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[FIX] fix lesion segmentation output (and refactor) #727

Merged
merged 25 commits into from
Jul 20, 2022
Merged

[FIX] fix lesion segmentation output (and refactor) #727

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c65c09e
upgrade transformers and allow for globbing patterns in conditions in…
Remi-Gau Jul 10, 2022
f0a7753
refactor
Remi-Gau Jul 10, 2022
b930418
refactor
Remi-Gau Jul 10, 2022
2741a9c
add demo and update
Remi-Gau Jul 10, 2022
0ff6f32
update bids matlab
Remi-Gau Jul 11, 2022
ad7354b
update bids-matlab
Remi-Gau Jul 11, 2022
e572543
adpat getOptionsFromModel to new schema
Remi-Gau Jul 11, 2022
5795c33
update demo
Remi-Gau Jul 11, 2022
8307689
Merge branch 'main' into enh_trans
Remi-Gau Jul 20, 2022
1b4588d
add more explicit error message for input parsing of getData
Remi-Gau Jul 20, 2022
7e3f24f
Merge branch 'main' into fixes
Remi-Gau Jul 20, 2022
91e3fed
Merge pull request #716 from Remi-Gau/enh_trans
Remi-Gau Jul 20, 2022
eeb9a71
Merge pull request #726 from Remi-Gau/fixes
Remi-Gau Jul 20, 2022
f00b36c
refactor renaming functions
Remi-Gau Jul 20, 2022
2df8fc7
misc
Remi-Gau Jul 20, 2022
bc32b93
Merge branch 'main' into lesion_seg
Remi-Gau Jul 20, 2022
9d55fff
refactor renaming config for lesion segmentation
Remi-Gau Jul 20, 2022
bb9765e
refactor renaming config lesion segmentation
Remi-Gau Jul 20, 2022
5ee1360
refactor renaming configuration
Remi-Gau Jul 20, 2022
e8d89c4
Merge branch 'dev' into lesion_seg
Remi-Gau Jul 20, 2022
0d2a105
adapt renaming of lesion segmentation to chosen options
Remi-Gau Jul 20, 2022
f78c17a
add dummy test data
Remi-Gau Jul 20, 2022
cc9db49
resize ALI mask in function of chosen options
Remi-Gau Jul 20, 2022
ee05cad
deal with multiple iterations renaming
Remi-Gau Jul 20, 2022
81f4f67
adapt tests
Remi-Gau Jul 20, 2022
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4 changes: 2 additions & 2 deletions demos/lesion_detection/run_lesion.m
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,10 @@

bidsCopyInputFolder(opt);

% Step 1: segmentation
%% Step 1: segmentation
bidsLesionSegmentation(opt);

% % Step 2: lesion abnormalities
%% Step 2: lesion abnormalities
bidsLesionAbnormalitiesDetection(opt);

% % Step 3: overlap map
Expand Down
3 changes: 3 additions & 0 deletions demos/transformers/.gitignore
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@@ -0,0 +1,3 @@
*.mat
new_events.tsv
transformers.json
175 changes: 175 additions & 0 deletions 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
0.000 1.358 BASE 0 0 0.000
1.358 2.026 CONG_LEFT 0 0 0.000
3.384 1.714 ISI 0 0 0.000
5.098 2.026 REST 0 0 0.000
7.124 2.047 ISI 0 0 0.000
9.171 2.046 P_LEFT 0 0 0.000
11.217 1.893 ISI 0 0 0.000
13.110 1.712 RESPONSE_P_LEFT 1 0 2147483.647
14.822 1.693 ISI 0 0 0.000
16.515 2.046 REST 0 0 0.000
18.561 2.381 ISI 0 0 0.000
20.942 2.028 INCONG_VR_PL 0 0 0.000
22.970 2.314 ISI 0 0 0.000
25.284 2.047 CONG_RIGHT 0 0 0.000
27.331 1.959 ISI 0 0 0.000
29.290 2.047 INCONG_VL_PR 0 0 0.000
31.337 1.712 ISI 0 0 0.000
33.049 2.027 V_LEFT 0 0 0.000
35.076 2.180 ISI 0 0 0.000
37.256 1.692 RESPONSE_V_LEFT 1 0 2147483.647
38.948 1.914 ISI 0 0 0.000
40.862 2.047 P_RIGHT 0 0 0.000
42.909 2.294 ISI 0 0 0.000
45.203 2.047 V_RIGHT 0 0 0.000
47.250 2.381 ISI 0 0 0.000
49.631 2.046 P_LEFT 0 0 0.000
51.677 1.693 ISI 0 0 0.000
53.370 2.046 INCONG_VL_PR 0 0 0.000
55.416 1.961 ISI 0 0 0.000
57.377 1.712 RESPONSE_INCONG_VL_PR 1 0 2147483.647
59.089 1.692 ISI 0 0 0.000
60.781 2.047 V_RIGHT 0 0 0.000
62.828 2.114 ISI 0 0 0.000
64.942 2.026 CONG_RIGHT 0 0 0.000
66.968 2.180 ISI 0 0 0.000
69.148 1.693 RESPONSE_CONG_RIGHT 1 0 2147483.647
70.841 2.046 ISI 0 0 0.000
72.887 2.048 INCONG_VR_PL 0 0 0.000
74.935 2.180 ISI 0 0 0.000
77.115 2.027 P_RIGHT 0 0 0.000
79.142 2.180 ISI 0 0 0.000
81.322 2.047 CONG_LEFT 0 0 0.000
83.369 2.160 ISI 0 0 0.000
85.529 2.047 V_LEFT 0 0 0.000
87.576 1.980 ISI 0 0 0.000
89.556 1.692 RESPONSE_V_LEFT 1 0 2147483.647
91.248 1.914 ISI 0 0 0.000
93.162 2.026 REST 0 0 0.000
95.188 2.114 ISI 0 0 0.000
97.302 2.047 REST 0 0 0.000
99.349 1.759 ISI 0 0 0.000
101.108 2.046 CONG_RIGHT 0 0 0.000
103.154 1.692 ISI 0 0 0.000
104.846 2.047 REST 0 0 0.000
106.893 2.381 ISI 0 0 0.000
109.274 2.028 P_LEFT 0 0 0.000
111.302 1.913 ISI 0 0 0.000
113.215 1.692 RESPONSE_P_LEFT 1 0 2147483.647
114.907 2.180 ISI 0 0 0.000
117.087 2.047 REST 0 0 0.000
119.134 2.113 ISI 0 0 0.000
121.247 2.027 V_LEFT 0 0 0.000
123.274 2.381 ISI 0 0 0.000
125.655 2.048 INCONG_VL_PR 0 0 0.000
127.703 1.826 ISI 0 0 0.000
129.529 2.046 P_RIGHT 0 0 0.000
131.575 1.846 ISI 0 0 0.000
133.421 2.027 INCONG_VR_PL 0 0 0.000
135.448 1.913 ISI 0 0 0.000
137.361 1.692 RESPONSE_INCONG_VR_PL 1 0 2147483.647
139.053 2.247 ISI 0 0 0.000
141.300 2.047 V_RIGHT 0 0 0.000
143.347 2.382 ISI 0 0 0.000
145.729 2.026 CONG_LEFT 0 0 0.000
147.755 1.980 ISI 0 0 0.000
149.735 2.047 CONG_LEFT 0 0 0.000
151.782 1.893 ISI 0 0 0.000
153.675 1.692 RESPONSE_CONG_LEFT 1 0 2147483.647
155.367 2.113 ISI 0 0 0.000
157.480 2.047 REST 0 0 0.000
159.527 1.759 ISI 0 0 0.000
161.286 2.048 P_RIGHT 0 0 0.000
163.334 1.979 ISI 0 0 0.000
165.313 2.027 INCONG_VR_PL 0 0 0.000
167.340 1.980 ISI 0 0 0.000
169.320 2.046 REST 0 0 0.000
171.366 1.759 ISI 0 0 0.000
173.125 2.047 INCONG_VL_PR 0 0 0.000
175.172 1.960 ISI 0 0 0.000
177.132 2.046 P_LEFT 0 0 0.000
179.178 1.760 ISI 0 0 0.000
180.938 2.047 V_RIGHT 0 0 0.000
182.985 2.114 ISI 0 0 0.000
185.099 1.692 RESPONSE_V_RIGHT 1 0 2147483.647
186.791 2.247 ISI 0 0 0.000
189.038 2.047 V_LEFT 0 0 0.000
191.085 1.692 ISI 0 0 0.000
192.777 2.047 CONG_RIGHT 0 0 0.000
194.824 2.093 ISI 0 0 0.000
196.917 2.048 INCONG_VR_PL 0 0 0.000
198.965 2.247 ISI 0 0 0.000
201.212 1.692 RESPONSE_INCONG_VR_PL 1 0 2147483.647
202.904 1.779 ISI 0 0 0.000
204.683 2.027 CONG_LEFT 0 0 0.000
206.710 1.846 ISI 0 0 0.000
208.556 2.047 INCONG_VL_PR 0 0 0.000
210.603 1.959 ISI 0 0 0.000
212.562 2.048 REST 0 0 0.000
214.610 2.113 ISI 0 0 0.000
216.723 2.027 CONG_RIGHT 0 0 0.000
218.750 1.712 ISI 0 0 0.000
220.462 1.692 RESPONSE_CONG_RIGHT 1 0 2147483.647
222.154 2.047 ISI 0 0 0.000
224.201 2.027 REST 0 0 0.000
226.228 2.046 ISI 0 0 0.000
228.274 2.047 V_LEFT 0 0 0.000
230.321 2.161 ISI 0 0 0.000
232.482 2.047 V_RIGHT 0 0 0.000
234.529 1.846 ISI 0 0 0.000
236.375 2.026 P_LEFT 0 0 0.000
238.401 2.315 ISI 0 0 0.000
240.716 2.046 P_RIGHT 0 0 0.000
242.762 2.381 ISI 0 0 0.000
245.143 1.692 RESPONSE_P_RIGHT 1 0 2147483.647
246.835 2.047 ISI 0 0 0.000
248.882 2.048 V_LEFT 0 0 0.000
250.930 2.294 ISI 0 0 0.000
253.224 2.047 V_RIGHT 0 0 0.000
255.271 2.046 ISI 0 0 0.000
257.317 2.027 CONG_LEFT 0 0 0.000
259.344 1.913 ISI 0 0 0.000
261.257 2.046 P_LEFT 0 0 0.000
263.303 2.227 ISI 0 0 0.000
265.530 2.048 INCONG_VR_PL 0 0 0.000
267.578 1.846 ISI 0 0 0.000
269.424 2.027 P_RIGHT 0 0 0.000
271.451 2.381 ISI 0 0 0.000
273.832 1.712 RESPONSE_P_RIGHT 1 0 2147483.647
275.544 1.960 ISI 0 0 0.000
277.504 2.046 REST 0 0 0.000
279.550 2.114 ISI 0 0 0.000
281.664 2.026 REST 0 0 0.000
283.690 2.115 ISI 0 0 0.000
285.805 2.047 CONG_RIGHT 0 0 0.000
287.852 1.759 ISI 0 0 0.000
289.611 2.046 INCONG_VL_PR 0 0 0.000
291.657 1.693 ISI 0 0 0.000
293.350 1.712 RESPONSE_INCONG_VL_PR 1 0 2147483.647
295.062 2.294 ISI 0 0 0.000
297.356 2.047 V_LEFT 0 0 0.000
299.403 1.846 ISI 0 0 0.000
301.249 2.027 P_RIGHT 0 0 0.000
303.276 2.314 ISI 0 0 0.000
305.590 2.047 CONG_LEFT 0 0 0.000
307.637 2.381 ISI 0 0 0.000
310.018 1.692 RESPONSE_CONG_LEFT 1 0 2147483.647
311.710 2.314 ISI 0 0 0.000
314.024 2.047 CONG_RIGHT 0 0 0.000
316.071 2.180 ISI 0 0 0.000
318.251 2.028 REST 0 0 0.000
320.279 2.180 ISI 0 0 0.000
322.459 2.047 V_RIGHT 0 0 0.000
324.506 1.826 ISI 0 0 0.000
326.332 1.712 RESPONSE_V_RIGHT 1 0 2147483.647
328.044 1.893 ISI 0 0 0.000
329.937 2.047 INCONG_VR_PL 0 0 0.000
331.984 2.093 ISI 0 0 0.000
334.077 2.047 P_LEFT 0 0 0.000
336.124 2.248 ISI 0 0 0.000
338.372 2.047 INCONG_VL_PR 0 0 0.000
340.419 1.959 ISI 0 0 0.000
342.378 2.047 REST 0 0 0.000
344.425 2.381 ISI 0 0 0.000
346.806 1.360 BASE 0 0 0.000
178 changes: 178 additions & 0 deletions demos/transformers/models/model-VisuoTact_smdl.json
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{
"Name": "demo transformers",
"BIDSModelVersion": "1.0.0",
"Description": "demo transformers",
"Input": {
"task": [
"VisuoTact"
],
"space": [
"IXI549Space"
]
},
"Nodes": [
{
"Level": "Run",
"Name": "run_level",
"GroupBy": [
"run",
"subject"
],
"Transformations": {
"Transformer": "bids-matlab_v0.1.0dev",
"Instructions": [
{
"Name": "Replace",
"Input": "trial_type",
"Replace": {
"key": "^RESPONSE.*",
"value": "RESPONSE"
},
"Attribute": "value"
},
{
"Name": "Filter",
"Input": "trial_type",
"Query": "trial_type==^.*LEFT$",
"Output": "tmp"
},
{
"Name": "LabelIdenticalRows",
"Cumulative": true,
"Input": [
"tmp"
],
"Output": [
"label"
]
},
{
"Name": "Concatenate",
"Input": [
"tmp",
"label"
],
"Output": [
"LEFT"
]
},
{
"Name": "Delete",
"Input": [
"tmp",
"label"
]
},
{
"Name": "Filter",
"Input": "trial_type",
"Query": "trial_type==^.*RIGHT$",
"Output": "tmp"
},
{
"Name": "LabelIdenticalRows",
"Cumulative": true,
"Input": [
"tmp"
],
"Output": [
"label"
]
},
{
"Name": "Concatenate",
"Input": [
"tmp",
"label"
],
"Output": [
"RIGHT"
]
},
{
"Name": "Delete",
"Input": [
"tmp",
"label"
]
},
{
"Name": "Filter",
"Input": "trial_type",
"Query": "trial_type==^INCONG.*$",
"Output": "tmp"
},
{
"Name": "LabelIdenticalRows",
"Cumulative": true,
"Input": [
"tmp"
],
"Output": [
"label"
]
},
{
"Name": "Concatenate",
"Input": [
"tmp",
"label"
],
"Output": [
"INCONG"
]
},
{
"Name": "Delete",
"Input": [
"tmp",
"label"
]
}
]
},
"Model": {
"X": [
"trial_type.REST",
"LEFT.P_LEFT_?",
"LEFT.V_LEFT_?",
"LEFT.CONG_LEFT_?",
"RIGHT.P_RIGHT_?",
"RIGHT.V_RIGHT_?",
"RIGHT.CONG_RIGHT_?",
"INCONG.INCONG*"
],
"HRF": {
"Variables": [
"trial_type.REST",
"LEFT.P_LEFT_?",
"LEFT.V_LEFT_?",
"LEFT.CONG_LEFT_?",
"RIGHT.P_RIGHT_?",
"RIGHT.V_RIGHT_?",
"RIGHT.CONG_RIGHT_?",
"INCONG.INCONG*"
],
"Model": "spm"
},
"Type": "glm",
"Options": {
"HighPassFilterCutoffHz": 0.0078,
"Mask": {
"suffix": [
"mask"
],
"desc": [
"brain"
]
}
},
"Software": {
"SPM": {
"SerialCorrelation": "AR(1)"
}
}
}
}
]
}
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