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Remi-GauRemi-Gau
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Merge pull request #716 from Remi-Gau/enh_trans
[FIX] support globbing patterns to specify conditions in design matrix
2 parents af0ee62 + 8307689 commit 91e3fed

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8 files changed

+652
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‎demos/transformers/.gitignore‎

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*.mat
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new_events.tsv
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transformers.json

‎demos/transformers/data/sub-03_task-VisuoTact_run-02_events.tsv‎

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onset duration trial_type expected_response given_response response_time
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0.000 1.358 BASE 0 0 0.000
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1.358 2.026 CONG_LEFT 0 0 0.000
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3.384 1.714 ISI 0 0 0.000
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5.098 2.026 REST 0 0 0.000
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7.124 2.047 ISI 0 0 0.000
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9.171 2.046 P_LEFT 0 0 0.000
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11.217 1.893 ISI 0 0 0.000
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13.110 1.712 RESPONSE_P_LEFT 1 0 2147483.647
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14.822 1.693 ISI 0 0 0.000
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16.515 2.046 REST 0 0 0.000
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18.561 2.381 ISI 0 0 0.000
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20.942 2.028 INCONG_VR_PL 0 0 0.000
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22.970 2.314 ISI 0 0 0.000
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25.284 2.047 CONG_RIGHT 0 0 0.000
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27.331 1.959 ISI 0 0 0.000
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29.290 2.047 INCONG_VL_PR 0 0 0.000
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31.337 1.712 ISI 0 0 0.000
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33.049 2.027 V_LEFT 0 0 0.000
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35.076 2.180 ISI 0 0 0.000
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37.256 1.692 RESPONSE_V_LEFT 1 0 2147483.647
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38.948 1.914 ISI 0 0 0.000
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40.862 2.047 P_RIGHT 0 0 0.000
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42.909 2.294 ISI 0 0 0.000
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45.203 2.047 V_RIGHT 0 0 0.000
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47.250 2.381 ISI 0 0 0.000
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49.631 2.046 P_LEFT 0 0 0.000
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51.677 1.693 ISI 0 0 0.000
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53.370 2.046 INCONG_VL_PR 0 0 0.000
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55.416 1.961 ISI 0 0 0.000
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57.377 1.712 RESPONSE_INCONG_VL_PR 1 0 2147483.647
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59.089 1.692 ISI 0 0 0.000
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60.781 2.047 V_RIGHT 0 0 0.000
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62.828 2.114 ISI 0 0 0.000
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64.942 2.026 CONG_RIGHT 0 0 0.000
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66.968 2.180 ISI 0 0 0.000
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69.148 1.693 RESPONSE_CONG_RIGHT 1 0 2147483.647
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70.841 2.046 ISI 0 0 0.000
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72.887 2.048 INCONG_VR_PL 0 0 0.000
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74.935 2.180 ISI 0 0 0.000
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77.115 2.027 P_RIGHT 0 0 0.000
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79.142 2.180 ISI 0 0 0.000
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81.322 2.047 CONG_LEFT 0 0 0.000
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83.369 2.160 ISI 0 0 0.000
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85.529 2.047 V_LEFT 0 0 0.000
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87.576 1.980 ISI 0 0 0.000
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89.556 1.692 RESPONSE_V_LEFT 1 0 2147483.647
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91.248 1.914 ISI 0 0 0.000
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93.162 2.026 REST 0 0 0.000
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95.188 2.114 ISI 0 0 0.000
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97.302 2.047 REST 0 0 0.000
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99.349 1.759 ISI 0 0 0.000
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101.108 2.046 CONG_RIGHT 0 0 0.000
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103.154 1.692 ISI 0 0 0.000
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104.846 2.047 REST 0 0 0.000
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106.893 2.381 ISI 0 0 0.000
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109.274 2.028 P_LEFT 0 0 0.000
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111.302 1.913 ISI 0 0 0.000
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113.215 1.692 RESPONSE_P_LEFT 1 0 2147483.647
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114.907 2.180 ISI 0 0 0.000
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117.087 2.047 REST 0 0 0.000
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119.134 2.113 ISI 0 0 0.000
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121.247 2.027 V_LEFT 0 0 0.000
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123.274 2.381 ISI 0 0 0.000
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125.655 2.048 INCONG_VL_PR 0 0 0.000
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127.703 1.826 ISI 0 0 0.000
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129.529 2.046 P_RIGHT 0 0 0.000
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131.575 1.846 ISI 0 0 0.000
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133.421 2.027 INCONG_VR_PL 0 0 0.000
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135.448 1.913 ISI 0 0 0.000
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137.361 1.692 RESPONSE_INCONG_VR_PL 1 0 2147483.647
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139.053 2.247 ISI 0 0 0.000
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141.300 2.047 V_RIGHT 0 0 0.000
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143.347 2.382 ISI 0 0 0.000
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145.729 2.026 CONG_LEFT 0 0 0.000
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147.755 1.980 ISI 0 0 0.000
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149.735 2.047 CONG_LEFT 0 0 0.000
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151.782 1.893 ISI 0 0 0.000
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153.675 1.692 RESPONSE_CONG_LEFT 1 0 2147483.647
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155.367 2.113 ISI 0 0 0.000
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157.480 2.047 REST 0 0 0.000
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159.527 1.759 ISI 0 0 0.000
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161.286 2.048 P_RIGHT 0 0 0.000
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163.334 1.979 ISI 0 0 0.000
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165.313 2.027 INCONG_VR_PL 0 0 0.000
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167.340 1.980 ISI 0 0 0.000
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169.320 2.046 REST 0 0 0.000
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171.366 1.759 ISI 0 0 0.000
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173.125 2.047 INCONG_VL_PR 0 0 0.000
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175.172 1.960 ISI 0 0 0.000
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177.132 2.046 P_LEFT 0 0 0.000
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179.178 1.760 ISI 0 0 0.000
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180.938 2.047 V_RIGHT 0 0 0.000
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182.985 2.114 ISI 0 0 0.000
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185.099 1.692 RESPONSE_V_RIGHT 1 0 2147483.647
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186.791 2.247 ISI 0 0 0.000
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189.038 2.047 V_LEFT 0 0 0.000
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191.085 1.692 ISI 0 0 0.000
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192.777 2.047 CONG_RIGHT 0 0 0.000
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194.824 2.093 ISI 0 0 0.000
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196.917 2.048 INCONG_VR_PL 0 0 0.000
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198.965 2.247 ISI 0 0 0.000
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201.212 1.692 RESPONSE_INCONG_VR_PL 1 0 2147483.647
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202.904 1.779 ISI 0 0 0.000
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204.683 2.027 CONG_LEFT 0 0 0.000
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206.710 1.846 ISI 0 0 0.000
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208.556 2.047 INCONG_VL_PR 0 0 0.000
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210.603 1.959 ISI 0 0 0.000
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212.562 2.048 REST 0 0 0.000
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214.610 2.113 ISI 0 0 0.000
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216.723 2.027 CONG_RIGHT 0 0 0.000
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218.750 1.712 ISI 0 0 0.000
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220.462 1.692 RESPONSE_CONG_RIGHT 1 0 2147483.647
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222.154 2.047 ISI 0 0 0.000
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224.201 2.027 REST 0 0 0.000
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226.228 2.046 ISI 0 0 0.000
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228.274 2.047 V_LEFT 0 0 0.000
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230.321 2.161 ISI 0 0 0.000
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232.482 2.047 V_RIGHT 0 0 0.000
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234.529 1.846 ISI 0 0 0.000
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236.375 2.026 P_LEFT 0 0 0.000
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238.401 2.315 ISI 0 0 0.000
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240.716 2.046 P_RIGHT 0 0 0.000
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242.762 2.381 ISI 0 0 0.000
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245.143 1.692 RESPONSE_P_RIGHT 1 0 2147483.647
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246.835 2.047 ISI 0 0 0.000
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248.882 2.048 V_LEFT 0 0 0.000
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250.930 2.294 ISI 0 0 0.000
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253.224 2.047 V_RIGHT 0 0 0.000
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255.271 2.046 ISI 0 0 0.000
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257.317 2.027 CONG_LEFT 0 0 0.000
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259.344 1.913 ISI 0 0 0.000
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261.257 2.046 P_LEFT 0 0 0.000
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263.303 2.227 ISI 0 0 0.000
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265.530 2.048 INCONG_VR_PL 0 0 0.000
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267.578 1.846 ISI 0 0 0.000
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269.424 2.027 P_RIGHT 0 0 0.000
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271.451 2.381 ISI 0 0 0.000
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273.832 1.712 RESPONSE_P_RIGHT 1 0 2147483.647
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275.544 1.960 ISI 0 0 0.000
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277.504 2.046 REST 0 0 0.000
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279.550 2.114 ISI 0 0 0.000
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281.664 2.026 REST 0 0 0.000
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283.690 2.115 ISI 0 0 0.000
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285.805 2.047 CONG_RIGHT 0 0 0.000
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287.852 1.759 ISI 0 0 0.000
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289.611 2.046 INCONG_VL_PR 0 0 0.000
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291.657 1.693 ISI 0 0 0.000
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293.350 1.712 RESPONSE_INCONG_VL_PR 1 0 2147483.647
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295.062 2.294 ISI 0 0 0.000
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297.356 2.047 V_LEFT 0 0 0.000
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299.403 1.846 ISI 0 0 0.000
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301.249 2.027 P_RIGHT 0 0 0.000
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303.276 2.314 ISI 0 0 0.000
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305.590 2.047 CONG_LEFT 0 0 0.000
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307.637 2.381 ISI 0 0 0.000
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310.018 1.692 RESPONSE_CONG_LEFT 1 0 2147483.647
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311.710 2.314 ISI 0 0 0.000
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314.024 2.047 CONG_RIGHT 0 0 0.000
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316.071 2.180 ISI 0 0 0.000
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318.251 2.028 REST 0 0 0.000
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320.279 2.180 ISI 0 0 0.000
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322.459 2.047 V_RIGHT 0 0 0.000
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324.506 1.826 ISI 0 0 0.000
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326.332 1.712 RESPONSE_V_RIGHT 1 0 2147483.647
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328.044 1.893 ISI 0 0 0.000
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329.937 2.047 INCONG_VR_PL 0 0 0.000
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331.984 2.093 ISI 0 0 0.000
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334.077 2.047 P_LEFT 0 0 0.000
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336.124 2.248 ISI 0 0 0.000
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338.372 2.047 INCONG_VL_PR 0 0 0.000
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340.419 1.959 ISI 0 0 0.000
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342.378 2.047 REST 0 0 0.000
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344.425 2.381 ISI 0 0 0.000
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346.806 1.360 BASE 0 0 0.000

‎demos/transformers/models/model-VisuoTact_smdl.json‎

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{
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"Name": "demo transformers",
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"BIDSModelVersion": "1.0.0",
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"Description": "demo transformers",
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"Input": {
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"task": [
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"VisuoTact"
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],
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"space": [
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"IXI549Space"
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]
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},
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"Nodes": [
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{
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"Level": "Run",
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"Name": "run_level",
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"GroupBy": [
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"run",
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"subject"
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],
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"Transformations": {
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"Transformer": "bids-matlab_v0.1.0dev",
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"Instructions": [
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{
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"Name": "Replace",
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"Input": "trial_type",
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"Replace": {
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"key": "^RESPONSE.*",
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"value": "RESPONSE"
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},
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"Attribute": "value"
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},
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{
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"Name": "Filter",
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"Input": "trial_type",
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"Query": "trial_type==^.*LEFT$",
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"Output": "tmp"
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},
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{
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"Name": "LabelIdenticalRows",
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"Cumulative": true,
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"Input": [
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"tmp"
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],
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"Output": [
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"label"
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]
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},
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{
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"Name": "Concatenate",
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"Input": [
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"tmp",
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"label"
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],
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"Output": [
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"LEFT"
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]
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},
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{
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"Name": "Delete",
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"Input": [
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"tmp",
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"label"
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]
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},
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{
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"Name": "Filter",
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"Input": "trial_type",
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"Query": "trial_type==^.*RIGHT$",
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"Output": "tmp"
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},
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{
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"Name": "LabelIdenticalRows",
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"Cumulative": true,
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"Input": [
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"tmp"
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],
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"Output": [
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"label"
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]
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},
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{
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"Name": "Concatenate",
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"Input": [
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"tmp",
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"label"
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],
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"Output": [
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"RIGHT"
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]
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},
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{
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"Name": "Delete",
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"Input": [
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"tmp",
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"label"
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]
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},
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{
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"Name": "Filter",
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"Input": "trial_type",
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"Query": "trial_type==^INCONG.*$",
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"Output": "tmp"
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},
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{
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"Name": "LabelIdenticalRows",
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"Cumulative": true,
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"Input": [
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"tmp"
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],
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"Output": [
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"label"
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]
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},
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{
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"Name": "Concatenate",
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"Input": [
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"tmp",
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"label"
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],
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"Output": [
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"INCONG"
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]
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},
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{
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"Name": "Delete",
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"Input": [
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"tmp",
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"label"
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]
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}
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]
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},
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"Model": {
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"X": [
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"trial_type.REST",
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"LEFT.P_LEFT_?",
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"LEFT.V_LEFT_?",
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"LEFT.CONG_LEFT_?",
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"RIGHT.P_RIGHT_?",
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"RIGHT.V_RIGHT_?",
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"RIGHT.CONG_RIGHT_?",
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"INCONG.INCONG*"
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],
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"HRF": {
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"Variables": [
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"trial_type.REST",
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"LEFT.P_LEFT_?",
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"LEFT.V_LEFT_?",
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"LEFT.CONG_LEFT_?",
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"RIGHT.P_RIGHT_?",
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"RIGHT.V_RIGHT_?",
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"RIGHT.CONG_RIGHT_?",
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"INCONG.INCONG*"
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],
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"Model": "spm"
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},
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"Type": "glm",
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"Options": {
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"HighPassFilterCutoffHz": 0.0078,
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"Mask": {
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"suffix": [
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"mask"
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],
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"desc": [
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"brain"
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]
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}
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},
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"Software": {
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"SPM": {
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"SerialCorrelation": "AR(1)"
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}
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}
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}
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}
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]
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}

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