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3dDegreeCentrality.json
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3dDegreeCentrality.json
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{
"command-line": "3dDegreeCentrality [PEARSON] [SPEARMAN] [THRESH] [SPARSITY] [POLORT] [AUTOCLIP] [AUTOMASK] [MASK] [PREFIX] [OUT1D] [DSET]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-pearson",
"description": "Correlation is the normal Pearson (product moment) correlation coefficient [default].",
"id": "PEARSON",
"name": "PEARSON",
"optional": true,
"type": "String",
"value-key": "[PEARSON]"
},
{
"command-line-flag": "-spearman",
"description": "-spearman AND -quadrant are disabled at this time :-(",
"id": "SPEARMAN",
"name": "SPEARMAN",
"optional": true,
"type": "String",
"value-key": "[SPEARMAN]"
},
{
"command-line-flag": "-thresh",
"description": "exclude correlations <= r from calculations",
"id": "THRESH",
"name": "THRESH",
"optional": true,
"type": "String",
"value-key": "[THRESH]"
},
{
"command-line-flag": "-sparsity",
"description": "only use top s percent of correlations in calculations s should be an integer between 0 and 100. Uses an an adaptive thresholding procedure to reduce memory. The speed of determining the adaptive threshold can be improved by specifying an initial threshold with the -thresh flag.",
"id": "SPARSITY",
"name": "SPARSITY",
"optional": true,
"type": "String",
"value-key": "[SPARSITY]"
},
{
"command-line-flag": "-polort",
"description": "Remove polynomical trend of order 'm', for m=-1..3. [default is m=1; removal is by least squares]. Using m=-1 means no detrending; this is only useful for data/information that has been pre-processed.",
"id": "POLORT",
"name": "POLORT",
"optional": true,
"type": "String",
"value-key": "[POLORT]"
},
{
"command-line-flag": "-autoclip",
"description": "Clip off low-intensity regions in the dataset,",
"id": "AUTOCLIP",
"name": "AUTOCLIP",
"optional": true,
"type": "String",
"value-key": "[AUTOCLIP]"
},
{
"command-line-flag": "-automask",
"description": "so that the correlation is only computed between high-intensity (presumably brain) voxels. The mask is determined the same way that 3dAutomask works.",
"id": "AUTOMASK",
"name": "AUTOMASK",
"optional": true,
"type": "String",
"value-key": "[AUTOMASK]"
},
{
"command-line-flag": "-mask",
"description": "Mask to define 'in-brain' voxels. Reducing the number the number of voxels included in the calculation will significantly speedup the calculation. Consider using a mask to constrain the calculations to the grey matter rather than the whole brain. This is also preferrable to using -autoclip or -automask.",
"id": "MASK",
"name": "MASK",
"optional": true,
"type": "String",
"value-key": "[MASK]"
},
{
"command-line-flag": "-prefix",
"description": "Save output into dataset with prefix 'p', this file will contain bricks for both 'weighted' or 'degree' centrality [default prefix is 'deg_centrality'].",
"id": "PREFIX",
"name": "PREFIX",
"optional": true,
"type": "String",
"value-key": "[PREFIX]"
},
{
"command-line-flag": "-out1D",
"description": "Save information about the above threshold correlations to 1D file 'f'. Each row of this file will contain: Voxel1 Voxel2 i1 j1 k1 i2 j2 k2 Corr Where voxel1 and voxel2 are the 1D indices of the pair of voxels, i j k correspond to their 3D coordinates, and Corr is the value of the correlation between the voxel time courses. Notes: * The output dataset is a bucket type of floats. * The program prints out an estimate of its memory used when it ends. It also prints out a progress 'meter' to keep you pacified. -- RWCox - 31 Jan 2002 and 16 Jul 2010 -- Cameron Craddock - 26 Sept 2015 ========================================================================= * This binary version of 3dDegreeCentrality is compiled using OpenMP, a semi- automatic parallelizer software toolkit, which splits the work across multiple CPUs/cores on the same shared memory computer. * OpenMP is NOT like MPI -- it does not work with CPUs connected only by a network (e.g., OpenMP doesn't work with 'cluster' setups). * For implementation and compilation details, please see https://afni.nimh.nih.gov/pub/dist/doc/misc/OpenMP.html * The number of CPU threads used will default to the maximum number on your system. You can control this value by setting environment variable OMP_NUM_THREADS to some smaller value (including 1). * Un-setting OMP_NUM_THREADS resets OpenMP back to its default state of using all CPUs available. ++ However, on some systems, it seems to be necessary to set variable OMP_NUM_THREADS explicitly, or you only get one CPU. ++ On other systems with many CPUS, you probably want to limit the CPU count, since using more than (say) 16 threads is probably useless. * You must set OMP_NUM_THREADS in the shell BEFORE running the program, since OpenMP queries this variable BEFORE the program actually starts. ++ You can't usefully set this variable in your ~/.afnirc file or on the command line with the '-D' option. * How many threads are useful? That varies with the program, and how well it was coded. You'll have to experiment on your own systems! * The number of CPUs on this particular computer system is ...... 4. * The maximum number of CPUs that will be used is now set to .... 4. ========================================================================= ++ Compile date = Sep 7 2018 {:}",
"id": "OUT1D",
"name": "OUT1D",
"optional": true,
"type": "String",
"value-key": "[OUT1D]"
},
{
"description": "NA",
"id": "dset",
"name": "dset",
"optional": false,
"type": "String",
"value-key": "[DSET]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}