TR air::alignlinear( in standard_hdr, in standard_img,
                     in reslice_hdr, in reslice_img,
                     out airfile, none args) {
   argument = ${standard_hdr};
   argument = ${reslice_hdr};
   argument = ${airfile};
   argument = args;
}

TR air::align_warp( in standard_hdr, in standard_img,
                     in reslice_hdr, in reslice_img,
                     out warpfile, none args) {
   argument = ${standard_hdr};
   argument = ${reslice_hdr};
   argument = ${warpfile};
   argument = args;
}

TR air::reslice( in input_hdr, in input_img,
                     out reslice_hdr, out reslice_img,
                     in airfile) {
   argument = ${airfile};
   argument = ${reslice_hdr};
}

TR air::reslice_warp( in input_hdr, in input_img,
                     out reslice_hdr, out reslice_img,
                     in warpfile) {
   argument = ${warpfile};
   argument = ${reslice_hdr};
}

TR air::definecommon_air(in in_airfiles[], out out_airfiles[],
                         none args) {
   argument = args;
   argument = ${in_airfiles};
}

TR air::softmean(in reslice_hdr[], in reslice_img[], out avg_hdr,
                 out avg_img, none args) {
   argument = ${avg_hdr};
   argument = args;
   argument = ${reslice_hdr};
}

TR fsl::slicer(in volume_hdr[], in volume_img[], out jpeg,
            none plane, none slice) {
   argument = ${volume_hdr};
   argument = plane;
   argument = slice;
   argument = ${jpeg};
}

TR fsl::convert (in input_img, out output_img) {
    argument = ${input_img};
    argument = ${output_img};
}

DV ipaw1::alignlinear_wf2_reference->air::alignlinear(
    standard_hdr = @{in:"reference.hdr"},
    standard_img = @{in:"reference.img"},
    reslice_hdr  = @{in:"reference.hdr"},
    reslice_img  = @{in:"reference.img"},
        airfile  = @{out:"soca/ipaw1/reference.air"},
           args  =  "-m 6 -t1 80 -t2 80 -s 81 27 3 -q"
);

DV ipaw1::reslice_wf2_reference->air::reslice(
   input_hdr = @{in:"reference.hdr"},
   input_img = @{in:"reference.img"},
   reslice_hdr = @{out:"soca/ipaw1/reference.sliced-linear.hdr"},
   reslice_img = @{out:"soca/ipaw1/reference.sliced-linear.img"},
     airfile = @{in:"soca/ipaw1/reference.air.aircommon"}
);

DV ipaw1::reslice_warp_wf2_reference->air::reslice_warp(
   input_hdr = @{in:"reference.hdr"},
   input_img = @{in:"reference.img"},
   reslice_hdr = @{out:"soca/ipaw1/reference.sliced-warp.hdr"},
   reslice_img = @{out:"soca/ipaw1/reference.sliced-warp.img"},
    warpfile = @{in:"soca/ipaw1/reference.warp"}
);

DV ipaw1::align_warp_wf2_reference->air::align_warp(
    standard_hdr = @{in:"soca/ipaw1/atlas-linear.hdr"},
    standard_img = @{in:"soca/ipaw1/atlas-linear.img"},
    reslice_hdr  = @{in:"reference.hdr"},
    reslice_img  = @{in:"reference.img"},
       warpfile  = @{out:"soca/ipaw1/reference.warp"},
           args  =  "-m 1 -t1 80 -t2 80 -s 81 27 18 -q"
);

DV ipaw1::alignlinear_wf2_101-3_anonymized->air::alignlinear(
    standard_hdr = @{in:"reference.hdr"},
    standard_img = @{in:"reference.img"},
    reslice_hdr  = @{in:"101-3_anonymized.hdr"},
    reslice_img  = @{in:"101-3_anonymized.img"},
        airfile  = @{out:"soca/ipaw1/101-3_anonymized.air"},
           args  =  "-m 6 -t1 80 -t2 80 -s 81 27 3 -q"
);

DV ipaw1::reslice_wf2_101-3_anonymized->air::reslice(
   input_hdr = @{in:"101-3_anonymized.hdr"},
   input_img = @{in:"101-3_anonymized.img"},
   reslice_hdr = @{out:"soca/ipaw1/101-3_anonymized.sliced-linear.hdr"},
   reslice_img = @{out:"soca/ipaw1/101-3_anonymized.sliced-linear.img"},
     airfile = @{in:"soca/ipaw1/101-3_anonymized.air.aircommon"}
);

DV ipaw1::reslice_warp_wf2_101-3_anonymized->air::reslice_warp(
   input_hdr = @{in:"101-3_anonymized.hdr"},
   input_img = @{in:"101-3_anonymized.img"},
   reslice_hdr = @{out:"soca/ipaw1/101-3_anonymized.sliced-warp.hdr"},
   reslice_img = @{out:"soca/ipaw1/101-3_anonymized.sliced-warp.img"},
    warpfile = @{in:"soca/ipaw1/101-3_anonymized.warp"}
);

DV ipaw1::align_warp_wf2_101-3_anonymized->air::align_warp(
    standard_hdr = @{in:"soca/ipaw1/atlas-linear.hdr"},
    standard_img = @{in:"soca/ipaw1/atlas-linear.img"},
    reslice_hdr  = @{in:"101-3_anonymized.hdr"},
    reslice_img  = @{in:"101-3_anonymized.img"},
       warpfile  = @{out:"soca/ipaw1/101-3_anonymized.warp"},
           args  =  "-m 1 -t1 80 -t2 80 -s 81 27 18 -q"
);

DV ipaw1::definecommon_air_wf2->air::definecommon_air(
      args = "null null null .aircommon y",
  in_airfiles = [
         @{in:"soca/ipaw1/reference.air"},
         @{in:"soca/ipaw1/101-3_anonymized.air"}
                ],
  out_airfiles = [
         @{out:"soca/ipaw1/reference.air.aircommon"},
         @{out:"soca/ipaw1/101-3_anonymized.air.aircommon"}
                ]
);

DV ipaw1::softmean_wf2_sliced-linear->air::softmean(
 avg_hdr = @{out:"soca/ipaw1/atlas-linear.hdr"},
 avg_img = @{out:"soca/ipaw1/atlas-linear.img"},
 args = " y null",
 reslice_hdr = [
       @{in:"soca/ipaw1/reference.sliced-linear.hdr"},
       @{in:"soca/ipaw1/101-3_anonymized.sliced-linear.hdr"}
               ],
 reslice_img = [
       @{in:"soca/ipaw1/reference.sliced-linear.img"},
       @{in:"soca/ipaw1/101-3_anonymized.sliced-linear.img"}
               ]
);

DV ipaw1::softmean_wf2_sliced-warp->air::softmean(
 avg_hdr = @{out:"soca/ipaw1/atlas.hdr"},
 avg_img = @{out:"soca/ipaw1/atlas.img"},
 args = " y null",
 reslice_hdr = [
       @{in:"soca/ipaw1/reference.sliced-warp.hdr"},
       @{in:"soca/ipaw1/101-3_anonymized.sliced-warp.hdr"}
               ],
 reslice_img = [
       @{in:"soca/ipaw1/reference.sliced-warp.img"},
       @{in:"soca/ipaw1/101-3_anonymized.sliced-warp.img"}
               ]
);

DV ipaw1::slicer_atlas_-x->fsl::slicer (
    volume_hdr = @{in:"soca/ipaw1/atlas.hdr"},
    volume_img = @{in:"soca/ipaw1/atlas.img"},
    jpeg = @{out:"soca/ipaw1/atlas-x.pgm"},
    plane = "-x",
    slice = ".5"
);

DV ipaw1::slicer_atlas_-y->fsl::slicer (
    volume_hdr = @{in:"soca/ipaw1/atlas.hdr"},
    volume_img = @{in:"soca/ipaw1/atlas.img"},
    jpeg = @{out:"soca/ipaw1/atlas-y.pgm"},
    plane = "-y",
    slice = ".5"
);

DV ipaw1::slicer_atlas_-z->fsl::slicer (
    volume_hdr = @{in:"soca/ipaw1/atlas.hdr"},
    volume_img = @{in:"soca/ipaw1/atlas.img"},
    jpeg = @{out:"soca/ipaw1/atlas-z.pgm"},
    plane = "-z",
    slice = ".5"
);

DV ipaw1::converter_atlas-x.pgm->fsl::convert (
 input_img = @{in:"soca/ipaw1/atlas-x.pgm"},
 output_img = @{out:"soca/ipaw1/atlas-x.gif"}
);

DV ipaw1::converter_atlas-y.pgm->fsl::convert (
 input_img = @{in:"soca/ipaw1/atlas-y.pgm"},
 output_img = @{out:"soca/ipaw1/atlas-y.gif"}
);

DV ipaw1::converter_atlas-z.pgm->fsl::convert (
 input_img = @{in:"soca/ipaw1/atlas-z.pgm"},
 output_img = @{out:"soca/ipaw1/atlas-z.gif"}
);
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