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1dBport.json
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{
"command-line": "1dBport [BAND] [INVERT] [NOZERO] [NOCONST] [QUAD] [INPUT] [INPUT1D] [NODATA] [TR] [CONCAT]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-band",
"description": "Specify lowest and highest frequencies in the passband. fbot can be 0 if you want to do a highpass filter only; on the other hand, if ftop > Nyquist frequency, then it's a lowpass filter only. ** This 'option' is actually mandatory! (At least once.) * For the un-enlightened, the Nyquist frequency is the highest frequency supported on the given grid, and is equal to 0.5/TR (units are Hz if TR is in s). * The lowest nonzero frequency supported on the grid is equaly to 1/(N*TR), where N=number of time points. ** Multiple -band options can be used, if needed. If the bands overlap, regressors will NOT be duplicated. * That is, '-band 0.01 0.05 -band 0.03 0.08' is the same as using '-band 0.01 0.08'. ** Note that if fbot==0 and ftop>=Nyquist frequency, you get a 'complete' set of trig functions, meaning that using these in regression is effectively a 'no-pass' filter -- probably not what you want! ** It is legitimate to set fbot = ftop. ** The 0 frequency (fbot = 0) component is all 1, of course. But unless you use the '-quad' option, nothing generated herein will deal well with linear-ish or quadratic-ish trends, which fall below the lowest nonzero frequency representable in a full cycle on the grid: f_low = 1 / ( NT * TR ) where NT = number of time points. ** See the fourth EXAMPLE to learn how to use 3dDeconvolve to generate a file of polynomials for regression fun.",
"id": "BAND",
"name": "BAND",
"optional": true,
"type": "String",
"value-key": "[BAND]"
},
{
"command-line-flag": "-invert",
"description": "After computing which frequency indexes correspond to the input band(s), invert the selection -- that is, output all those frequencies NOT selected by the -band option(s). See the fifth EXAMPLE.",
"id": "INVERT",
"name": "INVERT",
"optional": true,
"type": "String",
"value-key": "[INVERT]"
},
{
"command-line-flag": "-nozero",
"description": "Do NOT generate the 0 frequency (constant) component *OR } when fbot = 0; this has the effect of setting fbot to",
"id": "NOZERO",
"name": "NOZERO",
"optional": true,
"type": "String",
"value-key": "[NOZERO]"
},
{
"command-line-flag": "-noconst",
"description": "1/(N*TR), and is essentially a convenient way to say 'eliminate all oscillations below the ftop frequency'.",
"id": "NOCONST",
"name": "NOCONST",
"optional": true,
"type": "String",
"value-key": "[NOCONST]"
},
{
"command-line-flag": "-quad",
"description": "Add regressors for linear and quadratic trends. (These will be the last columns in the output.)",
"id": "QUAD",
"name": "QUAD",
"optional": true,
"type": "String",
"value-key": "[QUAD]"
},
{
"command-line-flag": "-input",
"description": "One of these options is used to specify the number of *OR* } time points to be created, as in 3dDeconvolve.",
"id": "INPUT",
"name": "INPUT",
"optional": false,
"type": "String",
"value-key": "[INPUT]"
},
{
"command-line-flag": "-input1D",
"description": "** '-input' allow catenated datasets, as in 3dDeconvolve. *OR* } ** '-input1D' assumes TR=1 unless you use the '-TR' option.",
"id": "INPUT1D",
"name": "INPUT1D",
"optional": true,
"type": "String",
"value-key": "[INPUT1D]"
},
{
"command-line-flag": "-nodata",
"description": "-nodata NT [TR] } ** One of these options is mandatory, to specify the length of the time series file to generate.",
"id": "NODATA",
"name": "NODATA",
"optional": true,
"type": "String",
"value-key": "[NODATA]"
},
{
"command-line-flag": "-TR",
"description": "Set the time step to 'del' rather than use the one given in the input dataset (if any). ** If TR is not specified by the -input dataset or by",
"id": "TR",
"name": "TR",
"optional": true,
"type": "String",
"value-key": "[TR]"
},
{
"command-line-flag": "-concat",
"description": "As in 3dDeconvolve, used to specify the list of start indexes for concatenated runs. ** Also as in 3dDeconvolve, if the -input dataset is auto- catenated (by providing a list of more than one dataset), the run start list is automatically generated. Otherwise, this option is needed if more than one run is involved. EXAMPLES -------- The first example provides basis functions to filter out all frequency components from 0 to 0.25 Hz: 1dBport -nodata 100 1 -band 0 0.25 > highpass.1D The second example provides basis functions to filter out all frequency components from 0.25 Hz up to the Nyquist freqency: 1dBport -nodata 100 1 -band 0.25 666 > lowpass.1D The third example shows how to examine the results visually, for fun: 1dBport -nodata 100 1 -band 0.41 0.43 | 1dplot -stdin -thick The fourth example shows how to use 3dDeconvolve to generate a file of polynomial 'orts', in case you find yourself needing this ability someday (e.g., when stranded on a desert isle, with Gilligan, the Skipper, et al.): 3dDeconvolve -nodata 100 1 -polort 2 -x1D_stop -x1D stdout: | 1dcat stdin: > pol3.1D The fifth example shows how to use 1dBport to generate a set of regressors to eliminate all frequencies EXCEPT those in the selected range: 1dBport -nodata 100 1 -band 0.03 0.13 -nozero -invert | 1dplot -stdin In this example, the '-nozero' flag is used because the next step will be to 3dDeconvolve with '-polort 2' and '-ortvec' to get rid of the undesirable stuff. ETYMOLOGICAL NOTES ------------------ * The word 'ort' was coined by Andrzej Jesmanowicz, as a shorthand name for a timeseries to which you want to 'orthogonalize' your data. * 'Ort' actually IS an English word, and means 'a scrap of food left from a meal'. As far as I know, its only usage in modern English is in crossword puzzles, and in Scrabble. * For other meanings of 'ort', see http://en.wikipedia.org/wiki/Ort * Do not confuse 'ort' with 'Oort': http://en.wikipedia.org/wiki/Oort_cloud AUTHOR -- RWCox -- Jan 2012 ++ Compile date = Sep 7 2018 {:}",
"id": "CONCAT",
"name": "CONCAT",
"optional": true,
"type": "String",
"value-key": "[CONCAT]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}