-
Notifications
You must be signed in to change notification settings - Fork 0
/
3dDWUncert.json
114 lines (114 loc) · 6.93 KB
/
3dDWUncert.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
{
"command-line": "3dDWUncert [INSET] [PREFIX] [INPUT] [INPUT_LIST] [GRADS] [BMATRIX_Z] [BMATRIX_FULL] [ITERS] [MASK] [CALC_THR_FA] [CSF_FA]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-inset",
"description": "ile with b0 and DWI subbricks (e.g., input to 3dDWtoDTI)",
"id": "INSET",
"name": "INSET",
"optional": true,
"type": "String",
"value-key": "[INSET]"
},
{
"command-line-flag": "-prefix",
"description": "utput file name part.",
"id": "PREFIX",
"name": "PREFIX",
"optional": true,
"type": "String",
"value-key": "[PREFIX]"
},
{
"command-line-flag": "-input",
"description": "asename of DTI volumes output by, e.g., 3dDWItoDT or TORTOISE. Assumes format of name is, e.g.: INPREF_FA+orig.HEAD or INPREF_FA.nii.gz . Files needed with same prefix are: *FA*, *L1*, *V1*, *V2*, *V3* .",
"id": "INPUT",
"name": "INPUT",
"optional": false,
"type": "String",
"value-key": "[INPUT]"
},
{
"command-line-flag": "-input_list",
"description": "n alternative way to specify DTI input files, where FILE is a NIML-formatted text file that lists the explicit/specific files for DTI input. This option is used in place of '-input INPREF'. See below for a 'INPUT LIST FILE EXAMPLE'.",
"id": "INPUT_LIST",
"name": "INPUT_LIST",
"optional": true,
"type": "String",
"value-key": "[INPUT_LIST]"
},
{
"command-line-flag": "-grads",
"description": "ile with 3 columns for x-, y-, and z-comps of DW-gradients (which have unit magnitude). NB: this option also assumes that only 1st DWI subbrick has a b=0 image (i.e., all averaging of multiple b=0 images has been done already); if such is not the case, then you should convert your grads to the bmatrix format and use `-bmatrix_FULL'. OR",
"id": "GRADS",
"name": "GRADS",
"optional": true,
"type": "String",
"value-key": "[GRADS]"
},
{
"command-line-flag": "-bmatrix_Z",
"description": "sing this means that file with gradient info is in b-matrix format, with 6 columns representing: b_xx b_yy b_zz b_xy b_xz b_yz. NB: here, bvalue per image is the trace of the bmatr, bval = b_xx+b_yy+b_zz, such as 1000 s/mm^2. This option might be used, for example, if multiple b-values were used to measure DWI data; this is an AFNI-style bmatrix that needs to be input.",
"id": "BMATRIX_Z",
"name": "BMATRIX_Z",
"optional": true,
"type": "String",
"value-key": "[BMATRIX_Z]"
},
{
"command-line-flag": "-bmatrix_FULL",
"description": "xact same as '-bmatrix_Z FF' above (i.e. there are N rows to the text file and N volumes in the matched data set) with just a lot more commonsensical name. Definitely would be preferred way to go, for ease of usage!",
"id": "BMATRIX_FULL",
"name": "BMATRIX_FULL",
"optional": true,
"type": "String",
"value-key": "[BMATRIX_FULL]"
},
{
"command-line-flag": "-iters",
"description": "umber of jackknife resample iterations, e.g. 50.",
"id": "ITERS",
"name": "ITERS",
"optional": true,
"type": "String",
"value-key": "[ITERS]"
},
{
"command-line-flag": "-mask",
"description": "an include a mask within which to calculate uncert. Otherwise, data should be masked already.",
"id": "MASK",
"name": "MASK",
"optional": true,
"type": "String",
"value-key": "[MASK]"
},
{
"command-line-flag": "-calc_thr_FA",
"description": "et a threshold for the minimum FA value above which one calculates uncertainty; useful if one doesn't want to waste time calculating uncertainty in very low-FA voxels that are likely GM/CSF. For example, in adult subjects one might set FF=0.1 or 0.15, depending on SNR and user's whims (default: FF=-1, i.e., do all).",
"id": "CALC_THR_FA",
"name": "CALC_THR_FA",
"optional": true,
"type": "String",
"value-key": "[CALC_THR_FA]"
},
{
"command-line-flag": "-csf_fa",
"description": "umber marking FA value of `bad' voxels, such as those with S0 value <=mean(S_i), which breaks DT assumptions due to, e.g., bulk/flow motion. Default value of this matches 3dDWItoDT value of csf_fa=0.012345678. * * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** + DTI LIST FILE EXAMPLE: Consider, for example, if you hadn't used the '-sep_dsets' option when outputting all the tensor information from 3dDWItoDT. Then one could specify the DTI inputs for this program with a file called, e.g., FILE_DTI_IN.niml.opts (the name *must* end with '.niml.opts'): <DTIFILE_opts dti_V1=\"SINGLEDT+orig[9..11]\" dti_V2=\"SINGLEDT+orig[12..14]\" dti_V3=\"SINGLEDT+orig[15..17]\" dti_FA=\"SINGLEDT+orig[18]\" dti_L1=\"SINGLEDT+orig[6]\" /> This represents the *minimum* set of input files needed when running 3dDWUncert. (Note that MD isn't needed here.) You can also recycle a NIMLly formatted file from '3dTrackID -dti_list'-- the extra inputs needed for the latter are a superset of those needed here, and won't affect anything detrimentally (I hope). **************************************************************************** + EXAMPLE: 3dDWUncert \\ -inset TEST_FILES/DTI/fin2_DTI_3mm_1+orig \\ -prefix TEST_FILES/DTI/o.UNCERT \\ -input TEST_FILES/DTI/DT \\ -grads TEST_FILES/Siemens_d30_GRADS.dat \\ -iters 50 If you use this program, please reference the jackknifing algorithm done with nonlinear fitting described in: Taylor PA, Biswal BB (2011). Geometric analysis of the b-dependent effects of Rician signal noise on diffusion tensor imaging estimates and determining an optimal b value. MRI 29:777-788. and the introductory/description paper for the FATCAT toolbox: Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional And Tractographic Connectivity Analysis Toolbox. Brain Connectivity 3(5):523-535. ____________________________________________________________________________",
"id": "CSF_FA",
"name": "CSF_FA",
"optional": true,
"type": "String",
"value-key": "[CSF_FA]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}