-
Notifications
You must be signed in to change notification settings - Fork 0
/
3dExtrema.json
211 lines (211 loc) · 7.78 KB
/
3dExtrema.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
{
"command-line": "3dExtrema [PREFIX] [OUTPUT] [SESSION] [QUIET] [MASK_FILE] [MASK_THR] [DATA_THR] [NBEST] [SEP_DIST] [MINIMA] [MAXIMA] [STRICT] [PARTIAL] [INTERIOR] [CLOSURE] [SLICE] [VOLUME] [REMOVE] [AVERAGE] [WEIGHT] [OPTIONS] [DATASETS]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-prefix",
"description": "Use 'pname' for the output dataset prefix name. OR [default = NONE; only screen output]",
"id": "PREFIX",
"name": "PREFIX",
"optional": true,
"type": "String",
"value-key": "[PREFIX]"
},
{
"command-line-flag": "-output",
"description": "-output pname",
"id": "OUTPUT",
"name": "OUTPUT",
"optional": true,
"type": "String",
"value-key": "[OUTPUT]"
},
{
"command-line-flag": "-session",
"description": "Use 'dir' for the output dataset session directory. [default='./'=current working directory]",
"id": "SESSION",
"name": "SESSION",
"optional": true,
"type": "String",
"value-key": "[SESSION]"
},
{
"command-line-flag": "-quiet",
"description": "Flag to suppress screen output",
"id": "QUIET",
"name": "QUIET",
"optional": true,
"type": "String",
"value-key": "[QUIET]"
},
{
"command-line-flag": "-mask_file",
"description": "Use mask statistic from file mname. Note: If file mname contains more than 1 sub-brick, the mask sub-brick must be specified!",
"id": "MASK_FILE",
"name": "MASK_FILE",
"optional": true,
"type": "String",
"value-key": "[MASK_FILE]"
},
{
"command-line-flag": "-mask_thr",
"description": "-mask_thr m Only voxels whose mask statistic is >= m in absolute value will be considered. A default value of 1 is assumed.",
"id": "MASK_THR",
"name": "MASK_THR",
"optional": true,
"type": "String",
"value-key": "[MASK_THR]"
},
{
"command-line-flag": "-data_thr",
"description": "-data_thr d Only voxels whose value (intensity) is greater than d in absolute value will be considered.",
"id": "DATA_THR",
"name": "DATA_THR",
"optional": true,
"type": "String",
"value-key": "[DATA_THR]"
},
{
"command-line-flag": "-nbest",
"description": "-nbest N Only print the first N extrema.",
"id": "NBEST",
"name": "NBEST",
"optional": true,
"type": "String",
"value-key": "[NBEST]"
},
{
"command-line-flag": "-sep_dist",
"description": "-sep_dist d Min. separation distance [mm] for distinct extrema Choose type of extrema (one and only one choice):",
"id": "SEP_DIST",
"name": "SEP_DIST",
"optional": true,
"type": "String",
"value-key": "[SEP_DIST]"
},
{
"command-line-flag": "-minima",
"description": "-minima Find local minima.",
"id": "MINIMA",
"name": "MINIMA",
"optional": true,
"type": "String",
"value-key": "[MINIMA]"
},
{
"command-line-flag": "-maxima",
"description": "-maxima [default] Find local maxima. Choose form of binary relation (one and only one choice):",
"id": "MAXIMA",
"name": "MAXIMA",
"optional": true,
"type": "String",
"value-key": "[MAXIMA]"
},
{
"command-line-flag": "-strict",
"description": "-strict [default] > for maxima, < for minima",
"id": "STRICT",
"name": "STRICT",
"optional": true,
"type": "String",
"value-key": "[STRICT]"
},
{
"command-line-flag": "-partial",
"description": "-partial >= for maxima, <= for minima Choose boundary criteria (one and only one choice):",
"id": "PARTIAL",
"name": "PARTIAL",
"optional": true,
"type": "String",
"value-key": "[PARTIAL]"
},
{
"command-line-flag": "-interior",
"description": "-interior [default]Extrema must be interior points (not on boundary)",
"id": "INTERIOR",
"name": "INTERIOR",
"optional": true,
"type": "String",
"value-key": "[INTERIOR]"
},
{
"command-line-flag": "-closure",
"description": "-closure Extrema may be boundary points Choose domain for finding extrema (one and only one choice):",
"id": "CLOSURE",
"name": "CLOSURE",
"optional": true,
"type": "String",
"value-key": "[CLOSURE]"
},
{
"command-line-flag": "-slice",
"description": "-slice [default] Each slice is considered separately",
"id": "SLICE",
"name": "SLICE",
"optional": true,
"type": "String",
"value-key": "[SLICE]"
},
{
"command-line-flag": "-volume",
"description": "-volume The volume is considered as a whole Choose option for merging of extrema (one and only one choice):",
"id": "VOLUME",
"name": "VOLUME",
"optional": true,
"type": "String",
"value-key": "[VOLUME]"
},
{
"command-line-flag": "-remove",
"description": "-remove [default] Remove all but strongest of neighboring extrema",
"id": "REMOVE",
"name": "REMOVE",
"optional": true,
"type": "String",
"value-key": "[REMOVE]"
},
{
"command-line-flag": "-average",
"description": "-average Replace neighboring extrema by average",
"id": "AVERAGE",
"name": "AVERAGE",
"optional": true,
"type": "String",
"value-key": "[AVERAGE]"
},
{
"command-line-flag": "-weight",
"description": "-weight Replace neighboring extrema by weighted average Command line arguments after the above are taken to be input datasets. Examples: Compute maximum value in amygdala region of Talairach-transformed dataset 3dExtrema -volume -closure -sep_dist 512 \\ -mask_file 'TT_Daemon::amygdala' func_slim+tlrc'[0]' Show minimum voxel values not on edge of mask, where the mask >= 0.95 3dExtrema -minima -volume -mask_file 'statmask+orig' \\",
"id": "WEIGHT",
"name": "WEIGHT",
"optional": true,
"type": "String",
"value-key": "[WEIGHT]"
},
{
"description": "NA",
"id": "options",
"name": "options",
"optional": false,
"type": "String",
"value-key": "[OPTIONS]"
},
{
"description": "NA",
"id": "datasets",
"name": "datasets",
"optional": false,
"type": "String",
"value-key": "[DATASETS]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}