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3dBrickStat.json
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{
"command-line": "3dBrickStat [QUICK] [SLOW] [MIN] [MAX] [MEAN] [SUM] [VAR] [STDEV] [COUNT] [VOLUME] [POSITIVE] [NEGATIVE] [ZERO] [NON-POSITIVE] [NON-NEGATIVE] [NON-ZERO] [ABSOLUTE] [NAN] [NONAN] [MASK] [MRANGE] [MVALUE] [AUTOMASK] [PERCENTILE] [MEDIAN] [VER] [HELP] [DATASET]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-quick",
"description": "get the information from the header only (default)",
"id": "QUICK",
"name": "QUICK",
"optional": true,
"type": "String",
"value-key": "[QUICK]"
},
{
"command-line-flag": "-slow",
"description": "read the whole dataset to find the min and max values all other options except min and max imply slow",
"id": "SLOW",
"name": "SLOW",
"optional": true,
"type": "String",
"value-key": "[SLOW]"
},
{
"command-line-flag": "-min",
"description": "print the minimum value in dataset",
"id": "MIN",
"name": "MIN",
"optional": true,
"type": "String",
"value-key": "[MIN]"
},
{
"command-line-flag": "-max",
"description": "print the maximum value in dataset (default)",
"id": "MAX",
"name": "MAX",
"optional": true,
"type": "String",
"value-key": "[MAX]"
},
{
"command-line-flag": "-mean",
"description": "print the mean value in dataset",
"id": "MEAN",
"name": "MEAN",
"optional": true,
"type": "String",
"value-key": "[MEAN]"
},
{
"command-line-flag": "-sum",
"description": "print the sum of values in the dataset",
"id": "SUM",
"name": "SUM",
"optional": true,
"type": "String",
"value-key": "[SUM]"
},
{
"command-line-flag": "-var",
"description": "print the variance in the dataset",
"id": "VAR",
"name": "VAR",
"optional": true,
"type": "String",
"value-key": "[VAR]"
},
{
"command-line-flag": "-stdev",
"description": "print the standard deviation in the dataset -stdev and -var are mutually exclusive",
"id": "STDEV",
"name": "STDEV",
"optional": true,
"type": "String",
"value-key": "[STDEV]"
},
{
"command-line-flag": "-count",
"description": "print the number of voxels included",
"id": "COUNT",
"name": "COUNT",
"optional": true,
"type": "String",
"value-key": "[COUNT]"
},
{
"command-line-flag": "-volume",
"description": "print the volume of voxels included in microliters",
"id": "VOLUME",
"name": "VOLUME",
"optional": true,
"type": "String",
"value-key": "[VOLUME]"
},
{
"command-line-flag": "-positive",
"description": "include only positive voxel values",
"id": "POSITIVE",
"name": "POSITIVE",
"optional": true,
"type": "String",
"value-key": "[POSITIVE]"
},
{
"command-line-flag": "-negative",
"description": "include only negative voxel values",
"id": "NEGATIVE",
"name": "NEGATIVE",
"optional": true,
"type": "String",
"value-key": "[NEGATIVE]"
},
{
"command-line-flag": "-zero",
"description": "include only zero voxel values",
"id": "ZERO",
"name": "ZERO",
"optional": true,
"type": "String",
"value-key": "[ZERO]"
},
{
"command-line-flag": "-non-positive",
"description": "-non-positive = include only voxel values 0 or negative",
"id": "NON-POSITIVE",
"name": "NON-POSITIVE",
"optional": true,
"type": "String",
"value-key": "[NON-POSITIVE]"
},
{
"command-line-flag": "-non-negative",
"description": "-non-negative = include only voxel values 0 or greater",
"id": "NON-NEGATIVE",
"name": "NON-NEGATIVE",
"optional": true,
"type": "String",
"value-key": "[NON-NEGATIVE]"
},
{
"command-line-flag": "-non-zero",
"description": "-non-zero = include only voxel values not equal to 0",
"id": "NON-ZERO",
"name": "NON-ZERO",
"optional": true,
"type": "String",
"value-key": "[NON-ZERO]"
},
{
"command-line-flag": "-absolute",
"description": "use absolute value of voxel values for all calculations can be combined with restrictive non-positive, non-negative, etc. even if not practical. Ignored for percentile and median computations.",
"id": "ABSOLUTE",
"name": "ABSOLUTE",
"optional": true,
"type": "String",
"value-key": "[ABSOLUTE]"
},
{
"command-line-flag": "-nan",
"description": "include only voxel values that are finite numbers, not NaN, or inf. -nan forces -slow mode.",
"id": "NAN",
"name": "NAN",
"optional": true,
"type": "String",
"value-key": "[NAN]"
},
{
"command-line-flag": "-nonan",
"description": "xclude voxel values that are not numbers",
"id": "NONAN",
"name": "NONAN",
"optional": true,
"type": "String",
"value-key": "[NONAN]"
},
{
"command-line-flag": "-mask",
"description": "use dset as mask to include/exclude voxels",
"id": "MASK",
"name": "MASK",
"optional": true,
"type": "String",
"value-key": "[MASK]"
},
{
"command-line-flag": "-mrange",
"description": "Only accept values between MIN and MAX (inclusive) from the mask. Default it to accept all non-zero voxels.",
"id": "MRANGE",
"name": "MRANGE",
"optional": true,
"type": "String",
"value-key": "[MRANGE]"
},
{
"command-line-flag": "-mvalue",
"description": "Only accept values equal to VAL from the mask.",
"id": "MVALUE",
"name": "MVALUE",
"optional": true,
"type": "String",
"value-key": "[MVALUE]"
},
{
"command-line-flag": "-automask",
"description": "automatically compute mask for dataset Can not be combined with -mask",
"id": "AUTOMASK",
"name": "AUTOMASK",
"optional": true,
"type": "String",
"value-key": "[AUTOMASK]"
},
{
"command-line-flag": "-percentile",
"description": "-percentile p0 ps p1 write the percentile values starting at p0% and ending at p1% at a step of ps% Output is of the form p% value p% value ... Percentile values are output first. Only one sub-brick is accepted as input with this option. Write the author if you REALLY need this option to work with multiple sub-bricks.",
"id": "PERCENTILE",
"name": "PERCENTILE",
"optional": true,
"type": "String",
"value-key": "[PERCENTILE]"
},
{
"command-line-flag": "-median",
"description": "-median a shortcut for -percentile 50 1 50",
"id": "MEDIAN",
"name": "MEDIAN",
"optional": true,
"type": "String",
"value-key": "[MEDIAN]"
},
{
"command-line-flag": "-ver",
"description": "print author and version info",
"id": "VER",
"name": "VER",
"optional": true,
"type": "String",
"value-key": "[VER]"
},
{
"command-line-flag": "-help",
"description": "print this help screen INPUT DATASET NAMES ------------------- This program accepts datasets that are modified on input according to the following schemes: 'r1+orig[3..5]' {sub-brick selector} 'r1+orig<100..200>' {sub-range selector} 'r1+orig[3..5]<100..200>' {both selectors} '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation} For the gruesome details, see the output of 'afni -help'. ++ Compile date = Sep 7 2018 {:}",
"id": "HELP",
"name": "HELP",
"optional": true,
"type": "String",
"value-key": "[HELP]"
},
{
"description": "NA",
"id": "dataset",
"name": "dataset",
"optional": false,
"type": "String",
"value-key": "[DATASET]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}