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# SET TRNS=air.func #SET $vars{"\\\$TRNS"}="air"; #air_path="@@@@@"; # # Transformations # #ANATOMICAL # reslice_warp TR air::reslice_warp2 ( none warp_in, none reslice_out, none overwrite, none menu_model, in input[], out output[]) { argument = warp_in; argument = reslice_out; argument = overwrite; argument = "-n " menu_model; } TR fsl::betpremask (none in_root, none out_root, input input[], output output[]) { argument = in_root; argument = out_root; } TR air::align_warp (none standard_file, none reslice_file, none model, in input[], out output[], out warp_out, none t1_thresh, none t2_thresh, none sampling, none initialization_file, none model, none final_model) { argument = standard_file; argument = reslice_file; argument = warp_out; argument = "-m " model; argument = final_model; argument = "-t1 " t1_thresh; argument = "-t2 " t2_thresh; argument = "-s " sampling; argument = initialization_file; } #FUNCTIONAL TR air::all (in input[]) { } TR air::reorient (in inhdr, in inimg, out outhdr, out outimg, none direction, none overwrite ) { argument = inhdr; argument = outhdr; argument = direction; argument = overwrite; } TR air::alignlinear (in stdhdr, in stdimg, in rshdr, in rsimg, out air, none args) { argument = stdhdr; argument = rshdr; argument = air; argument = args; } TR air::reslice (in air, in airimg, in airhdr, out img, out hdr, none args) { argument = air; argument = img; argument = args; } TR air::reslice2 (in air, in airimg, in airhdr, out img, out hdr, none args) { argument = air; argument = img; argument = args; } TR air::softmean (out img, out hdr, none args, in input[], in inputhdr[]) { argument = img; argument = args; argument = input; } TR air::combine_warp2 ( none warp_out, none overwrite, none air_file, none warp_in, in input[], out output[]) { argument = warp_out; argument = overwrite; argument = air_file; argument = warp_in; } TR air::combinewarp (out bnw, in shrink, in norm, in meanqa) { argument = bnw; argument = shrink; argument = norm; argument = meanqa; } # reslice_warp TR air::reslice_warp ( input boldnorm, out nrboldhdr, out nrboldimg, none arg1, in rboldhdr, in rboldimg, none arg2) { argument = boldnorm; argument = nrboldhdr; argument = arg1; argument = rboldhdr; argument = arg2; } TR air::strictmean (out img, out hdr, none args, in input[], inputimg[]) { argument = img; argument = args; argument = input; } TR air::binarize (in allimg, in allhdr, out maskimg, out maskhdr, none args) { argument = allimg; argument = maskimg; argument = args; } TR air::gsmooth (in hdr, none smoothing_kernel, in shdr, none args2, in boldimg, none args3, in img, out simg, in boldhdr) { argument = hdr; argument = smoothing_kernel; argument = shdr; argument = args2; argument = boldimg; argument = args3; } #ANATOMICAL # Eval: $vars{"\\\$user_directory"}="/home/yongzh/fmridc/output"; # Eval: $vars{"\\\$functional_dir"}="home/yongzh/fmridc/functional_data/"; # Eval: $vars{"\\\$anatomical_dir"}="home/yongzh/fmridc/anatomical_data/"; # Eval: $vars{"\\\$includes"}=""; DV dscheftn::reorient_0->air::reorient ( inhdr = @{input:"home/yongzh/fmridc/anatomical_data/hires.hdr"}, inimg = @{input:"home/yongzh/fmridc/anatomical_data/hires.img"}, outhdr = @{output:"home/yongzh/fmridc/anatomical_data/rhires-xy.hdr"}, outimg = @{output:"home/yongzh/fmridc/anatomical_data/rhires-xy.img"}, direction = "xy", overwrite = " " ); DV dscheftn::reorient_1->air::reorient ( inhdr = @{input:"home/yongzh/fmridc/anatomical_data/rhires-xy.hdr"}, inimg = @{input:"home/yongzh/fmridc/anatomical_data/rhires-xy.img"}, outhdr = @{output:"home/yongzh/fmridc/anatomical_data/rhires.hdr"}, outimg = @{output:"home/yongzh/fmridc/anatomical_data/rhires.img"}, direction = "xz", overwrite = " " ); DV dscheftn::betpremask_2->fsl::betpremask ( input = [ @{input:"home/yongzh/fmridc/anatomical_data/rhires.img"}, @{input:"home/yongzh/fmridc/anatomical_data/rhires.hdr"} ], output = [ @{output:"home/yongzh/fmridc/anatomical_data/brhires.img"}, @{output:"home/yongzh/fmridc/anatomical_data/brhires.hdr"} ], in_root = "home/yongzh/fmridc/anatomical_data/rhires", out_root = "home/yongzh/fmridc/anatomical_data/brhires" ); DV dscheftn::alignlinear_3->air::alignlinear ( stdhdr = @{input:"T1atlas.hdr"}, stdimg = @{input:"T1atlas.img"}, rshdr = @{input:"home/yongzh/fmridc/anatomical_data/brhires.hdr"}, rsimg = @{input:"home/yongzh/fmridc/anatomical_data/brhires.img"}, air = @{output:"home/yongzh/fmridc/anatomical_data/brhires.air"}, args = "-m 12 -t1 1000 -t2 1000 -s 81 3 3" ); DV dscheftn::align_warp_4->air::align_warp ( input = [ @{input:"T1atlas.hdr"}, @{input:"T1atlas.img"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.img"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.hdr"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.air"} ], output= [ @{output:"home/yongzh/fmridc/anatomical_data/brhires.warp"} ], standard_file = "T1atlas.hdr", reslice_file = "home/yongzh/fmridc/anatomical_data/brhires.hdr", warp_out = "home/yongzh/fmridc/anatomical_data/brhires.warp", initialization_file = "-f home/yongzh/fmridc/anatomical_data/brhires.air", sampling = "81 3 3", t1_thresh = "1000", t2_thresh = "1000", model = "1", final_model = "5" ); DV dscheftn::combine_warp2_5->air::combine_warp2 ( input = [ @{input:"shrink.air"}, # @{input:"reslice_hires"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.air"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.warp"} ], output = [ @{output:"home/yongzh/fmridc/anatomical_data/norm_hires.warp"} ], warp_out = "home/yongzh/fmridc/anatomical_data/norm_hires.warp", overwrite = " ", air_file = "home/yongzh/fmridc/anatomical_data/brhires.air", warp_in = "home/yongzh/fmridc/anatomical_data/brhires.warp" ); DV dscheftn::reslice_warp2_6->air::reslice_warp2 ( input = [ @{input:"home/yongzh/fmridc/anatomical_data/norm_hires.warp"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.img"}, @{input:"home/yongzh/fmridc/anatomical_data/brhires.hdr"} ], output = [ @{output:"home/yongzh/fmridc/anatomical_data/nhires.img"}, @{output:"home/yongzh/fmridc/anatomical_data/nhires.hdr"} ], reslice_out = "home/yongzh/fmridc/anatomical_data/nhires.hdr", warp_in = "home/yongzh/fmridc/anatomical_data/norm_hires.warp", menu_model = "2 9 9", overwrite = "-o" ); #FUNCTIONAL # BEGIN DATASET # Member bold1_i0002: DV dscheftn::reorient_7->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0002.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0002.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0002.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0002.img"}, direction = "y", overwrite = " " ); # Member bold1_i0003: DV dscheftn::reorient_8->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0003.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0003.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0003.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0003.img"}, direction = "y", overwrite = " " ); # Member bold1_i0004: DV dscheftn::reorient_9->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0004.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0004.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0004.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0004.img"}, direction = "y", overwrite = " " ); # Member bold1_i0005: DV dscheftn::reorient_10->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0005.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0005.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0005.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0005.img"}, direction = "y", overwrite = " " ); # Member bold1_i0006: DV dscheftn::reorient_11->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0006.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0006.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0006.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0006.img"}, direction = "y", overwrite = " " ); # Member bold1_i0007: DV dscheftn::reorient_12->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0007.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0007.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0007.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0007.img"}, direction = "y", overwrite = " " ); # Member bold1_i0008: DV dscheftn::reorient_13->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0008.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0008.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0008.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0008.img"}, direction = "y", overwrite = " " ); # Member bold1_i0009: DV dscheftn::reorient_14->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0009.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0009.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0009.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0009.img"}, direction = "y", overwrite = " " ); # Member bold1_i0010: DV dscheftn::reorient_15->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/bold1_i0010.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/bold1_i0010.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0010.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rbold1_i0010.img"}, direction = "y", overwrite = " " ); # END DATASET # BEGIN DATASET # Member bold1_i0002: DV dscheftn::reorient_16->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0002.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0002.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0002.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0002.img"}, direction = "x", overwrite = " " ); # Member bold1_i0003: DV dscheftn::reorient_17->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0003.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0003.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0003.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0003.img"}, direction = "x", overwrite = " " ); # Member bold1_i0004: DV dscheftn::reorient_18->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0004.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0004.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0004.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0004.img"}, direction = "x", overwrite = " " ); # Member bold1_i0005: DV dscheftn::reorient_19->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0005.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0005.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0005.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0005.img"}, direction = "x", overwrite = " " ); # Member bold1_i0006: DV dscheftn::reorient_20->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0006.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0006.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0006.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0006.img"}, direction = "x", overwrite = " " ); # Member bold1_i0007: DV dscheftn::reorient_21->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0007.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0007.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0007.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0007.img"}, direction = "x", overwrite = " " ); # Member bold1_i0008: DV dscheftn::reorient_22->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0008.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0008.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0008.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0008.img"}, direction = "x", overwrite = " " ); # Member bold1_i0009: DV dscheftn::reorient_23->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0009.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0009.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0009.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0009.img"}, direction = "x", overwrite = " " ); # Member bold1_i0010: DV dscheftn::reorient_24->air::reorient ( inhdr = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0010.hdr"}, inimg = @{in:"home/yongzh/fmridc/functional_data/rbold1_i0010.img"}, outhdr = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0010.hdr"}, outimg = @{out:"home/yongzh/fmridc/functional_data/rrbold1_i0010.img"}, direction = "x", overwrite = " " ); # END DATASET # Eval: $vars{"\\\$STDVOL"}=rr.$datasets{"BOLDSEQ"}[0]; # SETD STDVOL=RANDOM(4,$BOLDSEQ) #TR alignlinear (in stdhdr, in stdimg, in rshdr, in rsimg, out air, none args) #NEED TO TALK TO JED ABOUT THIS NEED TO FIND THE StandardVolume=`ls -1 ${FUNCTIONAL}/rbold*.img | head -1` # BEGIN DATASET # Member bold1_i0001: DV dscheftn::alignlinear_25->air::alignlinear ( stdhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.hdr"}, stdimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.img"}, rshdr = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0001.hdr"}, rsimg = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0001.img"}, air = @{output:"home/yongzh/fmridc/functional_data/rbold1_i0001.air"}, args = "-m 12 -t1 1000 -t2 1000 -s 81 3 3" ); # Member bold1_i0002: DV dscheftn::alignlinear_26->air::alignlinear ( stdhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.hdr"}, stdimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.img"}, rshdr = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0002.hdr"}, rsimg = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0002.img"}, air = @{output:"home/yongzh/fmridc/functional_data/rbold1_i0002.air"}, args = "-m 12 -t1 1000 -t2 1000 -s 81 3 3" ); # Member bold1_i0003: DV dscheftn::alignlinear_27->air::alignlinear ( stdhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.hdr"}, stdimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.img"}, rshdr = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0003.hdr"}, rsimg = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0003.img"}, air = @{output:"home/yongzh/fmridc/functional_data/rbold1_i0003.air"}, args = "-m 12 -t1 1000 -t2 1000 -s 81 3 3" ); # END DATASET # BEGIN DATASET # Member bold1_i0001: DV dscheftn::reslice_28->air::reslice ( air = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0001.air"}, airimg = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0001.img"}, airhdr = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0001.hdr"}, img = @{output:"home/yongzh/fmridc/functional_data/arbold1_i0001.img"}, hdr = @{output:"home/yongzh/fmridc/functional_data/arbold1_i0001.hdr"}, args = "-o -k" ); # Member bold1_i0002: DV dscheftn::reslice_29->air::reslice ( air = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0002.air"}, airimg = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0002.img"}, airhdr = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0002.hdr"}, img = @{output:"home/yongzh/fmridc/functional_data/arbold1_i0002.img"}, hdr = @{output:"home/yongzh/fmridc/functional_data/arbold1_i0002.hdr"}, args = "-o -k" ); # Member bold1_i0003: DV dscheftn::reslice_30->air::reslice ( air = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0003.air"}, airimg = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0003.img"}, airhdr = @{input:"home/yongzh/fmridc/functional_data/rrbold1_i0003.hdr"}, img = @{output:"home/yongzh/fmridc/functional_data/arbold1_i0003.img"}, hdr = @{output:"home/yongzh/fmridc/functional_data/arbold1_i0003.hdr"}, args = "-o -k" ); # END DATASET DV dscheftn::softmean_31->air::softmean ( img = @{output:"home/yongzh/fmridc/functional_data/mean.img"}, hdr = @{output:"home/yongzh/fmridc/functional_data/mean.hdr"}, args = "y null", input = [ # BEGIN DATASET # Member bold1_i0001: @{input:"home/yongzh/fmridc/functional_data/arbold1_i0001.img"}, # Member bold1_i0002: @{input:"home/yongzh/fmridc/functional_data/arbold1_i0002.img"}, # Member bold1_i0003: @{input:"home/yongzh/fmridc/functional_data/arbold1_i0003.img"}, # END DATASET ], inputhdr = [ # BEGIN DATASET # Member bold1_i0001: @{input:"home/yongzh/fmridc/functional_data/arbold1_i0001.hdr"}, # Member bold1_i0002: @{input:"home/yongzh/fmridc/functional_data/arbold1_i0002.hdr"}, # Member bold1_i0003: @{input:"home/yongzh/fmridc/functional_data/arbold1_i0003.hdr"}, # END DATASET ] ); DV dscheftn::alignlinear_32->air::alignlinear ( stdhdr = @{in:"home/yongzh/fmridc/anatomical_data/brhires.hdr"}, stdimg = @{in:"home/yongzh/fmridc/anatomical_data/brhires.img"}, rshdr = @{in:"home/yongzh/fmridc/functional_data/mean.hdr"}, rsimg = @{in:"home/yongzh/fmridc/functional_data/mean.img"}, air = @{out:"home/yongzh/fmridc/functional_data/mean-qa.air"}, args = "-m 6 -t1 1000 -p2 4" ); DV dscheftn::reslice2_33->air::reslice2 ( air = @{input:"home/yongzh/fmridc/functional_data/mean-qa.air"}, airimg = @{input:"home/yongzh/fmridc/functional_data/mean.img"}, airhdr = @{input:"home/yongzh/fmridc/functional_data/mean.hdr"}, img = @{output:"home/yongzh/fmridc/functional_data/mean-qa.img"}, hdr = @{output:"home/yongzh/fmridc/functional_data/mean-qa.hdr"}, args = "-o -k" ); DV dscheftn::combinewarp_34->air::combinewarp ( bnw = @{output:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, # shrink = @{input:"shrink.air"}, shrink = @{input:"shrink.air"}, norm = @{input:"home/yongzh/fmridc/anatomical_data/norm_hires.warp"}, meanqa = @{input:"home/yongzh/fmridc/functional_data/mean-qa.air"} ); # BEGIN DATASET # Member bold1_i0002: DV dscheftn::reslice_warp_35->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0002.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0002.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0002.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0002.img"}, arg2 = "-o" ); # Member bold1_i0003: DV dscheftn::reslice_warp_36->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0003.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0003.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0003.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0003.img"}, arg2 = "-o" ); # Member bold1_i0004: DV dscheftn::reslice_warp_37->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0004.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0004.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0004.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0004.img"}, arg2 = "-o" ); # Member bold1_i0005: DV dscheftn::reslice_warp_38->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0005.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0005.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0005.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0005.img"}, arg2 = "-o" ); # Member bold1_i0006: DV dscheftn::reslice_warp_39->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0006.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0006.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0006.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0006.img"}, arg2 = "-o" ); # Member bold1_i0007: DV dscheftn::reslice_warp_40->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0007.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0007.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0007.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0007.img"}, arg2 = "-o" ); # Member bold1_i0008: DV dscheftn::reslice_warp_41->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0008.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0008.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0008.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0008.img"}, arg2 = "-o" ); # Member bold1_i0009: DV dscheftn::reslice_warp_42->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0009.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0009.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0009.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0009.img"}, arg2 = "-o" ); # Member bold1_i0010: DV dscheftn::reslice_warp_43->air::reslice_warp ( boldnorm = @{input:"home/yongzh/fmridc/functional_data/bold_norm.warp"}, nrboldhdr = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0010.hdr"}, nrboldimg = @{output:"home/yongzh/fmridc/functional_data/nrbold1_i0010.img"}, arg1 = "-a", rboldhdr = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0010.hdr"}, rboldimg = @{input:"home/yongzh/fmridc/functional_data/rbold1_i0010.img"}, arg2 = "-o" ); # END DATASET DV dscheftn::strictmean_44->air::strictmean ( img = @{output:"home/yongzh/fmridc/functional_data/mean_all.img"}, hdr = @{output:"home/yongzh/fmridc/functional_data/mean_all.hdr"}, args = "y null", input = [ # BEGIN DATASET # Member bold1_i0002: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0002.hdr"}, # Member bold1_i0003: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0003.hdr"}, # Member bold1_i0004: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0004.hdr"}, # Member bold1_i0005: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0005.hdr"}, # Member bold1_i0006: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0006.hdr"}, # Member bold1_i0007: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0007.hdr"}, # Member bold1_i0008: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0008.hdr"}, # Member bold1_i0009: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0009.hdr"}, # Member bold1_i0010: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0010.hdr"}, # END DATASET ], inputimg = [ # BEGIN DATASET # Member bold1_i0002: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0002.img"}, # Member bold1_i0003: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0003.img"}, # Member bold1_i0004: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0004.img"}, # Member bold1_i0005: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0005.img"}, # Member bold1_i0006: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0006.img"}, # Member bold1_i0007: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0007.img"}, # Member bold1_i0008: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0008.img"}, # Member bold1_i0009: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0009.img"}, # Member bold1_i0010: @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0010.img"}, # END DATASET ] ); DV dscheftn::binarize_45->air::binarize ( allimg = @{input:"home/yongzh/fmridc/functional_data/mean_all.img"}, allhdr = @{input:"home/yongzh/fmridc/functional_data/mean_all.hdr"}, maskimg = @{output:"home/yongzh/fmridc/functional_data/bold_mask.img"}, maskhdr = @{output:"home/yongzh/fmridc/functional_data/bold_mask.hdr"}, args = "y" ); # BEGIN DATASET # Member bold1_i0002: DV dscheftn::gsmooth_46->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0002.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0002.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0002.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0002.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0003: DV dscheftn::gsmooth_47->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0003.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0003.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0003.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0003.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0004: DV dscheftn::gsmooth_48->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0004.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0004.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0004.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0004.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0005: DV dscheftn::gsmooth_49->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0005.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0005.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0005.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0005.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0006: DV dscheftn::gsmooth_50->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0006.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0006.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0006.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0006.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0007: DV dscheftn::gsmooth_51->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0007.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0007.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0007.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0007.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0008: DV dscheftn::gsmooth_52->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0008.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0008.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0008.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0008.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0009: DV dscheftn::gsmooth_53->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0009.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0009.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0009.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0009.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # Member bold1_i0010: DV dscheftn::gsmooth_54->air::gsmooth ( hdr = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0010.hdr"}, smoothing_kernel = "6 6 6", shdr = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0010.hdr"}, args2 = "-m", boldimg = @{input:"home/yongzh/fmridc/functional_data/bold_mask.img"}, args3 = "-o" img = @{input:"home/yongzh/fmridc/functional_data/nrbold1_i0010.img"}, simg = @{output:"home/yongzh/fmridc/functional_data/snrbold1_i0010.img"}, boldhdr = @{input:"home/yongzh/fmridc/functional_data/bold_mask.hdr"} ); # END DATASET DV dscheftn::all_55->air::all ( input = [ # BEGIN DATASET # Member bold1_i0002: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0002.hdr"}, # Member bold1_i0003: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0003.hdr"}, # Member bold1_i0004: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0004.hdr"}, # Member bold1_i0005: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0005.hdr"}, # Member bold1_i0006: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0006.hdr"}, # Member bold1_i0007: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0007.hdr"}, # Member bold1_i0008: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0008.hdr"}, # Member bold1_i0009: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0009.hdr"}, # Member bold1_i0010: @{input:"home/yongzh/fmridc/functional_data/snrbold1_i0010.hdr"}, # END DATASET ] );