Package 'niflowr'

Character; file path. input file A Required.

Character; file path. input file B Required.

Character. Additional parameters to the command

Logical. consider input datasets as masks

Character; file path. collect output to a file

Logical. be as quiet as possible (without being entirely mute)

Logical. print out some progress reports (to stderr)

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dAFNItoNIFTI Required.

Character. Additional parameters to the command

Logical. When writing the AFNI extension field, remove text notes that might contain subject identifying information.

Logical. Give the new dataset a new AFNI ID code, to distinguish it from the input dataset.

Logical. Give the new dataset the input datasets AFNI ID code.

Character; file path. output image file name

Logical. Do NOT write an AFNI extension field into the output file. Only use this option if needed. You can also use the 'nifti_tool' program to strip extensions from a file.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. name of structural dataset Required.

Character or numeric vector. the epi base used in alignmentshould be one of (0/mean/median/max/subbrick#) Required.

Character; file path. EPI dataset to align Required.

Logical. align anatomical to EPI dataset (default)

Character. Additional parameters to the command

Logical. align EPI to anatomical dataset

Character; one of: "3dSkullStrip", "3dAutomask", "None". method to mask brain in EPI datashould be one of[3dSkullStrip]/3dAutomask/None)

Logical. save skull-stripped (not aligned)

Character. append suffix to the original anat/epi dataset to usein the resulting dataset names (default is "_al")

Character; one of: "on", "off". do time shifting of EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on'

Character; one of: "on", "off". do volume registration on EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on'

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dAllineate Required.

Character; file path. Compute and print ALL available cost functionals for the un-warped inputsAND THEN QUIT. If you use this option none of the other expected outputs will be produced

Character. Additional parameters to the command

Logical. Expand the -automask function to enclose a rectangular box that holds the irregular mask.

Integer. Compute a mask function, set a value for dilation or 0.

Character. Compute a weight function using the 3dAutomask algorithm plus some blurring of the base image.

Character. Use the center-of-mass calculation to bracket the shifts.

Character or numeric vector. After cost functional optimization is done, start at the final parameters and RE-optimize using this new cost functions. If the results are too different, a warning message will be printed. However, the final parameters from the original optimization will be used to create the output dataset.

Numeric. Convergence test in millimeters (default 0.05mm).

Character; one of: "leastsq", "ls", "mutualinfo", "mi", "corratio_mul", "crM", "norm_mutualinfo", "nmi", "hellinger", "hel", "corratio_add", "crA", "corratio_uns", "crU". Defines the 'cost' function that defines the matching between the source and the base

Logical. Treat the source dataset as being composed of warped EPI slices, and the base as comprising anatomically 'true' images. Only phase-encoding direction image shearing and scaling will be allowed with this option.

Character; one of: "nearestneighbour", "linear", "cubic", "quintic", "wsinc5". Defines interpolation method used to create the output dataset

Numeric. Set the blurring radius to use in the fine resolution pass to 'x' mm. A small amount (1-2 mm?) of blurring at the fine step may help with convergence, if there is some problem, especially if the base volume is very noisy. [Default == 0 mm = no blurring at the final alignment pass]

Character; file path. matrix to align input file

Character; file path. Read warp parameters from file and apply them to the source dataset, and produce a new dataset

Character; one of: "nearestneighbour", "linear", "cubic", "quintic". Defines interpolation method to use during matching

Character; file path. Write the output dataset on the same grid as this file.

Numeric. Maximum allowed rotation in degrees.

Numeric. Maximum allowed scaling factor.

Numeric. Maximum allowed shift in mm.

Numeric. Maximum allowed shearing factor.

Numeric. Write the output dataset using isotropic grid spacing in mm.

Integer. Use at most n scattered points to match the datasets.

Logical. Do not use zero-padding on the base image.

Logical. Don't compute the autoweight/mask; if -weight is not also used, then every voxel will be counted equally.

Character; one of: "bilinear", "cubic", "quintic", "heptic", "nonic", "poly3", "poly5", "poly7", "poly9". Experimental nonlinear warping: bilinear or legendre poly.

Character or numeric vector. To fix non-linear warp dependency along directions.

Character or numeric vector. To fix motion along directions.

Logical. Use only the refining pass – do not try a coarse resolution pass first. Useful if you know that only small amounts of image alignment are needed.

Character; file path. output file from 3dAllineate

Character; file path. Save the transformation matrix for each volume.

Character; file path. Save the warp parameters in ASCII (.1D) format.

Character; file path. Write the weight volume to disk as a dataset

Logical. overwrite output file if it already exists

Logical. Don't print out verbose progress reports.

Character; file path. file to be used as reference, the first volume will be used if not given the reference will be the first volume of in_file.

Logical. If the source has more than one volume, then after the first volume is aligned to the base.

Character; one of: "leastsq", "ls", "mutualinfo", "mi", "corratio_mul", "crM", "norm_mutualinfo", "nmi", "hellinger", "hel", "corratio_add", "crA", "corratio_uns", "crU". After first volume is aligned, switch method for later volumes. For use with '-replacebase'.

Integer. Automatically mask the source dataset with dilation or 0.

Character; file path. mask the input dataset

Integer. In the coarse pass, use the best 'bb' set of initialpoints to search for the starting point for the finepass. If bb==0, then no search is made for the beststarting point, and the identity transformation isused as the starting point. [Default=5; min=0 max=11]

Numeric. Set the blurring radius for the first pass in mm.

Logical. Use -twopass on the first image to be registered, and then on all subsequent images from the source dataset, use results from the first image's coarse pass to start the fine pass.

Logical. Use a two pass alignment strategy for all volumes, searching for a large rotation+shift and then refining the alignment.

Logical. temporary file use

Logical. Print out verbose progress reports.

Character; one of: "shift_only", "shift_rotate", "shift_rotate_scale", "affine_general". Set the warp type.

Logical. Freeze the non-rigid body parameters after first volume.

Character or numeric vector. Set the weighting for each voxel in the base dataset; larger weights mean that voxel count more in the cost function. If an image file is given, the volume must be defined on the same grid as the base dataset

Character; file path. Set the weighting for each voxel in the base dataset; larger weights mean that voxel count more in the cost function. Must be defined on the same grid as the base dataset

Logical. Replace negative values in the input datasets (source & base) with zero.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. timeseries x space (volume or surface) file Required.

Character. Additional parameters to the command

Logical. eta^2 similarity

Character; file path. mask of voxels

Logical. use mask only on targets voxels

Character; file path. mask for source voxels

Character; file path. output image file name

Integer. Remove polynomial trend of order m or -1 for no detrending

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character. Reference anatomical volume. Usually this volume is in some standard space like TLRC or MNI space and with afni dataset view of (+tlrc). Preferably, this reference volume should have had the skull removed but that is not mandatory. AFNI's distribution contains several templates. For a longer list, use "whereami -show_templates" TT_N27+tlrc –> Single subject, skull stripped volume. This volume is also known as N27_SurfVol_NoSkull+tlrc elsewhere in AFNI and SUMA land. (www.loni.ucla.edu, www.bic.mni.mcgill.ca) This template has a full set of FreeSurfer (surfer.nmr.mgh.harvard.edu) surface models that can be used in SUMA. For details, see Talairach-related link: https://afni.nimh.nih.gov/afni/suma TT_icbm452+tlrc –> Average volume of 452 normal brains. Skull Stripped. (www.loni.ucla.edu) TT_avg152T1+tlrc –> Average volume of 152 normal brains. Skull Stripped.(www.bic.mni.mcgill.ca) TT_EPI+tlrc –> EPI template from spm2, masked as TT_avg152T1 TT_avg152 and TT_EPI volume sources are from SPM's distribution. (www.fil.ion.ucl.ac.uk/spm/) If you do not specify a path for the template, the script will attempt to locate the template AFNI's binaries directory. NOTE: These datasets have been slightly modified from their original size to match the standard TLRC dimensions (Jean Talairach and Pierre Tournoux Co-Planar Stereotaxic Atlas of the Human Brain Thieme Medical Publishers, New York, 1988). That was done for internal consistency in AFNI. You may use the original form of these volumes if you choose but your TLRC coordinates will not be consistent with AFNI's TLRC database (San Antonio Talairach Daemon database), for example. Required.

Character; file path. Original anatomical volume (+orig).The skull is removed by this scriptunless instructed otherwise (-no_ss). Required.

Character. Additional parameters to the command

Logical. Do not strip skull of input data set (because skull has already been removed or because template still has the skull) NOTE: The -no_ss option is not all that optional. Here is a table of when you should and should not use -no_ss +——————+————+—————+ | Dataset | Template | +==================+============+===============+ | | w/ skull | wo/ skull | +——————+————+—————+ | WITH skull | -no_ss | xxx | +——————+————+—————+ | WITHOUT skull | No Cigar | -no_ss | +——————+————+—————+ Template means: Your template of choice Dset. means: Your anatomical dataset -no_ss means: Skull stripping should not be attempted on Dset xxx means: Don't put anything, the script will strip Dset No Cigar means: Don't try that combination, it makes no sense.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file Required.

Character. Additional parameters to the command

Logical. Don't do any clustering to find box. Any non-zero voxel will be preserved in the cropped volume. The default method uses some clustering to find the cropping box, and will clip off small isolated blobs.

Character; file path

Integer. Number of extra voxels to pad on each side of box

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dAutomask Required.

Character. Additional parameters to the command

Character; file path. output file from 3dAutomask

Numeric. sets the clip level fraction (must be 0.1-0.9). A small value will tend to make the mask larger [default = 0.5].

Integer. dilate the mask outwards

Integer. erode the mask inwards

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3daxialize Required.

Character. Additional parameters to the command

Logical. Do axial slice order [-orient RAI]This is the default AFNI axial order, andis the one currently required by thevolume rendering plugin; this is alsothe default orientation output by thisprogram (hence the program's name).

Logical. Do coronal slice order [-orient RSA]

Character. new orientation code

Character; file path. output image file name

Logical. Do sagittal slice order [-orient ASL]

Logical. Print out a progerss report

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Numeric. highpass Required.

Character; file path. input file to 3dBandpass Required.

Numeric. lowpass Required.

Character. Additional parameters to the command

Logical. Create a mask from the input dataset.

Numeric. Blur (inside the mask only) with a filter width (FWHM) of 'fff' millimeters.

Logical. Despike each time series before other processing. Hopefully, you don't actually need to do this, which is why it is optional.

Numeric. Replace each vector by the local Principal Vector (AKA first singular vector) from a neighborhood of radius 'rrr' millimeters. Note that the PV time series is L2 normalized. This option is mostly for Bob Cox to have fun with.

Character; file path. mask file

Integer. Set the FFT length [must be a legal value].

Logical. Skip the quadratic detrending of the input that occurs before the FFT-based bandpassing. You would only want to do this if the dataset had been detrended already in some other program.

Logical. Make all output time series have L2 norm = 1 (i.e., sum of squares = 1).

Logical. Don't check for initial positive transients in the data. The test is a little slow, so skipping it is OK, if you KNOW the data time series are transient-free.

Character; file path. Orthogonalize each voxel to the corresponding voxel time series in dataset 'fset', which must have the same spatial and temporal grid structure as the main input dataset. At present, only one '-dsort' option is allowed.

Character or numeric vector. Also orthogonalize input to columns in f.1D. Multiple '-ort' options are allowed.

Character; file path. output file from 3dBandpass

Numeric. Set time step (TR) in sec [default=from dataset header].

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Numeric. fwhm kernel size Required.

Character; file path. input file to 3dSkullStrip Required.

Character. Additional parameters to the command

Logical. Create an automask from the input dataset.

Logical. Save dataset as floats, no matter what the input data type is.

Character; file path. Mask dataset, if desired. Blurring will occur only within the mask. Voxels NOT in the mask will be set to zero in the output.

Character; file path. Multi-mask dataset – each distinct nonzero value in dataset will be treated as a separate mask for blurring purposes.

Character. options

Character; file path. output to the file

Logical. Normally, voxels not in the mask will be set to zero in the output. If you want the original values in the dataset to be preserved in the output, use this option.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. The dataset that will be smoothed Required.

Character. Additional parameters to the command

Logical. Create an automask from the input dataset.

Character; file path. The dataset whose smoothness controls the process.

Numeric. Blur until the 3D FWHM reaches this value (in mm)

Numeric. Blur until the 2D (x,y)-plane FWHM reaches this value (in mm)

Character; file path. Mask dataset, if desired. Voxels NOT in mask will be set to zero in output.

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dmaskave Required.

Character. Additional parameters to the command

Character; file path. -mask dset = use dset as mask to include/exclude voxels

Logical. print the maximum value in the dataset

Logical. print the mean value in the dataset

Logical. print the minimum value in dataset

Character or numeric vector. p0 ps p1 write the percentile values starting at p0% and ending at p1% at a step of ps%. only one sub-brick is accepted.

Logical. read the whole dataset to find the min and max values

Logical. print the sum of values in the dataset

Logical. print the variance in the dataset

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector. List of tuples of input datasets and subbrick selection strings as described in more detail in the following afni help string Input dataset specified using one of these forms: prefix+view, prefix+view.HEAD, or prefix+view.BRIK. You can also add a sub-brick selection list after the end of the dataset name. This allows only a subset of the sub-bricks to be included into the output (by default, all of the input dataset is copied into the output). A sub-brick selection list looks like one of the following forms:: fred+orig[5] ==> use only sub-brick #5 fred+orig[5,9,17] ==> use #5, #9, and #17 fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8 fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13 Sub-brick indexes start at 0. You can use the character '$' to indicate the last sub-brick in a dataset; for example, you can select every third sub-brick by using the selection list ⁠fred+orig\[0..$(3)\]⁠ N.B.: The sub-bricks are output in the order specified, which may not be the order in the original datasets. For example, using ⁠fred+orig\[0..$(2),1..$(2)\]⁠ will cause the sub-bricks in fred+orig to be output into the new dataset in an interleaved fashion. Using ⁠fred+orig\[$..0\]⁠ will reverse the order of the sub-bricks in the output. N.B.: Bucket datasets have multiple sub-bricks, but do NOT have a time dimension. You can input sub-bricks from a 3D+time dataset into a bucket dataset. You can use the '3dinfo' program to see how many sub-bricks a 3D+time or a bucket dataset contains. N.B.: In non-bucket functional datasets (like the 'fico' datasets output by FIM, or the 'fitt' datasets output by 3dttest), sub-brick ⁠\[0\]⁠ is the 'intensity' and sub-brick [1] is the statistical parameter used as a threshold. Thus, to create a bucket dataset using the intensity from dataset A and the threshold from dataset B, and calling the output dataset C, you would type:: 3dbucket -prefix C -fbuc 'A+orig[0]' -fbuc 'B+orig[1] Required.

Character. Additional parameters to the command

Character; file path

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character. expr Required.

Character; file path. input file to 3dcalc Required.

Character. Additional parameters to the command

Character; file path. operand file to 3dcalc

Character; file path. operand file to 3dcalc

Character; file path. output image file name

Logical. overwrite output

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector Required.

Character; file path. output (concatenated) file name Required.

Character. Additional parameters to the command

Logical. Keep only columns that are marked as 'free' in the 3dAllineate header from '-1Dparam_save'. If there is no such header, all columns are kept.

Logical. Omit columns that are identically constant from output.

Logical. specify double data type for output

Logical. specify int, rounded down, data type for output

Character; one of: "int", "nice", "double", "fint", "cint". specify data type for output.

Logical. specify int data type for output

Logical. specify nice data type for output

Character. Apply the same column/row selection string to all filenames on the command line.

Logical. Stack the columns of the resultant matrix in the output.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector. list of tuples of mfiles and associated opkeys Required.

Character; file path. File to write concattenated matvecs to Required.

Character. Additional parameters to the command

Logical. Output matrix in augmented form (last row is 0 0 0 1)This option does not work with -MATRIX or -ONELINE

Logical. indicates that the resulting matrix willbe written to outfile in the 'MATRIX(...)' format (FORM 3).This feature could be used, with clever scripting, to inputa matrix directly on the command line to program 3dWarp.

Logical. indicates that the resulting matrixwill simply be written as 12 numbers on one line.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dCM Required.

Logical. Don't bother listing the values of ROIs you want: The program will find all of them and produce a full list

Character. Additional parameters to the command

Logical. Generate the mask automatically

Character; file path. File to write center of mass to

Logical. Output values as (i,j,k) in local orientation

Character; file path. Only voxels with nonzero values in the provided mask will be averaged.

Character or numeric vector. Compute center of mass for each blob with voxel value of v0, v1, v2, etc. This option is handy for getting ROI centers of mass.

Character or numeric vector. After computing the center of mass, set the origin fields in the header so that the center of mass will be at (x,y,z) in DICOM coords.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dClipLevel Required.

Character. Additional parameters to the command

Logical. Apply the algorithm to each sub-brick separately.

Character; file path. Also compute a 'gradual' clip level as a function of voxel position, and output that to a dataset.

Numeric. Use the number ff instead of 0.50 in the algorithm

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to ConvertDset Required.

Character; file path. output file for ConvertDset Required.

Character; one of: "niml", "niml_asc", "niml_bi", "1D", "1Dp", "1Dpt", "gii", "gii_asc", "gii_b64", "gii_b64gz". output type Required.

Character. Additional parameters to the command

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dcopy Required.

Character. Additional parameters to the command

Character; file path. output image file name

Logical. print progress reports

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. build a mask from provided file, and use this mask for the purpose of reporting truncation-to float issues AND for computing the FDR curves. The actual results ARE not masked with this option (only with 'mask' or 'automask' options).

Numeric. TR to use with 'input1D'. This option has no effect if you do not also use 'input1D'.

Logical. don't consider all zero matrix columns to be the type of error that 'gotforit' is needed to ignore.

Character. Additional parameters to the command

Logical. build a mask automatically from input data (will be slow for long time series datasets)

Character. Name for dataset in which to save the regression coefficients (no statistics). This dataset will be used in a -xrestore run [not yet implemented] instead of the bucket dataset, if possible.

Character; file path. filename of censor .1D time series. This is a file of 1s and 0s, indicating which time points are to be included (1) and which are to be excluded (0).

Logical. de-mean baseline time series (default if 'polort' >= 0)

Character or numeric vector. set environmental variable to provided value

Numeric. use this value instead of the TR in the 'input' dataset. (It's better to fix the input using Refit.)

Logical. output F-statistic for each stimulus

Logical. use global timing for stimulus timing files

Character or numeric vector. general linear test (i.e., contrast) labels

Character or numeric vector. general linear tests (i.e., contrasts) using symbolic conventions (e.g., '+Label1 -Label2')

Integer. use this to proceed even if the matrix has bad problems (e.g., duplicate columns, large condition number, etc.).

Character or numeric vector. filenames of 3D+time input datasets. More than one filename can be given and the datasets will be auto-catenated in time. You can input a 1D time series file here, but the time axis should run along the ROW direction, not the COLUMN direction as in the 'input1D' option.

Character; file path. filename of single (fMRI) .1D time series where time runs down the column.

Logical. use Legendre polynomials for null hypothesis (baseline model)

Logical. use local timing for stimulus timing files

Character; file path. filename of 3D mask dataset; only data time series from within the mask will be analyzed; results for voxels outside the mask will be set to zero.

Logical. normally, if you input multiple datasets with 'input', then the separate datasets are taken to be separate image runs that get separate baseline models. Use this options if you want to have the program consider these to be all one big run.* If any of the input dataset has only 1 sub-brick, then this option is automatically invoked!* If the auto-catenation feature isn't used, then this option has no effect, no how, no way.

Logical. DON'T calculate matrix condition number

Logical. don't de-mean baseline time series

Logical. Don't compute the statistic-vs-FDR curves for the bucket dataset.

Logical. use power polynomials for null hypotheses. Don't do this unless you are crazy!

Logical. use Gaussian elimination instead of SVD

Integer. number of general linear tests (i.e., contrasts)

Integer. number of stimulus timing files

Integer. run the program with provided number of sub-processes

Character or numeric vector. this option lets you input a rectangular array of 1 or more baseline vectors from a file. This method is a fast way to include a lot of baseline regressors in one step.

Character; file path. output statistics file

Integer. degree of polynomial corresponding to the null hypothesis [default: 1]

Numeric. minimum rms error to reject reduced model (default = 0; don't use this option normally!)

Logical. output the R^2 statistic for each stimulus

Logical. check the dataset time series for initial saturation transients, which should normally have been excised before data analysis.

Logical. print out the matrix singular values

Character or numeric vector. label for kth input stimulus (e.g., Label1)

Character or numeric vector. generate a response model from a set of stimulus times given in file.

Numeric. this option means to subtract specified seconds from each time encountered in any 'stim_times' option. The purpose of this option is to make it simple to adjust timing files for the removal of images from the start of each imaging run.

Logical. use SVD instead of Gaussian elimination (default)

Logical. output the T-statistic for each stimulus

Logical. check the dataset time series for initial saturation transients, which should normally have been excised before data analysis.

Logical. output the sample variance (MSE) for each stimulus

Character; file path. specify name for saved X matrix

Logical. stop running after writing .xmat.1D file

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dDegreeCentrality Required.

Character. Additional parameters to the command

Logical. Clip off low-intensity regions in the dataset

Logical. Mask the dataset to target brain-only voxels

Character; file path. mask file to mask input data

Character. output filepath to text dump of correlation matrix

Character; file path. output image file name

Integer

Numeric. only take the top percent of connections

Numeric. threshold to exclude connections where corr <= thresh

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dDespike Required.

Character. Additional parameters to the command

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dDetrend Required.

Character. Additional parameters to the command

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character. Additional parameters to the command

Logical. Remove the mean from each volume prior to computing the correlation

Logical. Return the least square fit coefficients {{a,b}} so that dset2 is approximately a + b\*dset1

Logical. Return the correlation coefficient (default).

Logical. Return the Dice coefficient (the Sorensen-Dice index).

Logical. Return the dot product (unscaled).

Logical. Return eta-squared (Cohen, NeuroImage 2008).

Logical. Return the 6 numbers xbar= ybar= <(x-xbar)^2> <(y-ybar)^2> <(x-xbar)(y-ybar)> and the correlation coefficient.

Logical. Compute the whole matrix. A waste of time, but handy for parsing.

Character or numeric vector. list of input files, possibly with subbrick selectors

Character; file path. Use this dataset as a mask

Character or numeric vector. Means to further restrict the voxels from 'mset' so thatonly those mask values within this range (inclusive) willbe used.

Character; file path. collect output to a file

Logical. Print sub-brick labels to help identify what is being correlated. This option is useful whenyou have more than 2 sub-bricks at input.

Logical. Compute upper triangular matrix

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dECM Required.

Character. Additional parameters to the command

Logical. Clip off low-intensity regions in the dataset

Logical. Mask the dataset to target brain-only voxels

Numeric. sets the stopping criterion for the power iteration; :math:⁠l2\\|v_\\text\{old\} - v_\\text\{new\}\\| < eps\\|v_\\text\{old\}\\|⁠; default = 0.001

Logical. Fast centrality method; substantial speed increase but cannot accommodate thresholding; automatically selected if -thresh or -sparsity are not set

Logical. Full power method; enables thresholding; automatically selected if -thresh or -sparsity are set

Character; file path. mask file to mask input data

Integer. sets the maximum number of iterations to use in the power iteration; default = 1000

Numeric. Limit memory consumption on system by setting the amount of GB to limit the algorithm to; default = 2GB

Character; file path. output image file name

Integer

Numeric. scale correlation coefficients in similarity matrix to after shifting, x >= 0.0; default = 1.0 for -full, 0.5 for -fecm

Numeric. shift correlation coefficients in similarity matrix to enforce non-negativity, s >= 0.0; default = 0.0 for -full, 1.0 for -fecm

Numeric. only take the top percent of connections

Numeric. threshold to exclude connections where corr <= thresh

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dedge3 Required.

Character. Additional parameters to the command

Character; one of: "byte", "short", "float". specify data type for output. Valid types are 'byte', 'short' and 'float'.

Logical. Force scaling of the output to the maximum integer range.

Logical. Same as '-fscale', but also forces each output sub-brick to to get the same scaling factor.

Logical. Don't do any scaling on output to byte or short datasets.

Character; file path. output image file name

Numeric. Multiply input by VAL, but only if the input datum is float. This is needed when the input dataset has a small range, like 0 to 2.0 for instance. With such a range, very few edges are detected due to what I suspect to be truncation problems. Multiplying such a dataset by 10000 fixes the problem and the scaling is undone at the output.

Logical. Print out some information along the way.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character. expr Required.

Character; file path. input file to 1deval Required.

Character. Additional parameters to the command

Character; file path. operand file to 1deval

Character; file path. operand file to 1deval

Logical. output in 1D

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. ideal time series file name Required.

Character; file path. input file to 3dfim+ Required.

Character. Additional parameters to the command

Numeric. fim internal mask threshold value

Character. Flag to output the specified parameter

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Numeric. highpass Required.

Character; file path. input file to 3dFourier Required.

Numeric. lowpass Required.

Character. Additional parameters to the command

Character; file path. output image file name

Logical. Any mean and linear trend are removed before filtering. This will restore the trend after filtering.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input dataset Required.

Character. computes the spatial autocorrelation

Character. Additional parameters to the command

Logical. if in_file has more than one sub-brick, compute the final estimate as the arithmetic mean of the individual sub-brick FWHM estimates

Logical. compute a mask from THIS dataset, a la 3dAutomask

Logical. combine the final measurements along each axis

Logical. be compatible with the older 3dFWHM

Logical. If the input dataset has more than one sub-brick (e.g., has a time axis), then subtract the median of each voxel's time series before processing FWHM. This will tend to remove intrinsic spatial structure and leave behind the noise.

Character. instead of demed (0th order detrending), detrend to the specified order. If order is not given, the program picks q=NT/30. -detrend disables -demed, and includes -unif.

Logical. if in_file has more than one sub-brick, compute the final estimate as the geometric mean of the individual sub-brick FWHM estimates

Character; file path. use only voxels that are nonzero in mask

Character; file path. Save the detrended file into a dataset

Character; file path. output file

Character; file path. output file listing the subbricks FWHM

Logical. If the input dataset has more than one sub-brick, then normalize each voxel's time series to have the same MAD before processing FWHM.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input dataset to compute the GCOR over Required.

Character. Additional parameters to the command

Character; file path. mask dataset, for restricting the computation

Integer. specify number of initial TRs to ignore

Logical. do not (need to) demean as first step

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dHist Required.

Character. Additional parameters to the command

Numeric. bin width

Character; file path. matrix to align input file

Numeric. maximum intensity value

Numeric. minimum intensity value

Integer. number of bins

Character; file path. Write histogram to niml file with this prefix

Character; file path. output image file name

Logical. write a text visual histogram

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dLFCD Required.

Character. Additional parameters to the command

Logical. Clip off low-intensity regions in the dataset

Logical. Mask the dataset to target brain-only voxels

Character; file path. mask file to mask input data

Character; file path. output image file name

Integer

Numeric. threshold to exclude connections where corr <= thresh

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. Filename of the first image Required.

Character; file path. Filename of the second image Required.

Character or numeric vector. The region around each voxel that will be extracted for the statistics calculation. Possible regions are: 'SPHERE', 'RHDD' (rhombic dodecahedron), 'TOHD' (truncated octahedron) with a given radius in mm or 'RECT' (rectangular block) with dimensions to specify in mm. Required.

Character or numeric vector. Statistics to compute. Possible names are: * pearson = Pearson correlation coefficient * spearman = Spearman correlation coefficient * quadrant = Quadrant correlation coefficient * mutinfo = Mutual Information * normuti = Normalized Mutual Information * jointent = Joint entropy * hellinger= Hellinger metric * crU = Correlation ratio (Unsymmetric) * crM = Correlation ratio (symmetrized by Multiplication) * crA = Correlation ratio (symmetrized by Addition) * L2slope = slope of least-squares (L2) linear regression of the data from dataset1 vs. the dataset2 (i.e., d2 = a + b*d1 ==> this is 'b') * L1slope = slope of least-absolute-sum (L1) linear regression of the data from dataset1 vs. the dataset2 * num = number of the values in the region: with the use of -mask or -automask, the size of the region around any given voxel will vary; this option lets you map that size. * ALL = all of the above, in that order More than one option can be used. Required.

Character. Additional parameters to the command

Logical. Compute the mask as in program 3dAutomask.

Character; file path. mask image file name. Voxels NOT in the mask will not be used in the neighborhood of any voxel. Also, a voxel NOT in the mask will have its statistic(s) computed as zero (0).

Character; file path. Output dataset.

Character; file path. File name of an image to use as a weight. Only applies to 'pearson' statistics.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input dataset Required.

Character or numeric vector. The region around each voxel that will be extracted for the statistics calculation. Possible regions are: 'SPHERE', 'RHDD' (rhombic dodecahedron), 'TOHD' (truncated octahedron) with a given radius in mm or 'RECT' (rectangular block) with dimensions to specify in mm. Required.

Character or numeric vector. statistics to compute. Possible names are: * mean = average of the values * stdev = standard deviation * var = variance (stdev\stdev) * cvar = coefficient of variation = stdev/fabs(mean) * median = median of the values * MAD = median absolute deviation * min = minimum * max = maximum * absmax = maximum of the absolute values * num = number of the values in the region: with the use of -mask or -automask, the size of the region around any given voxel will vary; this option lets you map that size. It may be useful if you plan to compute a t-statistic (say) from the mean and stdev outputs. * sum = sum of the values in the region * FWHM = compute (like 3dFWHM) image smoothness inside each voxel's neighborhood. Results are in 3 sub-bricks: FWHMx, FHWMy, and FWHMz. Places where an output is -1 are locations where the FWHM value could not be computed (e.g., outside the mask). * FWHMbar= Compute just the average of the 3 FWHM values (normally would NOT do this with FWHM also). * perc:P0:P1:Pstep = Compute percentiles between P0 and P1 with a step of Pstep. Default P1 is equal to P0 and default P2 = 1 * rank = rank of the voxel's intensity * frank = rank / number of voxels in neighborhood * P2skew = Pearson's second skewness coefficient 3 \ (mean - median) / stdev * ALL = all of the above, in that order (except for FWHMbar and perc). * mMP2s = Exactly the same output as: median, MAD, P2skew, but a little faster * mmMP2s = Exactly the same output as: mean, median, MAD, P2skew More than one option can be used. Required.

Character. Additional parameters to the command

Logical. Compute the mask as in program 3dAutomask.

Character; one of: "NN", "Li", "Cu", "Bk". Interpolant to use when resampling the output with thereduce_restore_grid option. The resampling method string RESAM should come from the set {'NN', 'Li', 'Cu', 'Bk'}. These stand for 'Nearest Neighbor', 'Linear', 'Cubic', and 'Blocky' interpolation, respectively.

Character; file path. Mask image file name. Voxels NOT in the mask will not be used in the neighborhood of any voxel. Also, a voxel NOT in the mask will have its statistic(s) computed as zero (0) unless the parameter 'nonmask' is set to true.

Logical. Voxels not in the mask WILL have their local statistics computed from all voxels in their neighborhood that ARE in the mask. For instance, this option can be used to compute the average local white matter time series, even at non-WM voxels.

Character; file path. Output dataset.

Logical. overwrite output file if it already exists

Logical. Stop the highly informative progress reports.

Character or numeric vector. Compute output on a grid that is reduced by the specified factors. If a single value is passed, output is resampled to the specified isotropic grid. Otherwise, the 3 inputs describe the reduction in the X, Y, and Z directions. This option speeds up computations at the expense of resolution. It should only be used when the nbhd is quite large with respect to the input's resolution, and the resultant stats are expected to be smooth.

Numeric. Like reduce_restore_grid, but automatically set Rx Ry Rz sothat the computation grid is at a resolution of nbhd/MAX_VOXvoxels.

Character or numeric vector. Like reduce_grid, but also resample output back to input grid.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector. input file or files to 3dmask_tool Required.

Character. Additional parameters to the command

Logical. Instead of created a binary 0/1 mask dataset, create one with counts of voxel overlap, i.e., each voxel will contain the number of masks that it is set in.

Character; one of: "byte", "short", "float". specify data type for output.

Character. Use this option to dilate and/or erode datasets as they are read. ex. '5 -5' to dilate and erode 5 times

Character. dilate and/or erode combined mask at the given levels.

Character. fill holes only in the given directions. This option is for use with -fill holes. should be a single string that specifies 1-3 of the axes using {x,y,z} labels (i.e. dataset axis order), or using the labels in {R,L,A,P,I,S}.

Logical. This option can be used to fill holes in the resulting mask, i.e. after all other processing has been done.

Numeric. When combining masks (across datasets and sub-bricks), use this option to restrict the result to a certain fraction of the set of volumes

Logical. intersection, this means -frac 1.0

Character; file path. output image file name

Logical. union, this means -frac 0

Integer. specify verbosity level, for 0 to 3

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dmaskave Required.

Character. Additional parameters to the command

Character; file path. matrix to align input file

Character; file path. output image file name

Logical. matrix to align input file

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dMean Required.

Character. Additional parameters to the command

Logical. compute count of non-zero voxels

Character. Sets the data type of the output dataset

Character; file path. another input file to 3dMean

Logical. create intersection mask

Logical. create union mask

Logical. use only non-zero values

Character; file path. output image file name

Character. scaling of output

Logical. mean square instead of value

Logical. calculate std dev

Logical. take sum, (not average)

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector Required.

Character. Additional parameters to the command

Integer. FWHM blur value (mm)

Logical. apply options to all sub-bricks in dataset

Character; file path. output image file name

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input time series file (4D data set) Required.

Character; file path. input set of ROIs, each labelled with distinct integers Required.

Character. Additional parameters to the command

Logical. switch to also output a matrix of Fisher Z-transform values for the corr coefs (r): Z = atanh(r) , (with Z=4 being output along matrix diagonals where r=1, as the r-to-Z conversion is ceilinged at Z = atanh(r=0.999329) = 4, which is still quite a high Pearson-r value

Logical. switch to ignore any label table labels in the '-in_rois' file, if there are any labels attached

Character; file path. can include a whole brain mask within which to calculate correlation. Otherwise, data should be masked already

Logical. output any correlation map files as NIFTI files (default is BRIK/HEAD). Only useful if using '-ts_wb_corr' and/or '-ts_wb_Z'

Character; file path. output file name part

Logical. internally, this program checks for where there are nonnull time series, because we don't like those, in general. With this flag, the user can output the determined mask of non-null time series.

Logical. output the partial correlation matrix

Logical. by default, this program will grind to a halt and refuse to calculate if any ROI contains >10 percent of voxels with null times series (i.e., each point is 0), as of April, 2017. This is because it seems most likely that hidden badness is responsible. However, if the user still wants to carry on the calculation anyways, then this option will allow one to push on through. However, if any ROI only has null time series, then the program will not calculate and the user will really, really, really need to address their masking

Logical. switch to create a directory for each network that contains the average time series for each ROI in individual files (each file has one line). The directories are labelled PREFIX_000_INDIV/, PREFIX_001_INDIV/, etc. (one per network). Within each directory, the files are labelled ROI_001.netts, ROI_002.netts, etc., with the numbers given by the actual ROI integer labels

Logical. additional switch when using '-ts_out'. Using this option will insert the integer ROI label at the start of each line of the *.netts file created. Thus, for a time series of length N, each line will have N+1 numbers, where the first is the integer ROI label and the subsequent N are scientific notation values

Logical. switch to output the mean time series of the ROIs that have been used to generate the correlation matrices. Output filenames mirror those of the correlation matrix files, with a '.netts' postfix

Logical. same as above in '-ts_wb_corr', except that the maps have been Fisher transformed to Z-scores the relation: Z=atanh(r). To avoid infinities in the transform, Pearson values are effectively capped at |r| = 0.999329 (where |Z| = 4.0). Files are labelled WB_Z_ROI_001+orig, etc

Logical. switch to create a set of whole brain correlation maps. Performs whole brain correlation for each ROI's average time series; this will automatically create a directory for each network that contains the set of whole brain correlation maps (Pearson 'r's). The directories are labelled as above for '-ts_indiv' Within each directory, the files are labelled WB_CORR_ROI_001+orig, WB_CORR_ROI_002+orig, etc., with the numbers given by the actual ROI integer labels

Logical. by default, '-ts_wb_{corr,Z}' output files are named using the int number of a given ROI, such as: WB_Z_ROI_001+orig. With this option, one can replace the int (such as '001') with the string label (such as 'L-thalamus') if one has a labeltable attached to the file

Character; file path. input a 1D file WTS of weights that will be applied multiplicatively to each ROI's average time series. WTS can be a column- or row-file of values, but it must have the same length as the input time series volume. If the initial average time series was A[n] for n=0,..,(N-1) time points, then applying a set of weights W[n] of the same length from WTS would produce a new time series: B[n] = A[n] * W[n]

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to 3dNotes Required.

Character. note to add

Character. note to add to history

Character. Additional parameters to the command

Integer. delete note number num

Character; file path. output image file name

Character. note with which to replace history

Logical. print to stdout the expanded notes

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector. List of input 3D warp datasets Required.

Character. Additional parameters to the command

Character or numeric vector. List of input 3D datasets to be warped by the adjusted warp datasets. There must be exactly as many of these datasets as there are input warps.

Character; file path. Output mean dataset, only needed if in_files are also given. The output dataset will be on the common grid shared by the source datasets.

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector. the name of the dataset to be warped can be multiple datasets Required.

Character. the name of the warp dataset. multiple warps can be concatenated (make sure they exist) Required.

Character; one of: "NN", "nearestneighbour", "nearestneighbor", "linear", "trilinear", "cubic", "tricubic", "quintic", "triquintic", "wsinc5". specify a different interpolation method than might be used for the warp

Character. Additional parameters to the command

Character; one of: "wsinc5", "NN", "nearestneighbour", "nearestneighbor", "linear", "trilinear", "cubic", "tricubic", "quintic", "triquintic". defines interpolation method to use during warp

Logical. After the warp specified in '-nwarp' is computed, invert it

Character; file path. the name of the master dataset, which defines the output grid

Character; file path. output image file name

Logical. don't be verbose :(

Logical. Write output dataset using 16-bit short integers, rather than the usual 32-bit floats.

Logical. be extra verbose :)

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character or numeric vector. list of tuples of 3D warps and associated functions Required.

Character. Additional parameters to the command

Integer. Pad the nonlinear warps by the given number of voxels in all directions. The warp displacements are extended by linear extrapolation from the faces of the input grid..

Character; one of: "wsinc5", "linear", "quintic". specify a different interpolation method than might be used for the warp

Logical. invert the final warp before output

Character; file path. output image file name

Character. string to attach to the output dataset as its atlas space marker.

Logical. be verbose

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input file to OneDTool Required.

Character. Additional parameters to the command

Character or numeric vector. Tuple of motion limit and outfile prefix. need to also set set_nruns -r set_run_lengths

Logical. for each censored TR, also censor previous

Logical. demean each run (new mean of each run = 0.0)

Logical. take the temporal derivative of each vector (done as first backward difference)

Character; file path. write the current 1D data to FILE

Integer. treat the input data as if it has nruns

Logical. display the total number of censored TRs Note : if input is a valid xmat.1D dataset, then the count will come from the header. Otherwise the input is assumed to be a binary censorfile, and zeros are simply counted.

Character; file path. Write cormat warnings to a file

Logical. display column indices for regs of interest

Integer. restrict -show_trs_[un]censored to the given 1-based run

Character; one of: "comma", "space", "encoded", "verbose". display a list of TRs which were not censored in the specified style

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input dataset Required.

Character. Additional parameters to the command

Logical. clip off small voxels

Logical. clip off small voxels

Logical. write out the fraction of masked voxels which are outliers at each timepoint

Logical. write out the median + 3.5 MAD of outlier count with each timepoint

Logical. use Legendre polynomials

Character; file path. only count voxels within the given mask

Character; file path. output image file name

Integer. detrend each voxel timeseries with polynomials

Character. indicate a value for q to compute alpha

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.

Character; file path. input dataset Required.

Character. Additional parameters to the command

Logical. clip off small voxels

Logical. clip off small voxels

Numeric. clip off values below

Logical. write out the median + 3.5 MAD of outlier count with each timepoint

Character; file path. compute correlation only across masked voxels

Character; file path. capture standard output

Logical. Similar to -spearman, but using 1 minus the quadrant correlation coefficient as the quality index.

Logical. Quality index is 1 minus the Spearman (rank) correlation coefficient of each sub-brick with the median sub-brick. (default).

Working directory override.

Named character vector of environment variables.

Execution engine override.

Runtime profile override.

Logical; preview command without executing.

Logical; echo stdout/stderr in real time.