ + | & awk '/^ / {print $14, $15, $16}' | head -n 1` ) +echo -- jumping to max coords: $maxcoords +afni -com "OPEN_WINDOW A.axialimage" \ + -com "OPEN_WINDOW A.sagittalimage" \ + -com "SWITCH_UNDERLAY anat_final.sub_001" \ + -com "SWITCH_OVERLAY stats.sub_001" \ + -com "SET_SUBBRICKS A 0 0 0" \ + -com "SET_THRESHNEW A $thresh" \ + -com "SET_DICOM_XYZ A $maxcoords" + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_1sided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_1sided.1D new file mode 100644 index 0000000..df7ea4d --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_1sided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# 1-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 1 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 647.7 663.9 683.0 705.6 722.0 752.0 793.0 845.0 913.0 1031.5 + 0.090000 477.2 488.6 500.9 515.3 531.9 550.3 579.0 611.4 652.7 747.0 + 0.080000 358.9 367.1 377.4 386.0 400.4 413.6 427.9 452.1 479.0 543.5 + 0.070000 269.6 275.6 281.9 288.5 297.9 309.7 323.4 337.6 358.7 397.3 + 0.060000 206.2 210.5 215.2 220.7 227.4 234.4 243.9 254.9 270.4 296.0 + 0.050000 155.6 158.2 161.3 165.0 169.3 173.8 179.9 189.1 200.9 220.7 + 0.040000 117.1 118.9 121.8 124.9 128.3 132.3 137.0 142.9 151.2 164.8 + 0.030000 85.5 87.2 88.8 90.9 93.4 95.9 99.3 103.1 108.6 118.4 + 0.020000 59.7 61.0 62.1 63.4 65.0 66.5 68.4 71.1 75.2 82.5 + 0.015000 47.8 48.6 49.5 50.5 51.6 53.1 54.8 57.1 59.8 64.8 + 0.010000 36.7 37.4 38.2 39.1 40.0 40.9 42.3 43.9 46.2 50.6 + 0.007000 29.5 30.0 30.7 31.4 32.3 33.4 34.6 36.1 38.0 41.4 + 0.005000 24.6 25.0 25.5 26.0 26.8 27.7 28.6 30.0 31.8 34.7 + 0.003000 19.0 19.4 19.8 20.3 20.8 21.5 22.3 23.3 24.7 26.9 + 0.002000 15.8 16.2 16.5 16.9 17.4 18.0 18.7 19.5 20.7 22.8 + 0.001500 14.0 14.3 14.6 14.9 15.4 15.9 16.5 17.3 18.5 20.4 + 0.001000 11.7 12.0 12.3 12.6 13.1 13.5 14.0 14.7 15.6 17.3 + 0.000700 10.2 10.5 10.7 11.0 11.3 11.7 12.2 12.8 13.7 15.2 + 0.000500 9.0 9.2 9.4 9.7 10.0 10.3 10.7 11.2 12.0 13.4 + 0.000300 7.5 7.7 7.9 8.1 8.3 8.6 9.0 9.5 10.1 11.3 + 0.000200 6.4 6.5 6.7 6.9 7.2 7.5 7.8 8.3 8.9 10.0 + 0.000150 5.8 5.9 6.1 6.3 6.5 6.8 7.1 7.5 8.2 9.2 + 0.000100 4.9 5.0 5.2 5.4 5.6 5.9 6.2 6.6 7.1 8.2 + 7.000e-5 4.3 4.4 4.6 4.7 4.9 5.2 5.5 5.9 6.4 7.3 + 5.000e-5 3.8 3.9 4.0 4.2 4.4 4.6 4.9 5.3 5.8 6.7 + 3.000e-5 3.1 3.2 3.3 3.5 3.6 3.8 4.0 4.4 4.8 5.6 + 2.000e-5 2.7 2.7 2.8 3.0 3.1 3.3 3.5 3.8 4.2 4.9 + 1.500e-5 2.4 2.5 2.6 2.7 2.8 3.0 3.2 3.4 3.8 4.5 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.6 2.8 3.0 3.4 4.0 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_1sided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_1sided.niml new file mode 100644 index 0000000..4ca4d3f --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_1sided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN1 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="1-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 647.7136 663.8995 683 705.554 722 752 793 845 913 1031.498 + 477.153 488.5705 500.8566 515.3324 531.8882 550.3327 579 611.4258 652.7482 747 + 358.9281 367.1245 377.4276 386 400.4272 413.5534 427.9156 452.1414 479 543.495 + 269.6295 275.5765 281.9085 288.4704 297.8993 309.7493 323.4417 337.598 358.7481 397.33 + 206.2065 210.5187 215.2335 220.7313 227.4258 234.3847 243.8561 254.9152 270.397 296 + 155.5817 158.2396 161.301 165.0428 169.2692 173.8175 179.8646 189.1096 200.855 220.6634 + 117.0532 118.8536 121.8309 124.9273 128.3156 132.2907 137 142.9152 151.2463 164.7921 + 85.5096 87.19159 88.84547 90.86127 93.36396 95.93936 99.25655 103.061 108.6349 118.3656 + 59.74778 60.97399 62.07258 63.41112 65.01368 66.48441 68.42413 71.08029 75.17361 82.54452 + 47.82853 48.62426 49.54956 50.51016 51.58645 53.08168 54.84631 57.11361 59.79022 64.79373 + 36.65577 37.3638 38.15169 39.08863 39.9622 40.87879 42.25825 43.93887 46.16824 50.64694 + 29.48989 29.99469 30.65436 31.4245 32.33146 33.36789 34.60448 36.11941 38.02314 41.37592 + 24.56395 24.95455 25.45064 26.02081 26.76887 27.65023 28.62955 29.98351 31.79847 34.71542 + 18.99242 19.37201 19.7936 20.26843 20.81318 21.48643 22.30665 23.31787 24.71319 26.851 + 15.83501 16.15011 16.48223 16.85668 17.35184 17.97272 18.66056 19.5041 20.71055 22.79293 + 13.98023 14.26346 14.57732 14.93118 15.37034 15.89485 16.51353 17.33988 18.48286 20.36728 + 11.74581 11.9802 12.29182 12.64789 13.05263 13.49888 14.03887 14.68148 15.59323 17.34548 + 10.23548 10.45478 10.69857 10.97344 11.30066 11.68685 12.15647 12.75739 13.66633 15.17092 + 9.005863 9.211467 9.440032 9.697732 9.993608 10.31523 10.70617 11.22579 11.99057 13.43971 + 7.500318 7.679178 7.878013 8.098725 8.347383 8.639902 8.996016 9.469398 10.13998 11.31479 + 6.388686 6.548267 6.72567 6.925687 7.172405 7.472252 7.837285 8.28768 8.90591 9.98436 + 5.757897 5.922163 6.097424 6.288868 6.508673 6.767251 7.091787 7.543435 8.168202 9.215364 + 4.891736 5.028778 5.199375 5.391717 5.612554 5.872344 6.177659 6.5597 7.109673 8.165321 + 4.287034 4.414818 4.556872 4.717035 4.900923 5.153855 5.49943 5.942611 6.419875 7.251079 + 3.780895 3.898936 4.034323 4.20269 4.395999 4.623407 4.900254 5.274338 5.809263 6.699744 + 3.069737 3.184157 3.311356 3.454768 3.619426 3.813128 4.049507 4.355421 4.784332 5.619211 + 2.650727 2.740258 2.839787 2.952004 3.099054 3.284761 3.510841 3.800777 4.199867 4.866426 + 2.386472 2.473741 2.570755 2.680136 2.805721 2.953458 3.156844 3.428211 3.808687 4.481433 + 2.017411 2.105374 2.20316 2.313411 2.439994 2.588907 2.770193 3.003122 3.38242 4.026022 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_2sided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_2sided.1D new file mode 100644 index 0000000..b3020ed --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_2sided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# 2-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 1 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 174.9 178.0 181.5 185.9 190.5 196.3 203.4 211.0 224.1 249.0 + 0.090000 152.4 154.9 157.9 161.0 165.5 170.4 176.7 183.6 193.9 214.0 + 0.080000 131.9 134.2 136.8 139.4 143.0 146.9 151.1 157.2 167.1 181.0 + 0.070000 112.9 115.2 117.4 119.7 122.8 126.1 129.8 134.4 140.6 154.0 + 0.060000 95.7 97.4 99.4 101.4 103.6 106.1 109.6 113.7 119.3 130.2 + 0.050000 79.8 81.2 82.8 84.5 86.6 89.0 92.2 95.5 102.1 109.3 + 0.040000 66.2 67.2 68.3 69.7 71.3 73.2 75.4 78.5 83.5 91.1 + 0.030000 52.8 53.7 54.8 55.8 57.2 58.4 60.2 62.5 65.9 73.1 + 0.020000 40.6 41.3 42.0 42.7 43.7 44.9 46.1 48.2 50.9 55.4 + 0.015000 34.4 35.0 35.5 36.2 37.0 37.8 39.1 40.6 42.9 47.5 + 0.010000 27.6 28.0 28.5 29.1 29.8 30.6 31.5 32.7 34.5 37.7 + 0.007000 23.0 23.4 23.9 24.4 25.0 25.7 26.6 27.6 29.1 31.5 + 0.005000 19.6 19.9 20.3 20.8 21.3 21.8 22.6 23.6 25.0 26.9 + 0.003000 15.6 15.9 16.2 16.6 17.1 17.6 18.3 19.0 20.1 21.9 + 0.002000 13.3 13.6 13.8 14.2 14.5 15.0 15.5 16.1 17.2 18.8 + 0.001500 11.9 12.1 12.4 12.6 12.9 13.4 14.0 14.6 15.5 17.2 + 0.001000 10.2 10.4 10.6 10.9 11.2 11.5 12.0 12.5 13.4 14.8 + 0.000700 9.0 9.2 9.4 9.6 9.9 10.2 10.6 11.1 11.8 13.0 + 0.000500 8.1 8.2 8.4 8.6 8.9 9.1 9.5 9.9 10.6 11.9 + 0.000300 6.7 6.9 7.0 7.3 7.5 7.8 8.1 8.5 9.2 10.3 + 0.000200 5.8 6.0 6.1 6.3 6.5 6.8 7.1 7.5 8.2 9.2 + 0.000150 5.2 5.4 5.6 5.7 5.9 6.2 6.5 6.9 7.5 8.4 + 0.000100 4.6 4.7 4.8 5.0 5.2 5.5 5.8 6.2 6.7 7.5 + 7.000e-5 4.0 4.1 4.3 4.4 4.6 4.8 5.1 5.5 6.0 6.8 + 5.000e-5 3.5 3.7 3.8 3.9 4.1 4.3 4.5 4.8 5.3 6.2 + 3.000e-5 2.9 3.0 3.1 3.3 3.4 3.6 3.9 4.1 4.5 5.2 + 2.000e-5 2.6 2.7 2.8 2.9 3.0 3.2 3.4 3.6 4.0 4.6 + 1.500e-5 2.3 2.4 2.5 2.6 2.7 2.8 3.0 3.3 3.6 4.2 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.5 2.7 2.9 3.2 3.8 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_2sided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_2sided.niml new file mode 100644 index 0000000..d787ddd --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_2sided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN1 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="2-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 174.865 177.9709 181.497 185.9187 190.526 196.2706 203.3971 211 224.1089 249 + 152.4413 154.9077 157.883 161 165.5369 170.4337 176.7323 183.5815 193.8978 214 + 131.8572 134.2271 136.7709 139.4239 142.9608 146.9213 151.1155 157.2475 167.0532 181 + 112.9086 115.1812 117.4417 119.7273 122.8026 126.0696 129.7573 134.3728 140.5761 154 + 95.6547 97.41637 99.38149 101.3505 103.6042 106.1448 109.5776 113.7073 119.2688 130.196 + 79.7816 81.17747 82.76731 84.53232 86.55299 89.03477 92.16354 95.48769 102.0643 109.3233 + 66.22449 67.18579 68.32789 69.70852 71.25952 73.16367 75.42413 78.51522 83.53909 91.07869 + 52.81401 53.74971 54.84575 55.84431 57.16221 58.42925 60.21259 62.47097 65.90859 73.12453 + 40.64025 41.25859 41.99223 42.73326 43.72218 44.92154 46.09672 48.20567 50.89002 55.39115 + 34.39783 34.95309 35.53691 36.19828 36.97482 37.84539 39.08927 40.56997 42.9383 47.51477 + 27.55301 28.03659 28.52211 29.07669 29.77007 30.58792 31.53598 32.70604 34.53733 37.65676 + 22.97254 23.39209 23.8592 24.37467 24.96183 25.66894 26.56696 27.61835 29.06312 31.45004 + 19.60088 19.939 20.3269 20.76688 21.26688 21.8499 22.62631 23.56089 25.01632 26.88443 + 15.62848 15.91214 16.24117 16.61811 17.0552 17.60752 18.25614 19.04384 20.14432 21.89395 + 13.3191 13.5673 13.84321 14.16005 14.53054 14.96639 15.47452 16.14937 17.22799 18.84166 + 11.92174 12.13971 12.3746 12.63942 12.94348 13.40088 13.9805 14.56225 15.47737 17.15958 + 10.22269 10.41769 10.63446 10.87886 11.17274 11.53033 11.96565 12.53938 13.39423 14.80168 + 9.013864 9.196611 9.399768 9.62882 9.891806 10.21351 10.61324 11.12446 11.83516 12.96743 + 8.051785 8.219197 8.405305 8.615137 8.856052 9.139428 9.484363 9.926723 10.59715 11.87953 + 6.72496 6.876881 7.04851 7.250329 7.482046 7.754638 8.089896 8.532241 9.168425 10.31614 + 5.819256 5.968312 6.133761 6.320231 6.534326 6.786185 7.104317 7.546337 8.183356 9.240799 + 5.243299 5.390182 5.553468 5.737569 5.948942 6.196503 6.497537 6.883598 7.482663 8.415504 + 4.565311 4.692964 4.834871 4.994868 5.212152 5.4689 5.781466 6.169015 6.690038 7.52108 + 3.993496 4.11838 4.257976 4.415366 4.596072 4.808653 5.078006 5.461839 6 6.821677 + 3.539346 3.653676 3.780773 3.924072 4.087296 4.277999 4.510161 4.807897 5.304372 6.201903 + 2.921767 3.009389 3.133976 3.274444 3.43572 3.625446 3.856417 4.138017 4.51357 5.164245 + 2.568017 2.654824 2.751326 2.860128 2.985049 3.153837 3.362331 3.629713 4.004376 4.610805 + 2.314862 2.396445 2.487138 2.589392 2.706794 2.844905 3.015744 3.276054 3.641026 4.237588 + 2.007983 2.084628 2.169832 2.265896 2.376192 2.505943 2.663903 2.866477 3.180589 3.760157 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_bisided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_bisided.1D new file mode 100644 index 0000000..62404f0 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_bisided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# bi-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 1 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 174.5 177.7 181.1 185.6 190.0 195.6 202.8 210.8 224.0 249.0 + 0.090000 152.3 154.7 157.7 160.9 165.3 170.1 176.6 183.4 193.8 214.0 + 0.080000 131.8 134.2 136.7 139.4 142.9 146.9 151.1 157.2 167.1 181.0 + 0.070000 112.9 115.2 117.4 119.7 122.8 126.0 129.7 134.4 140.6 154.0 + 0.060000 95.7 97.4 99.4 101.4 103.6 106.1 109.6 113.7 119.2 130.2 + 0.050000 79.8 81.2 82.8 84.5 86.6 89.0 92.2 95.5 102.1 109.3 + 0.040000 66.2 67.2 68.3 69.7 71.3 73.2 75.4 78.5 83.5 91.1 + 0.030000 52.8 53.7 54.8 55.8 57.2 58.4 60.2 62.5 65.9 73.1 + 0.020000 40.6 41.3 42.0 42.7 43.7 44.9 46.1 48.2 50.9 55.4 + 0.015000 34.4 35.0 35.5 36.2 37.0 37.8 39.1 40.6 42.9 47.5 + 0.010000 27.6 28.0 28.5 29.1 29.8 30.6 31.5 32.7 34.5 37.7 + 0.007000 23.0 23.4 23.9 24.4 25.0 25.7 26.6 27.6 29.1 31.5 + 0.005000 19.6 19.9 20.3 20.8 21.3 21.8 22.6 23.6 25.0 26.9 + 0.003000 15.6 15.9 16.2 16.6 17.1 17.6 18.3 19.0 20.1 21.9 + 0.002000 13.3 13.6 13.8 14.2 14.5 15.0 15.5 16.1 17.2 18.8 + 0.001500 11.9 12.1 12.4 12.6 12.9 13.4 14.0 14.6 15.5 17.2 + 0.001000 10.2 10.4 10.6 10.9 11.2 11.5 12.0 12.5 13.4 14.8 + 0.000700 9.0 9.2 9.4 9.6 9.9 10.2 10.6 11.1 11.8 13.0 + 0.000500 8.1 8.2 8.4 8.6 8.9 9.1 9.5 9.9 10.6 11.9 + 0.000300 6.7 6.9 7.0 7.3 7.5 7.8 8.1 8.5 9.2 10.3 + 0.000200 5.8 6.0 6.1 6.3 6.5 6.8 7.1 7.5 8.2 9.2 + 0.000150 5.2 5.4 5.6 5.7 5.9 6.2 6.5 6.9 7.5 8.4 + 0.000100 4.6 4.7 4.8 5.0 5.2 5.5 5.8 6.2 6.7 7.5 + 7.000e-5 4.0 4.1 4.3 4.4 4.6 4.8 5.1 5.5 6.0 6.8 + 5.000e-5 3.5 3.7 3.8 3.9 4.1 4.3 4.5 4.8 5.3 6.2 + 3.000e-5 2.9 3.0 3.1 3.3 3.4 3.6 3.9 4.1 4.5 5.2 + 2.000e-5 2.6 2.7 2.8 2.9 3.0 3.2 3.4 3.6 4.0 4.6 + 1.500e-5 2.3 2.4 2.5 2.6 2.7 2.8 3.0 3.3 3.6 4.2 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.5 2.7 2.9 3.2 3.8 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_bisided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_bisided.niml new file mode 100644 index 0000000..b9d30a7 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN1_bisided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN1 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="bi-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 174.4965 177.6817 181.0989 185.5959 190 195.6124 202.8441 210.7843 224 249 + 152.2845 154.7238 157.6768 160.8686 165.329 170.1316 176.5733 183.405 193.7961 214 + 131.8165 134.2018 136.7269 139.3527 142.9216 146.9213 151.1155 157.2475 167.0532 181 + 112.9086 115.1812 117.4417 119.7273 122.8026 126.0348 129.7091 134.3728 140.5761 154 + 95.6547 97.41637 99.38149 101.3505 103.6042 106.1448 109.5776 113.7073 119.2145 130.196 + 79.76957 81.15963 82.76411 84.53232 86.55299 89.03477 92.16354 95.48769 102.0643 109.3233 + 66.22449 67.18579 68.32789 69.70852 71.25952 73.16367 75.42413 78.51522 83.53909 91.07869 + 52.81401 53.74971 54.84575 55.84431 57.16221 58.42925 60.21259 62.47097 65.90859 73.12453 + 40.64025 41.25859 41.99223 42.73326 43.72218 44.92154 46.09672 48.20567 50.89002 55.39115 + 34.39783 34.95309 35.53691 36.19828 36.97482 37.84539 39.08927 40.56997 42.9383 47.51477 + 27.55301 28.03659 28.52211 29.07669 29.77007 30.58792 31.53598 32.70604 34.53733 37.65676 + 22.97254 23.39209 23.8592 24.37467 24.96183 25.66894 26.56696 27.61835 29.06312 31.45004 + 19.60088 19.939 20.3269 20.76688 21.26688 21.8499 22.62631 23.56089 25.01632 26.88443 + 15.62848 15.91214 16.24117 16.61811 17.0552 17.60752 18.25614 19.04384 20.14432 21.89395 + 13.3191 13.5673 13.84321 14.16005 14.53054 14.96639 15.47452 16.14937 17.22799 18.84166 + 11.92174 12.13971 12.3746 12.63942 12.94348 13.40088 13.9805 14.56225 15.47737 17.15958 + 10.22269 10.41769 10.63446 10.87886 11.17274 11.53033 11.96565 12.53938 13.39423 14.80168 + 9.013864 9.196611 9.399768 9.62882 9.891806 10.21351 10.61324 11.12446 11.83516 12.96743 + 8.051785 8.219197 8.405305 8.615137 8.856052 9.139428 9.484363 9.926723 10.59715 11.87953 + 6.72496 6.876881 7.04851 7.250329 7.482046 7.754638 8.089896 8.532241 9.168425 10.31614 + 5.819256 5.968312 6.133761 6.320231 6.534326 6.786185 7.104317 7.546337 8.183356 9.240799 + 5.243299 5.390182 5.553468 5.737569 5.948942 6.196503 6.497537 6.883598 7.482663 8.415504 + 4.565311 4.692964 4.834871 4.994868 5.212152 5.4689 5.781466 6.169015 6.690038 7.52108 + 3.993496 4.11838 4.257976 4.415366 4.596072 4.808653 5.078006 5.461839 6 6.821677 + 3.539346 3.653676 3.780773 3.924072 4.087296 4.277999 4.510161 4.807897 5.304372 6.201903 + 2.921767 3.009389 3.133976 3.274444 3.43572 3.625446 3.856417 4.138017 4.51357 5.164245 + 2.568017 2.654824 2.751326 2.860128 2.985049 3.153837 3.362331 3.629713 4.004376 4.610805 + 2.314862 2.396445 2.487138 2.589392 2.706794 2.844905 3.015744 3.276054 3.641026 4.237588 + 2.007983 2.084628 2.169832 2.265896 2.376192 2.505943 2.663903 2.866477 3.180589 3.760157 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_1sided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_1sided.1D new file mode 100644 index 0000000..dd6f926 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_1sided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# 1-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 2 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 1346.0 1381.6 1425.0 1479.7 1534.0 1591.7 1686.0 1786.0 1909.0 2143.0 + 0.090000 876.3 902.2 928.0 956.5 989.7 1039.0 1091.0 1158.7 1246.0 1415.5 + 0.080000 592.5 608.0 626.8 643.7 667.2 693.7 729.2 767.7 838.0 936.5 + 0.070000 405.9 416.4 425.6 439.0 451.7 469.0 494.2 521.3 560.5 624.0 + 0.060000 284.6 291.2 299.1 306.8 316.9 328.8 342.0 363.0 393.5 439.0 + 0.050000 201.8 206.2 211.4 217.1 223.6 230.9 239.2 251.0 265.0 298.0 + 0.040000 142.9 145.8 148.8 152.4 156.2 160.7 165.6 172.7 183.4 206.1 + 0.030000 99.5 101.8 104.1 106.1 108.6 111.7 115.4 119.8 125.9 139.4 + 0.020000 66.0 67.1 68.5 70.1 71.9 73.9 76.1 79.6 83.6 91.5 + 0.015000 51.9 52.9 54.0 55.2 56.5 58.0 59.7 62.2 65.4 72.3 + 0.010000 39.1 39.8 40.5 41.3 42.3 43.5 45.0 46.9 49.4 54.0 + 0.007000 31.0 31.6 32.3 33.1 34.0 35.2 36.3 37.8 40.0 43.4 + 0.005000 25.5 26.0 26.6 27.2 28.0 28.9 30.0 31.4 33.1 35.9 + 0.003000 19.7 20.1 20.5 21.0 21.6 22.3 23.1 24.1 25.6 27.7 + 0.002000 16.2 16.5 16.8 17.3 17.8 18.4 19.1 19.9 21.1 23.2 + 0.001500 14.3 14.6 14.9 15.3 15.8 16.3 16.9 17.8 18.9 20.7 + 0.001000 12.0 12.3 12.6 12.9 13.3 13.8 14.3 15.0 15.9 17.6 + 0.000700 10.4 10.6 10.9 11.2 11.5 11.9 12.4 13.0 13.8 15.3 + 0.000500 9.2 9.4 9.6 9.9 10.1 10.5 10.9 11.4 12.2 13.6 + 0.000300 7.6 7.8 8.0 8.2 8.4 8.8 9.1 9.6 10.3 11.4 + 0.000200 6.5 6.6 6.8 7.0 7.2 7.6 7.9 8.4 9.0 10.0 + 0.000150 5.8 6.0 6.2 6.3 6.6 6.8 7.1 7.6 8.2 9.3 + 0.000100 4.9 5.1 5.3 5.4 5.7 5.9 6.2 6.6 7.1 8.2 + 7.000e-5 4.4 4.5 4.6 4.8 5.0 5.2 5.5 6.0 6.4 7.3 + 5.000e-5 3.8 4.0 4.1 4.3 4.5 4.7 5.0 5.3 5.8 6.8 + 3.000e-5 3.1 3.2 3.4 3.5 3.7 3.9 4.1 4.4 4.8 5.7 + 2.000e-5 2.7 2.8 2.9 3.0 3.1 3.3 3.6 3.9 4.3 4.9 + 1.500e-5 2.4 2.5 2.6 2.7 2.8 3.0 3.2 3.5 3.9 4.5 + 1.000e-5 2.1 2.1 2.2 2.4 2.5 2.6 2.8 3.0 3.4 4.1 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_1sided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_1sided.niml new file mode 100644 index 0000000..d755023 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_1sided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN2 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="1-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 1346 1381.599 1425 1479.713 1534 1591.666 1686 1786 1909 2143 + 876.2717 902.2496 928 956.4996 989.6656 1039 1091 1158.666 1246 1415.498 + 592.4995 608 626.8328 643.6658 667.1993 693.7493 729.2491 767.6656 838 936.4975 + 405.8658 416.3987 425.6349 439 451.6656 469 494.2491 521.3322 560.4975 624 + 284.5884 291.1992 299.1418 306.7676 316.8564 328.7992 342 363 393.4975 439 + 201.7709 206.2361 211.4418 217.0619 223.6439 230.9324 239.2482 251 265 298 + 142.884 145.782 148.7555 152.4283 156.1974 160.6939 165.5693 172.7237 183.394 206.1385 + 99.52081 101.7745 104.056 106.0662 108.6377 111.6808 115.3847 119.8129 125.8707 139.394 + 66 67.14165 68.51146 70.06759 71.91863 73.88377 76.14755 79.62804 83.6162 91.48756 + 51.93305 52.91618 53.98867 55.17918 56.47147 57.98436 59.74284 62.22542 65.39629 72.29379 + 39.07147 39.75762 40.46856 41.26268 42.25185 43.50178 45.01662 46.93299 49.41793 54 + 30.9777 31.631 32.33418 33.10257 34.03249 35.16697 36.31435 37.84478 40 43.35606 + 25.49842 25.97014 26.55678 27.22733 28.0081 28.89241 29.95246 31.39094 33.08834 35.88704 + 19.67112 20.08047 20.51026 20.99483 21.59278 22.27769 23.08048 24.12043 25.55386 27.72814 + 16.17571 16.49197 16.84356 17.28714 17.83173 18.43653 19.1359 19.93462 21.13559 23.1836 + 14.28888 14.58391 14.91189 15.31112 15.78006 16.30089 16.91006 17.81401 18.87151 20.665 + 11.98618 12.25551 12.5568 12.89651 13.29022 13.75494 14.29461 14.96116 15.86297 17.58633 + 10.42144 10.64555 10.89469 11.18248 11.51767 11.91199 12.38094 12.97915 13.84528 15.34057 + 9.159887 9.367656 9.598627 9.85904 10.144 10.46451 10.85469 11.38108 12.15819 13.59369 + 7.575562 7.758055 7.960928 8.187462 8.447033 8.752392 9.130851 9.633379 10.31975 11.42838 + 6.456689 6.616239 6.793608 6.993586 7.24976 7.552021 7.919992 8.363493 8.977181 10.0321 + 5.821853 5.984529 6.151968 6.339336 6.554462 6.807534 7.127894 7.564929 8.180551 9.253895 + 4.945255 5.087261 5.253893 5.441765 5.657469 5.911222 6.210121 6.588262 7.137501 8.198461 + 4.350005 4.475782 4.615606 4.773252 4.954253 5.214829 5.547927 5.975108 6.44952 7.289969 + 3.840695 3.958416 4.100365 4.266229 4.456664 4.680691 4.953422 5.324574 5.849562 6.756187 + 3.127243 3.241209 3.367902 3.510745 3.674749 3.867683 4.102461 4.403388 4.825308 5.668004 + 2.69204 2.780722 2.879307 2.99046 3.149624 3.339864 3.571461 3.868473 4.261573 4.911755 + 2.429202 2.515571 2.611586 2.71984 2.84413 2.990345 3.207111 3.487953 3.881714 4.544996 + 2.059975 2.146917 2.243568 2.35254 2.477654 2.624838 2.80402 3.039754 3.41856 4.060665 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_2sided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_2sided.1D new file mode 100644 index 0000000..8e25f52 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_2sided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# 2-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 2 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 284.4 290.2 297.6 306.0 314.9 325.5 340.0 358.0 384.5 417.4 + 0.090000 225.3 229.7 234.8 239.8 246.3 253.4 262.8 276.6 297.8 329.9 + 0.080000 178.0 181.3 185.3 190.5 194.7 201.1 207.6 217.3 231.1 252.5 + 0.070000 143.6 146.2 149.9 153.2 156.6 161.3 166.6 174.1 183.1 201.7 + 0.060000 116.1 118.0 120.3 122.6 125.6 129.1 133.9 140.4 147.7 162.7 + 0.050000 94.0 95.5 97.3 99.6 101.7 103.9 107.4 111.5 118.8 130.0 + 0.040000 74.6 75.8 77.0 78.7 80.6 82.7 85.2 88.4 93.8 101.1 + 0.030000 58.1 59.1 60.0 61.2 62.5 64.3 66.4 69.5 73.2 80.2 + 0.020000 43.2 44.0 44.8 45.7 46.7 47.9 49.4 51.4 54.4 59.2 + 0.015000 36.1 36.8 37.5 38.2 39.1 40.1 41.3 42.9 45.4 49.6 + 0.010000 28.7 29.2 29.7 30.3 31.0 31.8 32.7 34.0 35.8 39.5 + 0.007000 23.8 24.2 24.7 25.2 25.8 26.6 27.4 28.4 29.9 32.6 + 0.005000 20.1 20.5 20.9 21.3 21.8 22.4 23.2 24.2 25.7 27.7 + 0.003000 16.0 16.3 16.7 17.0 17.5 18.1 18.7 19.5 20.6 22.3 + 0.002000 13.6 13.8 14.1 14.4 14.8 15.3 15.8 16.5 17.6 19.2 + 0.001500 12.1 12.3 12.6 12.8 13.2 13.6 14.1 14.7 15.7 17.4 + 0.001000 10.4 10.6 10.8 11.0 11.3 11.7 12.1 12.7 13.5 14.9 + 0.000700 9.1 9.3 9.5 9.7 10.0 10.3 10.7 11.2 11.9 13.1 + 0.000500 8.1 8.3 8.5 8.7 8.9 9.2 9.6 10.0 10.7 12.0 + 0.000300 6.8 6.9 7.1 7.3 7.5 7.8 8.1 8.6 9.2 10.4 + 0.000200 5.9 6.0 6.2 6.4 6.6 6.8 7.1 7.6 8.3 9.3 + 0.000150 5.3 5.4 5.6 5.8 6.0 6.2 6.5 6.9 7.5 8.5 + 0.000100 4.6 4.7 4.9 5.1 5.3 5.5 5.8 6.2 6.7 7.6 + 7.000e-5 4.1 4.2 4.3 4.5 4.7 4.9 5.1 5.5 6.0 6.8 + 5.000e-5 3.6 3.7 3.8 4.0 4.1 4.3 4.6 4.9 5.4 6.2 + 3.000e-5 3.0 3.1 3.2 3.3 3.5 3.7 3.9 4.2 4.6 5.2 + 2.000e-5 2.6 2.7 2.8 2.9 3.0 3.2 3.4 3.7 4.0 4.7 + 1.500e-5 2.4 2.4 2.5 2.6 2.7 2.9 3.1 3.3 3.7 4.3 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.5 2.7 2.9 3.2 3.8 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_2sided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_2sided.niml new file mode 100644 index 0000000..0f694c7 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_2sided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN2 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="2-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 284.4424 290.2296 297.5986 306 314.9159 325.4976 340 358 384.4975 417.394 + 225.3174 229.748 234.8498 239.8404 246.2913 253.4423 262.8162 276.6219 297.8313 329.8529 + 178 181.2665 185.2701 190.4704 194.7458 201.1448 207.6333 217.33 231.1089 252.4925 + 143.5569 146.2159 149.9299 153.1961 156.5521 161.3307 166.6116 174.0573 183.0886 201.7463 + 116.0617 118.0239 120.2857 122.6186 125.619 129.1174 133.8867 140.3519 147.7108 162.7463 + 94 95.54945 97.32002 99.5883 101.7203 103.8795 107.3926 111.5185 118.8292 130 + 74.58984 75.77315 77.01553 78.70134 80.56345 82.69262 85.18758 88.43649 93.79411 101.1066 + 58.06046 59.09653 60.03353 61.22114 62.51829 64.28261 66.41435 69.4659 73.18217 80.23869 + 43.19993 43.95993 44.84782 45.70842 46.66262 47.91367 49.36248 51.44286 54.42789 59.24249 + 36.12232 36.77089 37.46487 38.23928 39.12563 40.05411 41.27222 42.86945 45.44814 49.56886 + 28.67442 29.15956 29.69547 30.29719 30.98514 31.77077 32.68584 33.95435 35.82059 39.52943 + 23.77814 24.20627 24.66265 25.18642 25.80796 26.56159 27.44397 28.42921 29.86032 32.56034 + 20.12132 20.49145 20.90291 21.33155 21.81296 22.44851 23.24275 24.21616 25.67271 27.69538 + 16.03637 16.33208 16.66082 17.03525 17.51197 18.06655 18.6908 19.45211 20.59898 22.28177 + 13.57209 13.82765 14.11594 14.44828 14.82985 15.25435 15.75301 16.51568 17.57874 19.19053 + 12.10691 12.32016 12.55723 12.82451 13.16446 13.61636 14.1384 14.72486 15.68896 17.37552 + 10.36087 10.5586 10.77842 11.02712 11.32092 11.66656 12.09609 12.68983 13.54062 14.9029 + 9.128742 9.310686 9.512949 9.740993 10.00298 10.32789 10.72344 11.22973 11.93793 13.13583 + 8.135474 8.303812 8.49095 8.701942 8.94419 9.231374 9.581645 10.0325 10.69606 11.96172 + 6.768559 6.917745 7.089588 7.289989 7.520077 7.790751 8.124821 8.563396 9.203568 10.40325 + 5.873991 6.019865 6.18249 6.365846 6.576364 6.824017 7.147589 7.602256 8.26226 9.299053 + 5.300338 5.445507 5.606887 5.788839 5.997746 6.241412 6.538029 6.918425 7.533791 8.495185 + 4.620782 4.747834 4.889074 5.057006 5.272712 5.526468 5.835391 6.215466 6.732308 7.556303 + 4.050304 4.175682 4.315062 4.472208 4.652634 4.864886 5.138357 5.510255 6.028905 6.837885 + 3.595 3.708953 3.835631 3.978457 4.139009 4.327272 4.556464 4.85039 5.351784 6.222095 + 2.959488 3.059215 3.185213 3.327272 3.490376 3.682251 3.915839 4.190897 4.563121 5.212582 + 2.608137 2.694664 2.790855 2.899307 3.027842 3.199021 3.407414 3.674667 4.046863 4.651662 + 2.351405 2.432709 2.523093 2.624998 2.741999 2.879638 3.05705 3.316782 3.680944 4.279998 + 2.039972 2.116922 2.202466 2.298914 2.409649 2.539918 2.698508 2.901891 3.218945 3.786575 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_bisided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_bisided.1D new file mode 100644 index 0000000..17ed165 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_bisided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# bi-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 2 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 229.8 233.7 238.2 243.6 249.6 256.6 262.8 275.1 295.5 330.0 + 0.090000 192.9 196.1 200.7 205.6 210.7 216.6 223.9 233.5 246.2 270.5 + 0.080000 161.2 163.8 167.2 170.5 174.2 179.1 186.0 194.9 206.5 224.6 + 0.070000 134.6 137.2 139.6 142.6 146.2 150.6 154.5 160.7 169.4 184.5 + 0.060000 111.8 113.8 115.7 117.8 120.6 123.5 127.5 133.0 141.2 153.5 + 0.050000 91.9 93.4 95.1 97.0 99.2 101.7 104.4 108.6 114.5 125.7 + 0.040000 73.7 74.9 76.1 77.7 79.6 81.8 84.0 87.6 92.8 100.2 + 0.030000 57.8 58.8 59.8 60.9 62.3 64.0 66.0 69.2 73.0 79.9 + 0.020000 43.1 43.9 44.8 45.7 46.6 47.8 49.3 51.3 54.4 59.2 + 0.015000 36.1 36.7 37.4 38.2 39.1 40.0 41.3 42.9 45.4 49.6 + 0.010000 28.7 29.2 29.7 30.3 31.0 31.8 32.7 34.0 35.8 39.5 + 0.007000 23.8 24.2 24.7 25.2 25.8 26.6 27.4 28.4 29.9 32.6 + 0.005000 20.1 20.5 20.9 21.3 21.8 22.4 23.2 24.2 25.7 27.7 + 0.003000 16.0 16.3 16.7 17.0 17.5 18.1 18.7 19.5 20.6 22.3 + 0.002000 13.6 13.8 14.1 14.4 14.8 15.3 15.8 16.5 17.6 19.2 + 0.001500 12.1 12.3 12.6 12.8 13.2 13.6 14.1 14.7 15.7 17.4 + 0.001000 10.4 10.6 10.8 11.0 11.3 11.7 12.1 12.7 13.5 14.9 + 0.000700 9.1 9.3 9.5 9.7 10.0 10.3 10.7 11.2 11.9 13.1 + 0.000500 8.1 8.3 8.5 8.7 8.9 9.2 9.6 10.0 10.7 12.0 + 0.000300 6.8 6.9 7.1 7.3 7.5 7.8 8.1 8.6 9.2 10.4 + 0.000200 5.9 6.0 6.2 6.4 6.6 6.8 7.1 7.6 8.3 9.3 + 0.000150 5.3 5.4 5.6 5.8 6.0 6.2 6.5 6.9 7.5 8.5 + 0.000100 4.6 4.7 4.9 5.1 5.3 5.5 5.8 6.2 6.7 7.6 + 7.000e-5 4.1 4.2 4.3 4.5 4.7 4.9 5.1 5.5 6.0 6.8 + 5.000e-5 3.6 3.7 3.8 4.0 4.1 4.3 4.6 4.9 5.4 6.2 + 3.000e-5 3.0 3.1 3.2 3.3 3.5 3.7 3.9 4.2 4.6 5.2 + 2.000e-5 2.6 2.7 2.8 2.9 3.0 3.2 3.4 3.7 4.0 4.7 + 1.500e-5 2.4 2.4 2.5 2.6 2.7 2.9 3.1 3.3 3.7 4.3 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.5 2.7 2.9 3.2 3.8 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_bisided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_bisided.niml new file mode 100644 index 0000000..ccac190 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN2_bisided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN2 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="bi-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 229.7618 233.7113 238.2473 243.6224 249.6403 256.5953 262.7828 275.0818 295.4975 330 + 192.8509 196.086 200.6975 205.5679 210.747 216.5805 223.8551 233.4562 246.1646 270.495 + 161.2464 163.8175 167.2194 170.4945 174.1974 179.0824 186 194.8721 206.4938 224.594 + 134.6175 137.2181 139.5833 142.6079 146.227 150.554 154.5242 160.6645 169.4389 184.4925 + 111.7546 113.8202 115.6938 117.8092 120.5693 123.4772 127.4939 133 141.196 153.4901 + 91.90371 93.42738 95.05712 96.96165 99.2054 101.7103 104.3843 108.556 114.4574 125.7426 + 73.74778 74.88175 76.14503 77.67022 79.63074 81.80328 84.03452 87.57469 92.75719 100.192 + 57.7891 58.80799 59.79633 60.92647 62.28804 64.04802 66.03106 69.15372 73 79.85291 + 43.13611 43.89546 44.78783 45.65502 46.6077 47.8424 49.30056 51.32983 54.35468 59.24249 + 36.08595 36.73519 37.43564 38.21609 39.10867 40.03281 41.25825 42.86735 45.43047 49.56886 + 28.66512 29.15031 29.68824 30.29077 30.97772 31.76911 32.68584 33.95435 35.82059 39.52943 + 23.77735 24.20627 24.66265 25.18642 25.80796 26.56159 27.44397 28.42921 29.86032 32.56034 + 20.12132 20.49145 20.90291 21.33155 21.81296 22.44851 23.24275 24.21616 25.67271 27.69538 + 16.03637 16.33208 16.66082 17.03525 17.51197 18.06655 18.6908 19.45211 20.59898 22.28177 + 13.57209 13.82765 14.11594 14.44828 14.82985 15.25435 15.75301 16.51568 17.57874 19.19053 + 12.10691 12.32016 12.55723 12.82451 13.16446 13.61636 14.1384 14.72486 15.68896 17.37552 + 10.36087 10.5586 10.77842 11.02712 11.32092 11.66656 12.09609 12.68983 13.54062 14.9029 + 9.128742 9.310686 9.512949 9.740993 10.00298 10.32789 10.72344 11.22973 11.93793 13.13583 + 8.135474 8.303812 8.49095 8.701942 8.94419 9.231374 9.581645 10.0325 10.69606 11.96172 + 6.768559 6.917745 7.089588 7.289989 7.520077 7.790751 8.124821 8.563396 9.203568 10.40325 + 5.873991 6.019865 6.18249 6.365846 6.576364 6.824017 7.147589 7.602256 8.26226 9.299053 + 5.300338 5.445507 5.606887 5.788839 5.997746 6.241412 6.538029 6.918425 7.533791 8.495185 + 4.620782 4.747834 4.889074 5.057006 5.272712 5.526468 5.835391 6.215466 6.732308 7.556303 + 4.050304 4.175682 4.315062 4.472208 4.652634 4.864886 5.138357 5.510255 6.028905 6.837885 + 3.595 3.708953 3.835631 3.978457 4.139009 4.327272 4.556464 4.85039 5.351784 6.222095 + 2.959488 3.059215 3.185213 3.327272 3.490376 3.682251 3.915839 4.190897 4.563121 5.212582 + 2.608137 2.694664 2.790855 2.899307 3.027842 3.199021 3.407414 3.674667 4.046863 4.651662 + 2.351405 2.432709 2.523093 2.624998 2.741999 2.879638 3.05705 3.316782 3.680944 4.279998 + 2.039972 2.116922 2.202466 2.298914 2.409649 2.539918 2.698508 2.901891 3.218945 3.786575 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_1sided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_1sided.1D new file mode 100644 index 0000000..45a84a5 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_1sided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# 1-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 3 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 1857.5 1918.0 1972.7 2046.0 2120.0 2220.7 2329.7 2469.0 2654.0 2996.0 + 0.090000 1154.7 1185.8 1227.0 1269.0 1299.0 1361.0 1427.5 1512.0 1641.3 1904.0 + 0.080000 738.3 760.2 783.4 813.3 843.0 874.2 918.0 970.3 1052.0 1178.7 + 0.070000 486.3 501.2 514.3 528.2 544.0 566.0 592.0 627.0 682.0 756.0 + 0.060000 325.9 333.1 341.6 353.0 363.7 379.3 395.8 418.4 448.8 501.0 + 0.050000 224.8 229.5 234.7 242.3 248.8 257.9 267.3 280.2 302.7 342.0 + 0.040000 155.3 158.5 161.6 165.0 169.8 174.5 181.3 190.1 204.3 227.0 + 0.030000 106.0 107.9 109.9 112.6 115.5 118.7 122.9 128.2 135.3 148.3 + 0.020000 68.7 69.9 71.4 72.9 74.7 76.7 79.5 82.9 87.6 94.6 + 0.015000 53.5 54.5 55.5 56.7 58.0 59.7 61.9 64.5 68.3 73.8 + 0.010000 39.8 40.5 41.2 42.0 43.0 44.3 45.9 47.7 50.3 55.3 + 0.007000 31.6 32.2 32.9 33.7 34.6 35.7 36.9 38.4 40.8 44.1 + 0.005000 25.8 26.3 26.9 27.6 28.3 29.2 30.2 31.6 33.4 36.6 + 0.003000 19.8 20.2 20.7 21.2 21.8 22.5 23.3 24.3 25.7 27.9 + 0.002000 16.3 16.6 17.0 17.4 17.9 18.5 19.2 20.0 21.3 23.2 + 0.001500 14.4 14.7 15.0 15.4 15.9 16.4 17.0 17.9 18.9 20.8 + 0.001000 12.0 12.3 12.6 13.0 13.4 13.8 14.3 15.0 15.9 17.6 + 0.000700 10.5 10.7 10.9 11.2 11.6 12.0 12.4 13.0 13.9 15.4 + 0.000500 9.2 9.4 9.6 9.9 10.2 10.5 10.9 11.4 12.2 13.7 + 0.000300 7.6 7.8 8.0 8.2 8.5 8.8 9.1 9.6 10.3 11.4 + 0.000200 6.5 6.6 6.8 7.0 7.3 7.6 7.9 8.4 9.0 10.0 + 0.000150 5.8 6.0 6.2 6.3 6.6 6.8 7.1 7.6 8.2 9.3 + 0.000100 5.0 5.1 5.3 5.4 5.7 5.9 6.2 6.6 7.1 8.2 + 7.000e-5 4.4 4.5 4.6 4.8 5.0 5.2 5.6 6.0 6.5 7.3 + 5.000e-5 3.8 4.0 4.1 4.3 4.5 4.7 5.0 5.3 5.9 6.8 + 3.000e-5 3.1 3.2 3.4 3.5 3.7 3.9 4.1 4.4 4.8 5.7 + 2.000e-5 2.7 2.8 2.9 3.0 3.2 3.3 3.6 3.9 4.3 4.9 + 1.500e-5 2.4 2.5 2.6 2.7 2.8 3.0 3.2 3.5 3.9 4.5 + 1.000e-5 2.1 2.2 2.2 2.4 2.5 2.6 2.8 3.0 3.4 4.1 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_1sided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_1sided.niml new file mode 100644 index 0000000..4394dba --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_1sided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN3 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="1-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 1857.5 1918 1972.666 2046 2120 2220.666 2329.666 2469 2654 2996 + 1154.666 1185.8 1227 1269 1299 1361 1427.499 1512 1641.332 1904 + 738.333 760.2496 783.3993 813.3329 843 874.1992 918 970.3322 1052 1178.746 + 486.3327 501.2492 514.3317 528.1661 544 566 592 627 682 756 + 325.8563 333.1167 341.5816 353 363.6645 379.2843 395.8323 418.398 448.798 501 + 224.7671 229.4627 234.7316 242.3101 248.8215 257.8563 267.284 280.2488 302.6634 342 + 155.2616 158.496 161.6014 165.0393 169.7674 174.4971 181.2804 190.0985 204.3284 227 + 105.9791 107.8748 109.9178 112.5571 115.5451 118.7185 122.8729 128.2325 135.2673 148.2786 + 68.68697 69.92303 71.36015 72.94968 74.65099 76.74203 79.47501 82.88031 87.63749 94.5881 + 53.46863 54.46117 55.51794 56.67957 57.98606 59.71296 61.88593 64.45565 68.30556 73.82979 + 39.83496 40.46667 41.16011 41.98243 43 44.31827 45.87781 47.67999 50.27432 55.27134 + 31.55821 32.17836 32.88655 33.66731 34.61073 35.65356 36.86298 38.44996 40.75638 44.05072 + 25.80089 26.30902 26.8991 27.5681 28.3247 29.1872 30.22293 31.6379 33.41787 36.62756 + 19.84941 20.2479 20.67749 21.17567 21.77927 22.45942 23.27695 24.31787 25.68736 27.89324 + 16.28633 16.61691 16.9844 17.43296 17.9495 18.54255 19.2319 20.04867 21.2574 23.24903 + 14.38353 14.6838 15.01903 15.42562 15.89245 16.3925 16.98669 17.88355 18.92374 20.78348 + 12.0437 12.31589 12.61849 12.95965 13.35508 13.82076 14.34778 15 15.89826 17.64669 + 10.4565 10.68313 10.93507 11.2246 11.5589 11.95216 12.42384 13.02891 13.91138 15.36547 + 9.18874 9.398211 9.631073 9.89362 10.17887 10.50406 10.89995 11.43524 12.22674 13.6746 + 7.591378 7.773639 7.976254 8.20341 8.464046 8.770657 9.149136 9.645164 10.32834 11.43496 + 6.470781 6.631227 6.809592 7.011825 7.267183 7.567585 7.933294 8.373837 8.984891 10.0321 + 5.830786 5.993155 6.160641 6.348897 6.565041 6.819313 7.14084 7.574718 8.188518 9.264029 + 4.952906 5.09531 5.260472 5.446688 5.66049 5.912005 6.210121 6.588262 7.139352 8.215364 + 4.354384 4.480096 4.619848 4.777414 4.958322 5.218892 5.550266 5.975237 6.45371 7.304384 + 3.842591 3.959854 4.102629 4.269833 4.461807 4.687644 4.962578 5.333731 5.857204 6.757969 + 3.13344 3.246906 3.373044 3.515262 3.678547 3.870635 4.104593 4.404805 4.825723 5.668004 + 2.696158 2.784686 2.883101 2.99406 3.154072 3.344185 3.575629 3.872444 4.264198 4.912068 + 2.43477 2.521028 2.61692 2.725035 2.849166 2.995193 3.21296 3.493661 3.887223 4.547435 + 2.064631 2.151612 2.248307 2.357327 2.482499 2.62975 2.809013 3.045454 3.422011 4.060665 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_2sided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_2sided.1D new file mode 100644 index 0000000..3940931 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_2sided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# 2-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 3 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 504.3 516.8 529.9 546.4 562.0 582.2 607.6 639.6 695.0 781.0 + 0.090000 349.2 357.7 365.6 375.9 388.3 400.8 419.2 439.7 469.7 519.5 + 0.080000 251.2 256.2 262.4 269.5 278.3 287.0 296.5 309.1 330.0 370.0 + 0.070000 186.3 190.3 195.2 200.1 205.7 211.7 219.2 229.1 242.6 266.2 + 0.060000 140.0 142.5 145.7 149.0 153.4 158.3 164.4 171.4 181.8 199.5 + 0.050000 106.3 108.1 110.2 112.6 116.1 118.9 123.6 128.7 137.6 150.8 + 0.040000 81.4 83.0 84.7 86.6 88.6 91.1 93.7 97.8 102.9 112.8 + 0.030000 61.6 62.6 63.8 65.2 66.8 68.3 70.9 73.8 78.3 84.6 + 0.020000 44.7 45.5 46.2 47.1 48.3 49.5 51.1 53.2 56.3 61.3 + 0.015000 37.0 37.7 38.4 39.3 40.1 41.2 42.4 44.1 46.4 50.7 + 0.010000 29.1 29.6 30.1 30.7 31.4 32.2 33.2 34.5 36.5 39.9 + 0.007000 24.1 24.5 24.9 25.5 26.1 26.9 27.7 28.7 30.2 32.9 + 0.005000 20.3 20.7 21.1 21.5 22.0 22.6 23.4 24.4 25.8 27.9 + 0.003000 16.1 16.4 16.7 17.1 17.6 18.1 18.8 19.5 20.7 22.3 + 0.002000 13.6 13.9 14.2 14.5 14.9 15.3 15.8 16.6 17.7 19.3 + 0.001500 12.1 12.4 12.6 12.9 13.2 13.7 14.2 14.8 15.7 17.4 + 0.001000 10.4 10.6 10.8 11.1 11.4 11.7 12.2 12.7 13.6 15.0 + 0.000700 9.1 9.3 9.5 9.8 10.0 10.3 10.7 11.2 12.0 13.2 + 0.000500 8.1 8.3 8.5 8.7 9.0 9.2 9.6 10.0 10.7 12.0 + 0.000300 6.8 6.9 7.1 7.3 7.5 7.8 8.1 8.6 9.2 10.4 + 0.000200 5.9 6.0 6.2 6.4 6.6 6.8 7.2 7.6 8.3 9.3 + 0.000150 5.3 5.4 5.6 5.8 6.0 6.2 6.5 6.9 7.5 8.5 + 0.000100 4.6 4.8 4.9 5.1 5.3 5.5 5.8 6.2 6.7 7.6 + 7.000e-5 4.1 4.2 4.3 4.5 4.7 4.9 5.1 5.5 6.0 6.9 + 5.000e-5 3.6 3.7 3.8 4.0 4.1 4.3 4.6 4.9 5.4 6.2 + 3.000e-5 3.0 3.1 3.2 3.3 3.5 3.7 3.9 4.2 4.6 5.2 + 2.000e-5 2.6 2.7 2.8 2.9 3.0 3.2 3.4 3.7 4.0 4.7 + 1.500e-5 2.4 2.4 2.5 2.6 2.7 2.9 3.1 3.3 3.7 4.3 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.5 2.7 2.9 3.2 3.8 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_2sided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_2sided.niml new file mode 100644 index 0000000..357c6c1 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_2sided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN3 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="2-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 504.3327 516.8173 529.8566 546.4274 562 582.2493 607.5985 639.598 695 781 + 349.1659 357.6989 365.6136 375.9085 388.2845 400.7763 419.2482 439.7476 469.665 519.4975 + 251.1567 256.2206 262.3552 269.5308 278.3004 287 296.4969 309.1414 330 370 + 186.3194 190.2585 195.186 200.1099 205.7267 211.6896 219.1961 229.1236 242.597 266.196 + 140.0318 142.5397 145.672 149 153.3546 158.2685 164.3836 171.3941 181.7961 199.4925 + 106.2663 108.1249 110.2127 112.6255 116.0573 118.879 123.5762 128.7001 137.563 150.796 + 81.4026 83 84.67131 86.57608 88.55275 91.10673 93.6973 97.80425 102.8529 112.796 + 61.56893 62.5588 63.83511 65.175 66.78551 68.27982 70.89256 73.79092 78.34916 84.60014 + 44.72475 45.47106 46.24886 47.13666 48.25367 49.54482 51.11589 53.22543 56.34035 61.29379 + 36.99387 37.65658 38.41564 39.25491 40.13149 41.15611 42.38078 44.08481 46.36754 50.67055 + 29.0728 29.55441 30.0911 30.70345 31.38494 32.17809 33.18537 34.48938 36.54155 39.91703 + 24.05412 24.46293 24.91739 25.47141 26.11545 26.86644 27.73229 28.69836 30.2272 32.9244 + 20.28655 20.65058 21.05366 21.49675 22.00582 22.64169 23.41257 24.40619 25.83642 27.90581 + 16.12782 16.41385 16.73182 17.10604 17.58928 18.14244 18.7673 19.52377 20.69947 22.34492 + 13.64181 13.89822 14.18714 14.5153 14.89208 15.3155 15.82321 16.59509 17.66319 19.33413 + 12.14528 12.36438 12.60794 12.88255 13.24035 13.69096 14.20115 14.79191 15.73297 17.44991 + 10.39412 10.59367 10.81549 11.06831 11.36737 11.71917 12.15809 12.74694 13.59457 14.98036 + 9.145892 9.327175 9.528704 9.75592 10.01789 10.34466 10.74248 11.24953 11.956 13.17762 + 8.14922 8.316447 8.502349 8.711948 8.952598 9.237602 9.585035 10.0325 10.69606 11.96172 + 6.782255 6.932237 7.10455 7.303137 7.531143 7.799368 8.132707 8.574092 9.218503 10.41138 + 5.881294 6.02731 6.189209 6.371743 6.581319 6.827863 7.151674 7.607763 8.271178 9.305128 + 5.304162 5.449004 5.610021 5.791564 6 6.244241 6.54158 6.922902 7.541959 8.499448 + 4.625428 4.753118 4.895069 5.064701 5.280417 5.534185 5.843123 6.222803 6.739961 7.559435 + 4.051526 4.177086 4.316668 4.474043 4.654731 4.867292 5.142634 5.518116 6.040349 6.850897 + 3.599901 3.713782 3.840382 3.983119 4.144022 4.332906 4.562852 4.857747 5.362409 6.233515 + 2.963754 3.064675 3.190318 3.331978 3.494623 3.685958 3.91889 4.192914 4.56421 5.212582 + 2.61139 2.697774 2.793804 2.902076 3.030793 3.201452 3.409213 3.675655 4.046863 4.651662 + 2.354007 2.435205 2.52547 2.627243 2.744091 2.881552 3.059051 3.318231 3.68162 4.279998 + 2.044731 2.121515 2.206874 2.303113 2.41361 2.543598 2.701845 2.904788 3.221398 3.787245 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_bisided.1D b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_bisided.1D new file mode 100644 index 0000000..5c61f0c --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_bisided.1D @@ -0,0 +1,37 @@ +# 3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim +# bi-sided thresholding +# Grid: 54x64x50 3.00x3.00x3.00 mm^3 (70509 voxels in mask) +# +# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels +# -NN 3 | alpha = Prob(Cluster >= given size) +# pthr | .10000 .09000 .08000 .07000 .06000 .05000 .04000 .03000 .02000 .01000 +# ------ | ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ + 0.100000 256.2 260.6 265.0 272.0 279.5 289.6 300.4 316.4 337.4 375.7 + 0.090000 213.2 217.4 221.5 226.0 231.6 237.9 246.2 259.4 277.2 309.7 + 0.080000 174.9 177.9 181.6 185.7 191.5 197.1 204.0 212.4 224.9 249.4 + 0.070000 144.8 147.0 150.3 153.3 156.7 161.3 166.9 174.8 183.8 201.7 + 0.060000 118.9 120.9 123.2 125.7 128.7 132.0 136.6 142.7 150.4 164.2 + 0.050000 96.5 98.1 100.2 102.0 103.9 106.6 109.9 114.8 121.9 132.0 + 0.040000 76.6 78.0 79.3 81.0 82.9 85.3 88.1 91.5 95.9 104.8 + 0.030000 59.6 60.6 61.7 62.9 64.5 66.3 68.4 71.4 74.8 82.5 + 0.020000 44.1 44.9 45.7 46.6 47.7 48.9 50.4 52.5 55.7 60.6 + 0.015000 36.7 37.4 38.1 39.0 39.8 40.8 42.0 43.8 46.1 50.5 + 0.010000 29.0 29.5 30.0 30.6 31.3 32.1 33.1 34.4 36.5 39.9 + 0.007000 24.0 24.4 24.9 25.4 26.1 26.8 27.7 28.6 30.2 32.8 + 0.005000 20.3 20.6 21.0 21.5 22.0 22.6 23.4 24.4 25.8 27.9 + 0.003000 16.1 16.4 16.7 17.1 17.6 18.1 18.8 19.5 20.7 22.3 + 0.002000 13.6 13.9 14.2 14.5 14.9 15.3 15.8 16.6 17.7 19.3 + 0.001500 12.1 12.4 12.6 12.9 13.2 13.7 14.2 14.8 15.7 17.4 + 0.001000 10.4 10.6 10.8 11.1 11.4 11.7 12.2 12.7 13.6 15.0 + 0.000700 9.1 9.3 9.5 9.8 10.0 10.3 10.7 11.2 12.0 13.2 + 0.000500 8.1 8.3 8.5 8.7 9.0 9.2 9.6 10.0 10.7 12.0 + 0.000300 6.8 6.9 7.1 7.3 7.5 7.8 8.1 8.6 9.2 10.4 + 0.000200 5.9 6.0 6.2 6.4 6.6 6.8 7.2 7.6 8.3 9.3 + 0.000150 5.3 5.4 5.6 5.8 6.0 6.2 6.5 6.9 7.5 8.5 + 0.000100 4.6 4.8 4.9 5.1 5.3 5.5 5.8 6.2 6.7 7.6 + 7.000e-5 4.1 4.2 4.3 4.5 4.7 4.9 5.1 5.5 6.0 6.9 + 5.000e-5 3.6 3.7 3.8 4.0 4.1 4.3 4.6 4.9 5.4 6.2 + 3.000e-5 3.0 3.1 3.2 3.3 3.5 3.7 3.9 4.2 4.6 5.2 + 2.000e-5 2.6 2.7 2.8 2.9 3.0 3.2 3.4 3.7 4.0 4.7 + 1.500e-5 2.4 2.4 2.5 2.6 2.7 2.9 3.1 3.3 3.7 4.3 + 1.000e-5 2.0 2.1 2.2 2.3 2.4 2.5 2.7 2.9 3.2 3.8 diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_bisided.niml b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_bisided.niml new file mode 100644 index 0000000..c49d3c8 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.NN3_bisided.niml @@ -0,0 +1,45 @@ +<3dClustSim_NN3 + ni_type="10*float" + ni_dimen="29" + commandline="3dClustSim -both -mask full_mask.sub_001+tlrc -fwhmxyz 5.84829 5.82991 6.2316 -prefix ClustSim" + thresholding="bi-sided" + nxyz="54,64,50" + dxyz="3.000,3.000,3.000" + fwhmxyz="5.85,5.83,6.23" + iter="10000" + pthr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.015,0.01,0.007,0.005,0.003,0.002,0.0015,0.001,0.0007,0.0005,0.0003,0.0002,0.00015,0.0001,7e-05,5e-05,3e-05,2e-05,1.5e-05,1e-05" + athr="0.1,0.09,0.08,0.07,0.06,0.05,0.04,0.03,0.02,0.01" + mask_dset_idcode="AFN_QuU_eaCyIpqLjEz0QJE3xQ" + mask_dset_name="./full_mask.sub_001+tlrc.HEAD" + mask_count="70509" > + 256.1724 260.5532 265 272 279.4984 289.5805 300.3985 316.4258 337.397 375.6634 + 213.1651 217.3962 221.5183 226 231.6343 237.9222 246.2482 259.4408 277.1646 309.6634 + 174.9346 177.9048 181.6205 185.6785 191.5359 197.0579 204 212.4119 224.855 249.3656 + 144.7583 147.0298 150.3191 153.2892 156.6797 161.3294 166.9433 174.8155 183.798 201.7463 + 118.9035 120.8814 123.245 125.7383 128.6597 132.0313 136.6059 142.6931 150.377 164.2144 + 96.53384 98.14182 100.1947 101.9818 103.8826 106.6094 109.8857 114.8207 121.855 132 + 76.61415 78 79.33742 81.01893 82.94115 85.33515 88.10368 91.54463 95.87815 104.7701 + 59.59327 60.56303 61.70629 62.90099 64.46383 66.2759 68.38969 71.3982 74.8252 82.54452 + 44.0642 44.91052 45.6991 46.58054 47.66392 48.85994 50.42281 52.51987 55.71823 60.56886 + 36.73296 37.3751 38.11698 38.95513 39.80538 40.82841 42.01516 43.75431 46.05774 50.48008 + 28.97149 29.45368 29.98866 30.59911 31.28498 32.07101 33.06704 34.38543 36.45017 39.87181 + 24.01545 24.42188 24.87369 25.41739 26.05477 26.80647 27.66528 28.64635 30.16887 32.84998 + 20.2726 20.63515 21.03723 21.4803 21.98901 22.62549 23.39526 24.38277 25.816 27.90358 + 16.12279 16.40925 16.7277 17.10153 17.58401 18.13678 18.76025 19.51509 20.6834 22.34492 + 13.64181 13.89822 14.18714 14.5153 14.89208 15.3155 15.82321 16.59509 17.66319 19.33413 + 12.14528 12.36438 12.60794 12.88255 13.24035 13.69096 14.20115 14.79191 15.73297 17.44991 + 10.39121 10.59086 10.81281 11.0658 11.36566 11.71842 12.15809 12.74694 13.59457 14.98036 + 9.144528 9.3261 9.527951 9.755531 10.01789 10.34466 10.74248 11.24953 11.956 13.17762 + 8.14922 8.316447 8.502349 8.711948 8.952598 9.237602 9.585035 10.0325 10.69606 11.96172 + 6.782255 6.932237 7.10455 7.303137 7.531143 7.799368 8.132707 8.574092 9.218503 10.41138 + 5.881294 6.02731 6.189209 6.371743 6.581319 6.827863 7.151674 7.607763 8.271178 9.305128 + 5.304162 5.449004 5.610021 5.791564 6 6.244241 6.54158 6.922902 7.541959 8.499448 + 4.625428 4.753118 4.895069 5.064701 5.280417 5.534185 5.843123 6.222803 6.739961 7.559435 + 4.051526 4.177086 4.316668 4.474043 4.654731 4.867292 5.142634 5.518116 6.040349 6.850897 + 3.599901 3.713782 3.840382 3.983119 4.144022 4.332906 4.562852 4.857747 5.362409 6.233515 + 2.963754 3.064675 3.190318 3.331978 3.494623 3.685958 3.91889 4.192914 4.56421 5.212582 + 2.61139 2.697774 2.793804 2.902076 3.030793 3.201452 3.409213 3.675655 4.046863 4.651662 + 2.354007 2.435205 2.52547 2.627243 2.744091 2.881552 3.059051 3.318231 3.68162 4.279998 + 2.044731 2.121515 2.206874 2.303113 2.41361 2.543598 2.701845 2.904788 3.221398 3.787245 + + diff --git a/afni_no_motion_regressors/sub_001.results/ClustSim.mask b/afni_no_motion_regressors/sub_001.results/ClustSim.mask new file mode 100644 index 0000000..ab8adf6 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/ClustSim.mask @@ -0,0 +1,56 @@ +eNrtnEFu47gShikIaG4are1bBK0r9LIXjegdZY4wy7cYRMyqr6WgL6LcgEsuBHHI+kmqaFGS +kzgZTz8LQRSbtizXxypWFasixO24Hdd+PNDvoaOTaek0S/9b2dqftKXnJgz19FvJm+A++pgq 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a/afni_no_motion_regressors/sub_001.results/mask_group+tlrc.HEAD b/afni_no_motion_regressors/sub_001.results/mask_group+tlrc.HEAD new file mode 100644 index 0000000..052bdfd --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/mask_group+tlrc.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:76c62eb55658c96e543798d1ec16251d449e0c06365244419a851705338183f5 +size 2132 diff --git a/afni_no_motion_regressors/sub_001.results/mat.r01.vr.aff12.1D b/afni_no_motion_regressors/sub_001.results/mat.r01.vr.aff12.1D new file mode 100644 index 0000000..17128ec --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/mat.r01.vr.aff12.1D @@ -0,0 +1,105 @@ +# 3dvolreg matrices (DICOM-to-DICOM, row-by-row): + 1 -0.000273018 0.000198518 -0.00189945 0.00027273 0.999999 0.00144846 0.0811217 -0.000198913 -0.00144841 0.999999 0.0395884 + 1 -9.61105e-05 -6.07152e-05 0.00138822 9.61524e-05 1 0.00068988 0.0362836 6.06489e-05 -0.000689886 1 -0.0181741 + 1 8.49712e-11 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b/afni_no_motion_regressors/sub_001.results/motion_sub_001_CENSORTR.txt new file mode 100644 index 0000000..d759ac8 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/motion_sub_001_CENSORTR.txt @@ -0,0 +1 @@ +-CENSORTR 1:20..24,1:50..52,1:75,1:76,1:78,1:79 diff --git a/afni_no_motion_regressors/sub_001.results/motion_sub_001_censor.1D b/afni_no_motion_regressors/sub_001.results/motion_sub_001_censor.1D new file mode 100644 index 0000000..14d4c4f --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/motion_sub_001_censor.1D @@ -0,0 +1,104 @@ +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +0 +0 +1 +0 +0 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 diff --git a/afni_no_motion_regressors/sub_001.results/motion_sub_001_enorm.1D b/afni_no_motion_regressors/sub_001.results/motion_sub_001_enorm.1D new file mode 100644 index 0000000..15d5279 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/motion_sub_001_enorm.1D @@ -0,0 +1,104 @@ +0 +0.0854264 +0.0562189 +0.0294637 +0.0690088 +0.0147251 +0.0207832 +0.0170655 +0.04365 +0.0394919 +0.289925 +0.163749 +0.115999 +0.0370042 +0.152587 +0.0895549 +0.033803 +0.0580387 +0.0497418 +0.0429767 +0.204197 +0.572462 +0.386764 +0.281657 +0.422455 +0.0858537 +0.0831197 +0.0646937 +0.0564853 +0.0277364 +0.050176 +0.0359443 +0.0266745 +0.0384926 +0.0355963 +0.128928 +0.084972 +0.035958 +0.0797067 +0.0338494 +0.0448574 +0.0676797 +0.0447921 +0.0559862 +0.0520531 +0.0447399 +0.0318226 +0.0245444 +0.039301 +0.0669572 +0.0991943 +0.812363 +0.580431 +0.291556 +0.243107 +0.091504 +0.143233 +0.0535129 +0.110969 +0.0310747 +0.0347677 +0.0289707 +0.0575936 +0.0476427 +0.0309066 +0.0329792 +0.0255875 +0.0415911 +0.0438297 +0.0184158 +0.130805 +0.0318675 +0.104309 +0.0702893 +0.0511497 +0.0637823 +0.434613 +0.036242 +0.181528 +0.455586 +0.275262 +0.0780648 +0.166573 +0.0573753 +0.0847906 +0.0314798 +0.0305794 +0.0153353 +0.0865798 +0.0753118 +0.0315732 +0.0791279 +0.0378338 +0.0579022 +0.0218364 +0.0479361 +0.084811 +0.0281563 +0.0610426 +0.0353853 +0.0682534 +0.0571855 +0.0589526 +0.0633023 diff --git a/afni_no_motion_regressors/sub_001.results/out.cormat_warn.txt b/afni_no_motion_regressors/sub_001.results/out.cormat_warn.txt new file mode 100644 index 0000000..f43ab3c --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/out.cormat_warn.txt @@ -0,0 +1,7 @@ + +Warnings regarding Correlation Matrix: X.xmat.1D + + severity correlation cosine regressor pair + -------- ----------- ------ ---------------------------------------- + medium: -0.439 0.214 ( 3 vs. 4) tone_counting#0 vs. probe#0 + diff --git a/afni_no_motion_regressors/sub_001.results/out.gcor.1D b/afni_no_motion_regressors/sub_001.results/out.gcor.1D new file mode 100644 index 0000000..282e8ea --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/out.gcor.1D @@ -0,0 +1 @@ + 0.0786602 diff --git a/afni_no_motion_regressors/sub_001.results/out.mask_ae_dice.txt b/afni_no_motion_regressors/sub_001.results/out.mask_ae_dice.txt new file mode 100644 index 0000000..16d1be5 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/out.mask_ae_dice.txt @@ -0,0 +1 @@ +0.875027 diff --git a/afni_no_motion_regressors/sub_001.results/out.mask_ae_overlap.txt b/afni_no_motion_regressors/sub_001.results/out.mask_ae_overlap.txt new file mode 100644 index 0000000..75da3d0 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/out.mask_ae_overlap.txt @@ -0,0 +1,4 @@ +++ 3dOverlap: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit] +#A=./full_mask.sub_001+tlrc.BRIK B=./mask_anat.sub_001+tlrc.BRIK +#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) +70509 57071 71762 55818 14691 1253 20.8356 2.1955 0.8509 0.8183 0.9191 diff --git a/afni_no_motion_regressors/sub_001.results/out.pre_ss_warn.txt b/afni_no_motion_regressors/sub_001.results/out.pre_ss_warn.txt new file mode 100644 index 0000000..e69de29 diff --git a/afni_no_motion_regressors/sub_001.results/out.ss_review.sub_001.txt b/afni_no_motion_regressors/sub_001.results/out.ss_review.sub_001.txt new file mode 100644 index 0000000..845376b --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/out.ss_review.sub_001.txt @@ -0,0 +1,44 @@ + +subject ID : sub_001 +TRs removed (per run) : 0 +num stim classes provided : 2 +final anatomy dset : anat_final.sub_001+tlrc.HEAD +final stats dset : stats.sub_001+tlrc.HEAD +final voxel resolution : 3.000000 3.000000 3.000000 + +motion limit : 0.3 +num TRs above mot limit : 7 +average motion (per TR) : 0.102228 +average censored motion : 0.0674361 +max motion displacement : 1.8772 +max censored displacement : 1.67669 +outlier limit : 0.1 +average outlier frac (TR) : 0.00361683 +num TRs above out limit : 0 + +num runs found : 1 +num TRs per run : 104 +num TRs per run (applied) : 92 +num TRs per run (censored): 12 +fraction censored per run : 0.115385 +TRs total (uncensored) : 104 +TRs total : 92 +degrees of freedom used : 5 +degrees of freedom left : 87 + +TRs censored : 12 +censor fraction : 0.115385 +num regs of interest : 2 +num TRs per stim (orig) : 93 59 +num TRs censored per stim : 12 11 +fraction TRs censored : 0.129 0.186 +ave mot per sresp (orig) : 0.106833 0.132941 +ave mot per sresp (cens) : 0.067166 0.071088 + +TSNR average : 106.852 +global correlation (GCOR) : 0.0786602 +anat/EPI mask Dice coef : 0.875027 +maximum F-stat (masked) : 89.4711 +blur estimates : 5.84829 5.82991 6.2316 + + diff --git a/afni_no_motion_regressors/sub_001.results/outcount.r01.1D b/afni_no_motion_regressors/sub_001.results/outcount.r01.1D new file mode 100644 index 0000000..f5ccc3e --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/outcount.r01.1D @@ -0,0 +1,104 @@ +0.01409 +0.00265 +0.00154 +0.00102 +0.00102 +0.00059 +0.00066 +0.00088 +0.00121 +0.00098 +0.00102 +0.00059 +0.00016 +0.00043 +0.00111 +0.00095 +0.00121 +0.00088 +0.00043 +0.00062 +0.00213 +0.01720 +0.00374 +0.02012 +0.00167 +0.00023 +0.00013 +0.00026 +0.00020 +0.00036 +0.00098 +0.00039 +0.00046 +0.00043 +0.00033 +0.00144 +0.00039 +0.00033 +0.00036 +0.00056 +0.00075 +0.00066 +0.00039 +0.00043 +0.00023 +0.00010 +0.00033 +0.00049 +0.00072 +0.00046 +0.00092 +0.08914 +0.06459 +0.03080 +0.00600 +0.00764 +0.00220 +0.00174 +0.00049 +0.00069 +0.00154 +0.00082 +0.00046 +0.00043 +0.00039 +0.00026 +0.00029 +0.00007 +0.00036 +0.00115 +0.00079 +0.00056 +0.00043 +0.00020 +0.00020 +0.00039 +0.01235 +0.00239 +0.00380 +0.02405 +0.01311 +0.00688 +0.00125 +0.00075 +0.00059 +0.00151 +0.00167 +0.00082 +0.00056 +0.00033 +0.00013 +0.00023 +0.00066 +0.00046 +0.00029 +0.00016 +0.00020 +0.00013 +0.00072 +0.00062 +0.00039 +0.00043 +0.00029 +0.00052 diff --git a/afni_no_motion_regressors/sub_001.results/outcount_rall.1D b/afni_no_motion_regressors/sub_001.results/outcount_rall.1D new file mode 100644 index 0000000..f5ccc3e --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/outcount_rall.1D @@ -0,0 +1,104 @@ +0.01409 +0.00265 +0.00154 +0.00102 +0.00102 +0.00059 +0.00066 +0.00088 +0.00121 +0.00098 +0.00102 +0.00059 +0.00016 +0.00043 +0.00111 +0.00095 +0.00121 +0.00088 +0.00043 +0.00062 +0.00213 +0.01720 +0.00374 +0.02012 +0.00167 +0.00023 +0.00013 +0.00026 +0.00020 +0.00036 +0.00098 +0.00039 +0.00046 +0.00043 +0.00033 +0.00144 +0.00039 +0.00033 +0.00036 +0.00056 +0.00075 +0.00066 +0.00039 +0.00043 +0.00023 +0.00010 +0.00033 +0.00049 +0.00072 +0.00046 +0.00092 +0.08914 +0.06459 +0.03080 +0.00600 +0.00764 +0.00220 +0.00174 +0.00049 +0.00069 +0.00154 +0.00082 +0.00046 +0.00043 +0.00039 +0.00026 +0.00029 +0.00007 +0.00036 +0.00115 +0.00079 +0.00056 +0.00043 +0.00020 +0.00020 +0.00039 +0.01235 +0.00239 +0.00380 +0.02405 +0.01311 +0.00688 +0.00125 +0.00075 +0.00059 +0.00151 +0.00167 +0.00082 +0.00056 +0.00033 +0.00013 +0.00023 +0.00066 +0.00046 +0.00029 +0.00016 +0.00020 +0.00013 +0.00072 +0.00062 +0.00039 +0.00043 +0.00029 +0.00052 diff --git a/afni_no_motion_regressors/sub_001.results/pb00.sub_001.r01.tcat+orig.HEAD b/afni_no_motion_regressors/sub_001.results/pb00.sub_001.r01.tcat+orig.HEAD new file mode 100644 index 0000000..7dea249 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/pb00.sub_001.r01.tcat+orig.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:578ce62a2cb6320a4d7de1530865fba2fb26cba4a5e7fed592de351846017e2c +size 9446 diff --git a/afni_no_motion_regressors/sub_001.results/pb01.sub_001.r01.tshift+orig.HEAD b/afni_no_motion_regressors/sub_001.results/pb01.sub_001.r01.tshift+orig.HEAD new file mode 100644 index 0000000..ae2abcf --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/pb01.sub_001.r01.tshift+orig.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c6437005467e2bcbc0ad420ffaa872e8b841ea761ab9039c732485d8623e5d1f +size 9427 diff --git a/afni_no_motion_regressors/sub_001.results/pb02.sub_001.r01.volreg+tlrc.HEAD b/afni_no_motion_regressors/sub_001.results/pb02.sub_001.r01.volreg+tlrc.HEAD new file mode 100644 index 0000000..2fc1e43 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/pb02.sub_001.r01.volreg+tlrc.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:306b677e04c3e7e7d3546aed5721b77c22e57510b29701b231f7cc416bbb42d0 +size 10791 diff --git a/afni_no_motion_regressors/sub_001.results/pb03.sub_001.r01.blur+tlrc.HEAD b/afni_no_motion_regressors/sub_001.results/pb03.sub_001.r01.blur+tlrc.HEAD new file mode 100644 index 0000000..dce55dd --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/pb03.sub_001.r01.blur+tlrc.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:aa6ce2b0e13c8951852b33e78002ba0510ecc6370dc214bf085fdf999fe9f2fc +size 10951 diff --git a/afni_no_motion_regressors/sub_001.results/pb04.sub_001.r01.scale+tlrc.HEAD b/afni_no_motion_regressors/sub_001.results/pb04.sub_001.r01.scale+tlrc.HEAD new file mode 100644 index 0000000..1ccb457 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/pb04.sub_001.r01.scale+tlrc.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b6c2926f07d2944971e65ad718841b489e3e5063b3e27641f63f863b63517443 +size 13783 diff --git a/afni_no_motion_regressors/sub_001.results/stats.REML_cmd b/afni_no_motion_regressors/sub_001.results/stats.REML_cmd new file mode 100644 index 0000000..02724e2 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/stats.REML_cmd @@ -0,0 +1,5 @@ +# 3dDeconvolve -input pb04.sub_001.r01.scale+tlrc.HEAD -censor motion_sub_001_censor.1D -polort 2 -num_stimts 2 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt dmBLOCK -stim_label 2 probe -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_001 -errts errts.sub_001 -bucket stats.sub_001 + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_001.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_001_REML -Rvar stats.sub_001_REMLvar \ + -Rfitts fitts.sub_001_REML -Rerrts errts.sub_001_REML -verb $* diff --git a/afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.BRIK b/afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.BRIK new file mode 100644 index 0000000..6668e62 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.BRIK @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fd822a668452cc420ed6251e23e9016a1a17b9474bb295f89bce8e6831a40232 +size 4838400 diff --git a/afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.HEAD b/afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.HEAD new file mode 100644 index 0000000..5b065dd --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/stats.sub_001+tlrc.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e4883ff0891faa4033ef2ea551e62d98db7bf443b43972c6a74044457af12adc +size 54277 diff --git a/afni_no_motion_regressors/sub_001.results/stimuli/tone_counting_onset_times.txt b/afni_no_motion_regressors/sub_001.results/stimuli/tone_counting_onset_times.txt new file mode 100755 index 0000000..aaf9124 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/stimuli/tone_counting_onset_times.txt @@ -0,0 +1,2 @@ +2.1932636000000003 6.7816266 11.371288999999999 15.954114 20.597725 25.18076 29.770214000000003 34.353722999999995 58.146115 62.735347 67.371975 71.955564 76.544209 81.235098 85.81789 90.408253 114.09236000000001 118.73118000000001 123.48092 128.10946 132.74601 137.33543999999998 141.91796000000002 146.50836999999999 170.09179 174.67803999999998 179.31413 183.95771000000002 188.59818 193.22709 197.8111 202.50274 + diff --git a/afni_no_motion_regressors/sub_001.results/stimuli/tone_counting_probe_duration.txt b/afni_no_motion_regressors/sub_001.results/stimuli/tone_counting_probe_duration.txt new file mode 100755 index 0000000..58fc1f1 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/stimuli/tone_counting_probe_duration.txt @@ -0,0 +1,2 @@ + +0.0:2.0 38.853722999999995:3.0 56.0:2.0 94.908253:3.0 112.0:2.0 151.00836999999999:3.0 168.0:2.0 207.00274:3.0 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w+orig.HEAD b/afni_no_motion_regressors/sub_001.results/sub-01_T1w+orig.HEAD new file mode 100644 index 0000000..5e1cf5c --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w+orig.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2ef9c32681553c125e41c993d898dbcb0ea95237b9a26ceacc34a3c34c78d457 +size 5423 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk+orig.BRIK.gz b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk+orig.BRIK.gz new file mode 100644 index 0000000..bbcdd1d --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk+orig.BRIK.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d507069343ee535a58318ac554705f5d74144bba177f72c967825d09a1aac061 +size 864566 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk+orig.HEAD b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk+orig.HEAD new file mode 100644 index 0000000..47f3525 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk+orig.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1e91707a9cd5cf7f1e5cf5fd8511309fdb68ca81040b6d952c7ab51e07642493 +size 3616 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk_mat.aff12.1D b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk_mat.aff12.1D new file mode 100644 index 0000000..e94cdbf --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_al_junk_mat.aff12.1D @@ -0,0 +1,2 @@ +# 3dAllineate matrices (DICOM-to-DICOM, row-by-row): + 1.02794 0.00577474 -0.0236742 3.23274 0.0128962 1.05417 0.110378 7.50673 0.0134358 -0.191984 0.972287 9.9994 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+orig.BRIK.gz b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+orig.BRIK.gz new file mode 100644 index 0000000..24bbd94 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+orig.BRIK.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c50ff2744d8f8f54314596aae4fcfce73f0784d8cd7094d126a5db7ded620af9 +size 891507 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+orig.HEAD b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+orig.HEAD new file mode 100644 index 0000000..281cfbf --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+orig.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c48a03d8fddb61975c58b0a9495aec829bd5b2d118592198fcf5fe744fc500b4 +size 2210 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+tlrc.HEAD b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+tlrc.HEAD new file mode 100644 index 0000000..43d1bb7 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns+tlrc.HEAD @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:319c03337d948d1cc0de98e629bb93aa416daac066e30741a47095fb445320cd +size 8558 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xaff12.1D b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xaff12.1D new file mode 100644 index 0000000..46b4b37 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xaff12.1D @@ -0,0 +1,2 @@ +# 3dWarpDrive matrices (DICOM-to-DICOM, row-by-row): + 0.969572 -0.0273696 0.0143933 6.16267 0.0384888 0.937003 0.266185 -7.07547 -0.0502717 -0.308966 0.97552 1.96274 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xat.1D b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xat.1D new file mode 100644 index 0000000..2d7f729 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns.Xat.1D @@ -0,0 +1,3 @@ + 0.969572 -0.0273696 0.0143933 6.16267 + 0.0384888 0.937003 0.266185 -7.07547 + -0.0502717 -0.308966 0.97552 1.96274 diff --git a/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns_WarpDrive.log b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns_WarpDrive.log new file mode 100644 index 0000000..b9e43d8 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sub-01_T1w_ns_WarpDrive.log @@ -0,0 +1 @@ +RMS[0] = 70.673 47.3833 ITER = 12/137 diff --git a/afni_no_motion_regressors/sub_001.results/sum_ideal.1D b/afni_no_motion_regressors/sub_001.results/sum_ideal.1D new file mode 100644 index 0000000..b42aed4 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/sum_ideal.1D @@ -0,0 +1,113 @@ +# + 0 + 0.269509 + 1.81918 + 3.46654 + 4.32523 + 4.34228 + 4.55292 + 4.39359 + 4.49986 + 4.45202 + 4.4324 + 4.50978 + 4.33082 + 4.5201 + 4.37151 + 4.52247 + 4.42823 + 4.44817 + 4.49935 + 4.39708 + 4.56211 + 4.45564 + 4.30506 + 2.85819 + 1.28754 + 0.445667 + 0.130356 + 0.0311898 + 0.00745076 + 0.269509 + 1.83727 + 3.51352 + 4.34803 + 4.35294 + 4.55648 + 4.35631 + 4.46208 + 4.43273 + 4.42468 + 4.51929 + 4.38264 + 4.55101 + 4.29822 + 4.43771 + 4.39871 + 4.43424 + 4.50208 + 4.38757 + 4.55928 + 4.45351 + 4.3249 + 2.90684 + 1.321 + 0.459875 + 0.135042 + 0.0323933 + 0.00775527 + 0.269509 + 1.85915 + 3.56717 + 4.3651 + 4.31986 + 4.52523 + 4.26134 + 4.35049 + 4.37804 + 4.35107 + 4.49695 + 4.32205 + 4.51691 + 4.37443 + 4.49894 + 4.4468 + 4.43628 + 4.51738 + 4.38332 + 4.55973 + 4.45343 + 4.35885 + 2.99632 + 1.38411 + 0.486986 + 0.144054 + 0.0347189 + 0.00834596 + 0.269509 + 1.85938 + 3.56773 + 4.374 + 4.36899 + 4.56346 + 4.3543 + 4.47091 + 4.39715 + 4.37137 + 4.47767 + 4.32093 + 4.51665 + 4.33488 + 4.48144 + 4.41898 + 4.44185 + 4.47662 + 4.28984 +# diff --git a/afni_no_motion_regressors/sub_001.results/warp.anat.Xat.1D b/afni_no_motion_regressors/sub_001.results/warp.anat.Xat.1D new file mode 100644 index 0000000..2d7f729 --- /dev/null +++ b/afni_no_motion_regressors/sub_001.results/warp.anat.Xat.1D @@ -0,0 +1,3 @@ + 0.969572 -0.0273696 0.0143933 6.16267 + 0.0384888 0.937003 0.266185 -7.07547 + -0.0502717 -0.308966 0.97552 1.96274