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automated nidm example computation from github action
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GitHub Actions Bot committed Oct 4, 2024
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112 changes: 56 additions & 56 deletions examples/from_parsers/afni/afni_alt_onesided_proc.jsonld

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26 changes: 13 additions & 13 deletions examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
{
"@id": "urn:autobloc-v8H5Ogxq",
"Label": "auto block: setup",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
"bids::afni_one_sided_t_test/tone_counting_onset_times.txt",
Expand All @@ -26,7 +26,7 @@
{
"@id": "urn:autobloc-X3Kz90HY",
"Label": "auto block: tcat",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
"bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
Expand All @@ -35,7 +35,7 @@
{
"@id": "urn:autobloc-GVYJczpS",
"Label": "auto block: outcount",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
"bids::pb00.$subj.r$run.tcat+orig",
Expand All @@ -45,7 +45,7 @@
{
"@id": "urn:tshift-HGyQiLrF",
"Label": "tshift",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
"bids::pb00.$subj.r$run.tcat+orig"
Expand All @@ -54,7 +54,7 @@
{
"@id": "urn:align-dbfMq7NE",
"Label": "align",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
"bids::pb01.$subj.r01.tshift+orig",
Expand All @@ -64,7 +64,7 @@
{
"@id": "urn:tlrc-RV1CChcN",
"Label": "tlrc",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
"bids::TT_N27+tlrc",
Expand All @@ -75,7 +75,7 @@
{
"@id": "urn:volreg-qY8NgHG7",
"Label": "volreg",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$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$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
"bids::pb01.$subj.r$run.tshift+orig",
Expand All @@ -98,7 +98,7 @@
{
"@id": "urn:blur-2ufpOLNQ",
"Label": "blur",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
"bids::pb02.$subj.r$run.volreg+tlrc",
Expand All @@ -108,7 +108,7 @@
{
"@id": "urn:mask-YfQVxxPi",
"Label": "mask",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
"bids::pb03.$subj.r$run.blur+tlrc",
Expand All @@ -127,7 +127,7 @@
{
"@id": "urn:scale-GmmL0l7Q",
"Label": "scale",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dTstat -prefix rm.mean_r$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$run.scale; ",
"Used": [
"bids::pb03.$subj.r$run.blur+tlrc",
Expand All @@ -139,7 +139,7 @@
{
"@id": "urn:regress-JwuObKc8",
"Label": "regress",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -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 -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$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.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
"bids::dfile_rall.1D",
Expand All @@ -166,7 +166,7 @@
{
"@id": "urn:bluresti-QW19fifr",
"Label": "blur estimation",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
"bids::full_mask.$subj+tlrc",
Expand All @@ -177,7 +177,7 @@
{
"@id": "urn:autobloc-44jc0p9G",
"Label": "auto block: generate review scripts",
"AssociatedWith": "urn:urn:afni-CUfM2GF9",
"AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
"bids::pb00.$subj.r*.tcat+orig.HEAD"
Expand Down
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