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github | mccahill/docker-novnc-fmri-master | ft_apply_montage.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/ft_apply_montage.m | 19,718 | utf_8 | 34eed8e1a072416d95136c30453c3456 | function [input] = ft_apply_montage(input, montage, varargin)
% FT_APPLY_MONTAGE changes the montage of an electrode or gradiometer array. A
% montage can be used for EEG rereferencing, MEG synthetic gradients, MEG
% planar gradients or unmixing using ICA. This function applies the montage
% to the inputor array. The ... |
github | mccahill/docker-novnc-fmri-master | ft_headmodel_slab.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/ft_headmodel_slab.m | 3,466 | utf_8 | 757f6a05af6be4410be4b60f68219358 | function vol = ft_headmodel_slab(geom1, geom2, Pc, varargin)
% FT_HEADMODEL_SLAB creates an EEG volume conduction model that
% is described with an infinite conductive slab. You can think
% of this as two parallel planes containing a mass of conductive
% material (e.g. water) and externally to them a non-conductive ma... |
github | mccahill/docker-novnc-fmri-master | ft_prepare_vol_sens.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/ft_prepare_vol_sens.m | 25,042 | utf_8 | 09e581182e947bc57e0bd964452fb46e | function [vol, sens] = ft_prepare_vol_sens(vol, sens, varargin)
% FT_PREPARE_VOL_SENS does some bookkeeping to ensure that the volume
% conductor model and the sensor array are ready for subsequent forward
% leadfield computations. It takes care of some pre-computations that can
% be done efficiently prior to the lead... |
github | mccahill/docker-novnc-fmri-master | ft_headmodel_halfspace.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/ft_headmodel_halfspace.m | 3,240 | utf_8 | d78abbad6c8d161643451f71b14c2877 | function vol = ft_headmodel_halfspace(geom, Pc, varargin)
% FT_HEADMODEL_HALFSPACE creates an EEG volume conduction model that
% is described with an infinite conductive halfspace. You can think
% of this as a plane with on one side a infinite mass of conductive
% material (e.g. water) and on the other side non-conduc... |
github | mccahill/docker-novnc-fmri-master | ft_headmodel_dipoli.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/ft_headmodel_dipoli.m | 6,998 | utf_8 | 934fad76a00f27acb4e2605a1a832349 | function vol = ft_headmodel_dipoli(geom, varargin)
% FT_HEADMODEL_DIPOLI creates a volume conduction model of the head
% using the boundary element method (BEM) for EEG. This function takes
% as input the triangulated surfaces that describe the boundaries and
% returns as output a volume conduction model which can be ... |
github | mccahill/docker-novnc-fmri-master | ft_headmodel_openmeeg.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/ft_headmodel_openmeeg.m | 6,795 | utf_8 | 87148f44ed9665567ea7313dccaf0754 | function vol = ft_headmodel_openmeeg(geom, varargin)
% FT_HEADMODEL_OPENMEEG creates a volume conduction model of the
% head using the boundary element method (BEM). This function takes
% as input the triangulated surfaces that describe the boundaries and
% returns as output a volume conduction model which can be used... |
github | mccahill/docker-novnc-fmri-master | ft_datatype_sens.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/ft_datatype_sens.m | 20,793 | utf_8 | 1a5161e33bdd52cc9dc548f1382cb532 | function [sens] = ft_datatype_sens(sens, varargin)
% FT_DATATYPE_SENS describes the FieldTrip structure that represents
% an EEG, ECoG, or MEG sensor array. This structure is commonly called
% "elec" for EEG and "grad" for MEG, or more general "sens" for either
% one.
%
% The structure for MEG gradiometers and/or magn... |
github | mccahill/docker-novnc-fmri-master | pinvNx2.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/pinvNx2.m | 1,115 | utf_8 | f3995af2f68c58ae1810bd10b370ed07 | function y = pinvNx2(x)
% PINVNX2 computes a pseudo-inverse of the slices of an Nx2xM real-valued matrix.
% Output has dimensionality 2xNxM. This implementation is generally faster
% than calling pinv in a for-loop, once M > 2
siz = [size(x) 1];
xtx = zeros([2,2,siz(3:end)]);
xtx(1,1,:,:) = sum(x(:,1,:,:).^2,1);
xtx... |
github | mccahill/docker-novnc-fmri-master | normals.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/normals.m | 2,582 | utf_8 | f93d9961689cac7e03d07628eb89665d | function [nrm] = normals(pnt, tri, opt)
% NORMALS compute the surface normals of a triangular mesh
% for each triangle or for each vertex
%
% [nrm] = normals(pnt, tri, opt)
% where opt is either 'vertex' or 'triangle'
% Copyright (C) 2002-2007, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.ru.n... |
github | mccahill/docker-novnc-fmri-master | meg_ini.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/meg_ini.m | 5,415 | utf_8 | 42866ed86f2046f15b9d2e8a7b899b49 | function forwpar=meg_ini(vc,center,order,sens,refs,gradlocs,weights)
% initializes MEG-forward calculation
% usage: forwpar=meg_ini(vc,center,order,sens,refs,gradlocs,weights)
%
% input:
% vc: Nx6 matrix; N is the number of surface points
% the first three numbers in each row are the location
% and the seco... |
github | mccahill/docker-novnc-fmri-master | eeg_halfspace_monopole.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/eeg_halfspace_monopole.m | 3,531 | utf_8 | a30cd5fd8a55c538ea729282dd92336a | function [lf] = eeg_halfspace_monopole(rd, elc, vol)
% EEG_HALFSPACE_MONOPOLE calculate the halfspace medium leadfield
% on positions pnt for a monopole at position rd and conductivity cond
% The halfspace solution requires a plane dividing a conductive zone of
% conductivity cond, from a non coductive zone (cond = 0)... |
github | mccahill/docker-novnc-fmri-master | eeg_halfspace_medium_leadfield.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/eeg_halfspace_medium_leadfield.m | 3,539 | utf_8 | 1e8b5e9c0f452dc034f74f1a4035efd7 | function [lf] = eeg_halfspace_medium_leadfield(rd, elc, vol)
% HALFSPACE_MEDIUM_LEADFIELD calculate the halfspace medium leadfield
% on positions pnt for a dipole at position rd and conductivity cond
% The halfspace solution requires a plane dividing a conductive zone of
% conductivity cond, from a non coductive zone ... |
github | mccahill/docker-novnc-fmri-master | warning_once.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/warning_once.m | 7,284 | utf_8 | ea3a917360f20c39c7ff823b1c1c5028 | function [ws warned] = warning_once(varargin)
%
% WARNING_ONCE will throw a warning for every unique point in the
% stacktrace only, e.g. in a for-loop a warning is thrown only once.
%
% Use as one of the following
% warning_once(string)
% warning_once(id, string)
% Alternatively, you can use warning_once using a t... |
github | mccahill/docker-novnc-fmri-master | leadsphere_all.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/leadsphere_all.m | 2,351 | utf_8 | 8a0c7658993d13ebbeafaa335b06386a | function out=leadsphere_chans(xloc,sensorloc,sensorori)
% usage: out=leadsphere_chans(xloc,sensorloc,sensorori)
% Copyright (C) 2003, Guido Nolte
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute ... |
github | mccahill/docker-novnc-fmri-master | ft_hastoolbox.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/ft_hastoolbox.m | 25,228 | utf_8 | 0972697d520199424e9b41666dc33c04 | function [status] = ft_hastoolbox(toolbox, autoadd, silent)
% FT_HASTOOLBOX tests whether an external toolbox is installed. Optionally
% it will try to determine the path to the toolbox and install it
% automatically.
%
% Use as
% [status] = ft_hastoolbox(toolbox, autoadd, silent)
%
% autoadd = 0 means that it will ... |
github | mccahill/docker-novnc-fmri-master | mesh2edge.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/mesh2edge.m | 3,477 | utf_8 | 787befab8f09407ac0979720168bc0bd | function [newbnd] = mesh2edge(bnd)
% MESH2EDGE finds the edge lines from a triangulated mesh or the edge surfaces
% from a tetrahedral or hexahedral mesh.
%
% Use as
% [bnd] = mesh2edge(bnd)
% Copyright (C) 2013, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip
% for... |
github | mccahill/docker-novnc-fmri-master | project_elec.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/project_elec.m | 3,850 | utf_8 | ef202b133e8b7ab407250b6761a4c4d4 | function [el, prj] = project_elec(elc, pnt, tri)
% PROJECT_ELEC projects electrodes on a triangulated surface
% and returns triangle index, la/mu parameters and distance
%
% Use as
% [el, prj] = project_elec(elc, pnt, tri)
% which returns
% el = Nx4 matrix with [tri, la, mu, dist] for each electrode
% prj ... |
github | mccahill/docker-novnc-fmri-master | eeg_slab_monopole.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/eeg_slab_monopole.m | 4,438 | utf_8 | a73da4acab82be2e433ef6b96c5da222 | function [lf] = eeg_slab_monopole(rd, elc, vol)
% EEG_SLAB_MONOPOLE calculate the strip medium leadfield
% on positions pnt for a monopole at position rd and conductivity cond
% The halfspace solution requires a plane dividing a conductive zone of
% conductivity cond, from a non coductive zone (cond = 0)
%
% [l... |
github | mccahill/docker-novnc-fmri-master | eeg_leadfield1.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/eeg_leadfield1.m | 3,928 | utf_8 | 5ebef73728bb0598cf55671093fde0a8 | function lf = eeg_leadfield1(R, elc, vol)
% EEG_LEADFIELD1 electric leadfield for a dipole in a single sphere
%
% [lf] = eeg_leadfield1(R, elc, vol)
%
% with input arguments
% R position dipole (vector of length 3)
% elc position electrodes
% and vol being a structure with the elements
% vol.r ... |
github | mccahill/docker-novnc-fmri-master | meg_forward.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/meg_forward.m | 4,011 | utf_8 | cf177fb071a706f75303c6892e243203 | function field=meg_forward(dip_par,forwpar)
% calculates the magnetic field of n dipoles
% in a realistic volume conductor
% usage: field=meg_forward(dip_par,forwpar)
%
% input:
% dip_par nx6 matrix where each row contains location (first 3 numbers)
% and moment (second 3 numbers) of a dipole
% forwpar structur... |
github | mccahill/docker-novnc-fmri-master | leadfield_openmeeg.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/forward/private/leadfield_openmeeg.m | 12,868 | utf_8 | 1b1fafd4e9a5c31f46f2f9cc19206bf7 | function [lp, voxels_in] = ft_leadfield_openmeeg ( voxels, vol, sens, varargin )
% FT_OM_COMPUTE_LEAD uses OpenMEEG to compute the lead fields / potentials
% using the boundary element method (BEM).
% The inputs are as follows:
% voxels = an [Nx3] array of voxel locations.
% vol = the volume structure... |
github | mccahill/docker-novnc-fmri-master | firwsord.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/firwsord.m | 3,019 | utf_8 | 23bd2678844e6a2383a02791e4eebaaf | % firwsord() - Estimate windowed sinc FIR filter order depending on
% window type and requested transition band width
%
% Usage:
% >> [m, dev] = firwsord(wtype, fs, df);
% >> m = firwsord('kaiser', fs, df, dev);
%
% Inputs:
% wtype - char array window type. 'rectangular', 'bartlett', 'hann',
% ... |
github | mccahill/docker-novnc-fmri-master | minphaserceps.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/minphaserceps.m | 2,202 | utf_8 | 8d00f7a35a48083dbd40a95ba8e70051 | % rcepsminphase() - Convert FIR filter coefficient to minimum phase
%
% Usage:
% >> b = minphaserceps(b);
%
% Inputs:
% b - FIR filter coefficients
%
% Outputs:
% bMinPhase - minimum phase FIR filter coefficients
%
% Author: Andreas Widmann, University of Leipzig, 2013
%
% References:
% [1] Smith III, O. J. (20... |
github | mccahill/docker-novnc-fmri-master | firws.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/firws.m | 3,260 | utf_8 | 30758d690d0f223b6effa30f8b70d570 | %firws() - Designs windowed sinc type I linear phase FIR filter
%
% Usage:
% >> b = firws(m, f);
% >> b = firws(m, f, w);
% >> b = firws(m, f, t);
% >> b = firws(m, f, t, w);
%
% Inputs:
% m - filter order (mandatory even)
% f - vector or scalar of cutoff frequency/ies (-6 dB;
% pi rad / sample)
%
% O... |
github | mccahill/docker-novnc-fmri-master | kaiserbeta.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/kaiserbeta.m | 1,617 | utf_8 | 9b7de189360083d6a5e30b5553f8e19e | % kaiserbeta() - Estimate Kaiser window beta
%
% Usage:
% >> beta = pop_kaiserbeta(dev);
%
% Inputs:
% dev - scalar maximum passband deviation/ripple
%
% Output:
% beta - scalar Kaiser window beta
%
% References:
% [1] Proakis, J. G., & Manolakis, D. G. (1996). Digital Signal
% Processing: Prin... |
github | mccahill/docker-novnc-fmri-master | invfirwsord.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/invfirwsord.m | 2,949 | utf_8 | 53515c03f2d68457a67dab0e508f5480 | % invfirwsord() - Estimate windowed sinc FIR filter transition band width
% depending on filter order and window type
%
% Usage:
% >> [df, dev] = invfirwsord(wtype, fs, m);
% >> df = invfirwsord('kaiser', fs, m, dev);
%
% Inputs:
% wtype - char array window type. 'rectangular', 'bartlett', 'hann'... |
github | mccahill/docker-novnc-fmri-master | windows.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/windows.m | 3,197 | utf_8 | 3d2efd1b24b86ce24f5c4a9f2522e159 | % windows() - Symmetric window functions
%
% Usage:
% >> h = windows(t, m);
% >> h = windows(t, m, a);
%
% Inputs:
% t - char array 'rectangular', 'bartlett', 'hann', 'hamming',
% 'blackman', 'blackmanharris', 'kaiser', or 'tukey'
% m - scalar window length
%
% Optional inputs:
% a - scalar or vector wi... |
github | mccahill/docker-novnc-fmri-master | warning_once.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/warning_once.m | 7,284 | utf_8 | ea3a917360f20c39c7ff823b1c1c5028 | function [ws warned] = warning_once(varargin)
%
% WARNING_ONCE will throw a warning for every unique point in the
% stacktrace only, e.g. in a for-loop a warning is thrown only once.
%
% Use as one of the following
% warning_once(string)
% warning_once(id, string)
% Alternatively, you can use warning_once using a t... |
github | mccahill/docker-novnc-fmri-master | fir_filterdcpadded.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/fir_filterdcpadded.m | 2,990 | utf_8 | 2c1959c076d333949cf5cb85caffbd0b | % fir_filterdcpadded() - Pad data with DC constant and filter
%
% Usage:
% >> data = fir_filterdcpadded(b, a, data, causal);
%
% Inputs:
% b - vector of filter coefficients
% a - 1
% data - raw data (times x chans)
% causal - boolean perform causal filtering {default 0}... |
github | mccahill/docker-novnc-fmri-master | plotfresp.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/preproc/private/plotfresp.m | 5,260 | utf_8 | b69fa45956658456be0c947b87f4dabc | % plotfresp() - Plot a filter's impulse, step, magnitude, and phase response
%
% Usage:
% >> plotfresp(b, a, nfft, fs, causal);
%
% Inputs:
% b - vector numerator coefficients
%
% Optional inputs:
% a - scalar or vector denominator coefficients (IIR support is
% experimental!) {default 1}
% nf... |
github | mccahill/docker-novnc-fmri-master | ft_statfun_roc.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/statfun/ft_statfun_roc.m | 5,402 | utf_8 | c82923f7c59493a2f64b4a008d27f14e | function [s, cfg] = ft_statfun_roc(cfg, dat, design)
% FT_STATFUN_ROC computes the area under the curve (AUC) of the
% Receiver Operator Characteristic (ROC). This is a measure of the
% separability of the data divided over two conditions. The AUC can
% be used to test statistical significance of being able to predict... |
github | mccahill/docker-novnc-fmri-master | warning_once.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/statfun/private/warning_once.m | 7,284 | utf_8 | ea3a917360f20c39c7ff823b1c1c5028 | function [ws warned] = warning_once(varargin)
%
% WARNING_ONCE will throw a warning for every unique point in the
% stacktrace only, e.g. in a for-loop a warning is thrown only once.
%
% Use as one of the following
% warning_once(string)
% warning_once(id, string)
% Alternatively, you can use warning_once using a t... |
github | mccahill/docker-novnc-fmri-master | tukeywin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/tukeywin.m | 2,102 | utf_8 | 92cee22ee44a0bf1650a07edd3ef943a | % Copyright (C) 2007 Laurent Mazet <mazet@crm.mot.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%
% This progra... |
github | mccahill/docker-novnc-fmri-master | rectwin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/rectwin.m | 990 | utf_8 | 6fcae9032382b3785fa1a5fc7d35d0bd | % Copyright (C) 2007 Sylvain Pelissier <sylvain.pelissier@gmail.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%... |
github | mccahill/docker-novnc-fmri-master | triang.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/triang.m | 2,254 | utf_8 | 922302c6c872d9c51d61c97a76761328 | % Copyright (C) 2000-2002 Paul Kienzle <pkienzle@users.sf.net>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%
% Thi... |
github | mccahill/docker-novnc-fmri-master | bohmanwin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/bohmanwin.m | 1,381 | utf_8 | b837d6f243c8cd46b91ac9846a12da56 | % Copyright (C) 2007 Sylvain Pelissier <sylvain.pelissier@gmail.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%... |
github | mccahill/docker-novnc-fmri-master | hanning.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/hanning.m | 2,015 | utf_8 | 5ea7ba326e52371880cab2d3032552da | function [tap] = hanning(n, str)
%HANNING Hanning window.
% HANNING(N) returns the N-point symmetric Hanning window in a column
% vector. Note that the first and last zero-weighted window samples
% are not included.
%
% HANNING(N,'symmetric') returns the same result as HANNING(N).
%
% HANNING(N,'periodic'... |
github | mccahill/docker-novnc-fmri-master | filtfilt.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/filtfilt.m | 3,297 | iso_8859_1 | d01a26a827bc3379f05bbc57f46ac0a9 | % Copyright (C) 1999 Paul Kienzle
% Copyright (C) 2007 Francesco Potortì
% Copyright (C) 2008 Luca Citi
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (a... |
github | mccahill/docker-novnc-fmri-master | nuttallwin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/nuttallwin.m | 1,316 | utf_8 | 2a8b412e307f23d07700757c675abcc1 | % Copyright (C) 2007 Sylvain Pelissier <sylvain.pelissier@gmail.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%... |
github | mccahill/docker-novnc-fmri-master | hann.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/hann.m | 66 | utf_8 | 779d38839745c5c57530f4c470cc1352 | % w = hann(n)
% see hanning
function w = hann(n), w=hanning(n);
|
github | mccahill/docker-novnc-fmri-master | kaiser.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/kaiser.m | 1,745 | utf_8 | bae51aff1f9eb7c65b82a58fb3049d34 | % Copyright (C) 1995, 1996, 1997 Kurt Hornik <Kurt.Hornik@ci.tuwien.ac.at>
% Copyright (C) 2000 Paul Kienzle <pkienzle@users.sf.net>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either vers... |
github | mccahill/docker-novnc-fmri-master | window.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/window.m | 1,240 | utf_8 | a1ed726ea9ff030e26b60e47cd280d12 | % Copyright (C) 2008 David Bateman
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%
% This program is distributed in... |
github | mccahill/docker-novnc-fmri-master | blackmanharris.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/blackmanharris.m | 1,188 | utf_8 | 58ad36fc97b524266d6a9db98fb6e6ee | % Copyright (C) 2007 Sylvain Pelissier <sylvain.pelissier@gmail.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%... |
github | mccahill/docker-novnc-fmri-master | butter.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/butter.m | 3,559 | utf_8 | ad82b4c04911a5ea11fd6bd2cc5fd590 | % Copyright (C) 1999 Paul Kienzle
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in t... |
github | mccahill/docker-novnc-fmri-master | parzenwin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/parzenwin.m | 1,301 | utf_8 | 5e0e2262856d9c53bb520b02b54f2653 | % Copyright (C) 2007 Sylvain Pelissier <sylvain.pelissier@gmail.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%... |
github | mccahill/docker-novnc-fmri-master | gausswin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/gausswin.m | 1,116 | utf_8 | 17daab2749d4ce5c84bb5e676271e8f0 | % Copyright (C) 1999 Paul Kienzle <pkienzle@users.sf.net>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%
% This pro... |
github | mccahill/docker-novnc-fmri-master | barthannwin.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/barthannwin.m | 1,173 | utf_8 | c90d57c40549a232f05664d193b8cb7a | % Copyright (C) 2007 Sylvain Pelissier <sylvain.pelissier@gmail.com>
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 3 of the License, or (at your option) any later
% version.
%... |
github | mccahill/docker-novnc-fmri-master | postpad.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/private/postpad.m | 2,013 | utf_8 | 2c9539d77ff0f85c9f89108f4dc811e0 | % Copyright (C) 1994, 1995, 1996, 1997, 1998, 2000, 2002, 2004, 2005,
% 2006, 2007, 2008, 2009 John W. Eaton
%
% This file is part of Octave.
%
% Octave is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Founda... |
github | mccahill/docker-novnc-fmri-master | sftrans.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/private/sftrans.m | 7,947 | utf_8 | f64cb2e7d19bcdc6232b39d8a6d70e7c | % Copyright (C) 1999 Paul Kienzle
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in t... |
github | mccahill/docker-novnc-fmri-master | bilinear.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/signal/private/bilinear.m | 4,339 | utf_8 | 17250db27826cad87fa3384823e1242f | % Copyright (C) 1999 Paul Kienzle
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in t... |
github | mccahill/docker-novnc-fmri-master | betapdf.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/betapdf.m | 4,091 | utf_8 | 22972826a645e022df6b35f62bc7c557 | % Copyright (C) 2012 Rik Wehbring
% Copyright (C) 1995-2012 Kurt Hornik
% Copyright (C) 2010 Christos Dimitrakakis
%
% This file is part of Octave.
%
% Octave is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; ei... |
github | mccahill/docker-novnc-fmri-master | nansum.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/nansum.m | 178 | utf_8 | 09c40b9f7168d919e88cbaf011675a72 | % NANSUM provides a replacement for MATLAB's nanmean.
%
% For usage see SUM.
function y = nansum(x, dim)
x(isnan(x)) = 0;
if nargin==1
y = sum(x);
else
y = sum(x,dim);
end
|
github | mccahill/docker-novnc-fmri-master | betacdf.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/betacdf.m | 2,801 | utf_8 | e1af8d1223714ddeef6f5d873bf36c57 | % Copyright (C) 2012 Rik Wehbring
% Copyright (C) 1995-2012 Kurt Hornik
%
% This file is part of Octave.
%
% Octave is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 3 of the License, or (at
% you... |
github | mccahill/docker-novnc-fmri-master | nanstd.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/nanstd.m | 231 | utf_8 | 0ff62b1c345b5ad76a9af59cf07c2983 | % NANSTD provides a replacement for MATLAB's nanstd that is almost
% compatible.
%
% For usage see STD. Note that the three-argument call with FLAG is not
% supported.
function Y = nanstd(varargin)
Y = sqrt(nanvar(varargin{:}));
|
github | mccahill/docker-novnc-fmri-master | finv.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/finv.m | 1,923 | utf_8 | fd552f83d58acd399ecde455a11523d0 | % Copyright (C) 2012 Rik Wehbring
% Copyright (C) 1995-2012 Kurt Hornik
%
% This file is part of Octave.
%
% Octave is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 3 of the License, or (at
% you... |
github | mccahill/docker-novnc-fmri-master | nanmean.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/nanmean.m | 164 | utf_8 | 4e1ca86ec8485f1958f38543f8d5d224 | % NANMEAN provides a replacement for MATLAB's nanmean.
%
% For usage see MEAN.
function y = nanmean(x, dim)
N = sum(~isnan(x), dim);
y = nansum(x, dim) ./ N;
end |
github | mccahill/docker-novnc-fmri-master | tinv.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/tinv.m | 7,634 | utf_8 | 8fe66ec125f91e1a7ac5f8d3cb2ac51a | function x = tinv(p,v);
% TINV Inverse of Student's T cumulative distribution function (cdf).
% X=TINV(P,V) returns the inverse of Student's T cdf with V degrees
% of freedom, at the values in P.
%
% The size of X is the common size of P and V. A scalar input
% functions as a constant matrix of the same s... |
github | mccahill/docker-novnc-fmri-master | betainv.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/external/stats/betainv.m | 2,699 | utf_8 | 105a6134b0eb25f2c863062d582e2040 | % Copyright (C) 2012 Rik Wehbring
% Copyright (C) 1995-2012 Kurt Hornik
%
% This file is part of Octave.
%
% Octave is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 3 of the License, or (at
% you... |
github | mccahill/docker-novnc-fmri-master | ft_connectivity_corr.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/connectivity/ft_connectivity_corr.m | 8,655 | utf_8 | 25e44e5dd146fb9241a777918e64d7fc | function [c, v, outcnt] = ft_connectivity_corr(input, varargin)
% FT_CONNECTIVITY_CORR computes correlation, coherence or a related
% quantity from a data-matrix containing a covariance or cross-spectral
% density.
%
% Use as
% [c, v, n] = ft_connectivity_corr(input, varargin)
%
% The input data input should be an a... |
github | mccahill/docker-novnc-fmri-master | ft_connectivity_psi.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/connectivity/ft_connectivity_psi.m | 5,704 | utf_8 | 1c94dc974eeff21301a4aa0a3e6cd0b3 | function [c, v, n] = ft_connectivity_psi(input, varargin)
% FT_CONNECTIVITY_PSI computes the phase slope index from a data-matrix
% containing the cross-spectral density. It implements the method described
% in: Nolte et al., Robustly estimating the flow direction of information
% in complex physical systems. Physical... |
github | mccahill/docker-novnc-fmri-master | sfactorization_wilson2x2.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/connectivity/private/sfactorization_wilson2x2.m | 8,478 | utf_8 | 8702e7907257ec57f4c63a04e29e2692 | function [H, Z, S, psi] = sfactorization_wilson2x2(S,freq,Niterations,tol,cmbindx,fb,init,checkflag)
% SFACTORIZATION_WILSON2X2 performs pairwise non-parametric spectral factorization on
% cross-spectra, based on Wilson's algorithm.
%
% Usage : [H, Z, psi] = sfactorization_wilson(S,freq);
%
% Inputs : S (1-sided, 3D-... |
github | mccahill/docker-novnc-fmri-master | warning_once.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/connectivity/private/warning_once.m | 7,284 | utf_8 | ea3a917360f20c39c7ff823b1c1c5028 | function [ws warned] = warning_once(varargin)
%
% WARNING_ONCE will throw a warning for every unique point in the
% stacktrace only, e.g. in a for-loop a warning is thrown only once.
%
% Use as one of the following
% warning_once(string)
% warning_once(id, string)
% Alternatively, you can use warning_once using a t... |
github | mccahill/docker-novnc-fmri-master | sfactorization_wilson.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/connectivity/private/sfactorization_wilson.m | 7,895 | utf_8 | d21143e6877072af098a2393e724e6a0 | function [H, Z, S, psi] = sfactorization_wilson(S,freq,Niterations,tol,fb,init,checkflag)
% SFACTORIZATION_WILSON performs multivariate non-parametric spectral factorization on
% cross-spectra, based on Wilson's algorithm.
%
% Usage : [H, Z, S, psi] = sfactorization_wilson(S,freq);
%
% Inputs : S (1-sided, 3D-spectra... |
github | mccahill/docker-novnc-fmri-master | beamformer_pcc.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/inverse/beamformer_pcc.m | 12,952 | utf_8 | 75a451c35ccee4c1c38b1573fb5e0756 | function [dipout] = beamformer_pcc(dip, grad, vol, dat, Cf, varargin)
% BEAMFORMER_PCC implements an experimental beamformer based on partial
% canonical correlations or coherences. Dipole locations that are outside
% the head will return a NaN value.
%
% Use as
% [dipout] = beamformer_pcc(dipin, grad, vol, dat, cov... |
github | mccahill/docker-novnc-fmri-master | beamformer_dics.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/inverse/beamformer_dics.m | 26,365 | utf_8 | de8e9379f1a63e113355cfc45d1210cf | function [dipout] = beamformer_dics(dip, grad, vol, dat, Cf, varargin)
% BEAMFORMER_DICS scans on pre-defined dipole locations with a single dipole
% and returns the beamformer spatial filter output for a dipole on every
% location. Dipole locations that are outside the head will return a
% NaN value.
%
% Use as
% [... |
github | mccahill/docker-novnc-fmri-master | beamformer_lcmv.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/inverse/beamformer_lcmv.m | 16,577 | utf_8 | 11e3b9386286c4fe46e27685a94b890e | function [dipout] = beamformer_lcmv(dip, grad, vol, dat, Cy, varargin)
% BEAMFORMER_LCMV scans on pre-defined dipole locations with a single dipole
% and returns the beamformer spatial filter output for a dipole on every
% location. Dipole locations that are outside the head will return a
% NaN value.
%
% Use as
% [... |
github | mccahill/docker-novnc-fmri-master | dipole_fit.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/inverse/dipole_fit.m | 13,734 | utf_8 | 520adef60da8ec99cad7fc49f1e7e9df | function [dipout] = dipole_fit(dip, sens, vol, dat, varargin)
% DIPOLE_FIT performs an equivalent current dipole fit with a single
% or a small number of dipoles to explain an EEG or MEG scalp topography.
%
% Use as
% [dipout] = dipole_fit(dip, sens, vol, dat, ...)
%
% Additional input arguments should be specified ... |
github | mccahill/docker-novnc-fmri-master | ft_hastoolbox.m | .m | docker-novnc-fmri-master/mri/spm12/external/fieldtrip/inverse/private/ft_hastoolbox.m | 25,228 | utf_8 | 0972697d520199424e9b41666dc33c04 | function [status] = ft_hastoolbox(toolbox, autoadd, silent)
% FT_HASTOOLBOX tests whether an external toolbox is installed. Optionally
% it will try to determine the path to the toolbox and install it
% automatically.
%
% Use as
% [status] = ft_hastoolbox(toolbox, autoadd, silent)
%
% autoadd = 0 means that it will ... |
github | mccahill/docker-novnc-fmri-master | subsasgn.m | .m | docker-novnc-fmri-master/mri/spm12/@nifti/subsasgn.m | 15,573 | utf_8 | 19262917223b7c67e5afb2e51a04da11 | function obj = subsasgn(obj,subs,varargin)
% Subscript assignment
% See subsref for meaning of fields.
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: subsasgn.m 5985 2014-05-14 18:32:51Z john $
switch subs(1).type,
case {... |
github | mccahill/docker-novnc-fmri-master | subsref.m | .m | docker-novnc-fmri-master/mri/spm12/@nifti/subsref.m | 8,802 | utf_8 | 785fbaa0ea7a537b43ed943a1df76694 | function varargout = subsref(opt,subs)
% Subscript referencing
%
% Fields are:
% dat - a file-array representing the image data
% mat0 - a 9-parameter affine transform (from qform0)
% Note that the mapping is from voxels (where the first
% is considered to be at [1,1,1], to m... |
github | mccahill/docker-novnc-fmri-master | getdict.m | .m | docker-novnc-fmri-master/mri/spm12/@nifti/private/getdict.m | 5,809 | utf_8 | 978117bee604b08ea902109325778180 | function d = getdict
% Dictionary of NIFTI stuff
% _________________________________________________________________________
% Copyright (C) 2005-2013 Wellcome Trust Centre for Neuroimaging
%
% $Id: getdict.m 5759 2013-11-21 14:01:14Z guillaume $
persistent dict;
if ~isempty(dict)
d = dict;
return;
end
% Da... |
github | mccahill/docker-novnc-fmri-master | overlay2.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/overlay2.m | 71,088 | utf_8 | c517c3f5c1f39f099a57208b85c6a082 | function [fused,cmap]=overlay2(base,over1,over2,bColor,o1Color,o2Color,...
bClip,o1Clip,o2Clip,bFill,o1Fill,o2Fill,bMap,o1Map,o2Map)
%OVERLAY2 Overlay one or two images over another using specified colormaps.
%
% [fused,cmap]=OVERLAY2(base,over1,over2,bColor,o1Color,o2Color,...
% bClip,o1Clip,o2Clip,bFill,... |
github | mccahill/docker-novnc-fmri-master | overlay2_roiloader.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/overlay2_roiloader.m | 26,166 | utf_8 | b63a291be08eefa74a4ae06097d39a55 | function varargout = overlay2_roiloader(varargin)
%OVERLAY2_ROILOADER - Tools loading ROIs using OVERLAY2
%
% gui_h = OVERLAY2_ROILOADER(h)
% Launch ROI loader GUI for overlay2 figure h. Or if GUI already
% exists, make it the current figure. gui_h is the handle of
% the ROI loader GUI.
%
% ... |
github | mccahill/docker-novnc-fmri-master | winlev.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/winlev.m | 22,649 | utf_8 | e23a8036bdc443590153a6edb09bbd5c | function actReturned_h=winlev(action)
% WINLEV - GUI to window and level an image interactively
%
% WINLEV_H = WINLEV(HANDLE)
%
% handle - Handle of the image(s) to be windowed and leveled
% - OR handle of the axes containing the image
% - OR handle of the figure containing the image
%
% ... |
github | mccahill/docker-novnc-fmri-master | tstatprofile2.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/tstatprofile2.m | 45,879 | utf_8 | 93ab455cb9abd858e6d8e4406cb60bc0 | function varargout=tstatprofile2(varargin)
%TSTATPROFILE2 Calculate statistics on functional, TRAligned data, with the
% baseline subtracted. Uses the new BIAC XML header data.
%
% USAGE
% tstatprofile2;
% tstatprofile2(controlfname);
% out=tstatprofile2(controlfname);
%
% INPUTS
% controlfname i... |
github | mccahill/docker-novnc-fmri-master | roilimits.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/roilimits.m | 7,872 | utf_8 | 1fce5d59dd565121059d5f348b09f11d | function [srs,limits]=roilimits(defSrs,varargin)
%ROILIMITS Get ROI limits for MR series in overlay2 window.
%
% [srs,limits]=roilimits(defSrs,defLimits,...);
%
% defSrs is 0 for the base series, 1 for overlay 1, 2 for overlay 2 and
% indicates which series is the default in the GUI.
% ... |
github | mccahill/docker-novnc-fmri-master | iswinlevforfig.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/iswinlevforfig.m | 3,245 | utf_8 | a39099520bcd0284588d3c1a7509a5ef | function figwinlev_h=iswinlevforfig(fig)
% ISWINLEVFORFIG - Is there a window & level GUI for a particular figure?
%
% WINLEV_H = ISWINLEVFORFIG(FIG)
%
% winlev_h - handle(s) of winlev GUIs controlling FIGURE (empty if none)
% figure - handle of figure to test for open winlev GUIs
%
% See also: WINLEV, ISWIN... |
github | mccahill/docker-novnc-fmri-master | readparadigm.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/readparadigm.m | 8,449 | utf_8 | d74ab8a0ab9df44a8b682a2322a6b65b | function [pMatrix,binnames]=readparadigm(paradigmFile,standardValue)
%READPARADIGM Read a paradigm file
%
% [pMatrix,binnames]=readparadigm(paradigmFile)
% [pMatrix,binnames]=readparadigm(paradigmFile,standardValue)
%
% paradigmFile
% standardValue - Optional: default = 0
% CVS ID and authorship of thi... |
github | mccahill/docker-novnc-fmri-master | readmr.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/readmr.m | 132,922 | utf_8 | 16e6e74286af5140c098fe7787aed144 | function varargout=readmr(varargin)
%READMR Read MR images from filename or structure.
%
% mrstruct = readmr; % Use GUI
% mrstruct = readmr(filenames, typespec, dataselect, '=>returnelemtype');
% mrstruct = readmr(filenames, typespec, dataselect, '=>returnelemtype', 'NOPROGRESSBAR');
% data = mrstruct.data;
% ... |
github | mccahill/docker-novnc-fmri-master | roianalysis_count.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/roianalysis_count.m | 30,094 | utf_8 | 7c4e617e598642e1b71fe9072dbd87fe | function outputData=roianalysis_count(dataPath,dataFileSpec,typeSpec,zoom,roiPath,roiFileSpec,...
studies,bins,gyri,sides,slices,outputExcelFileName, ...
writeMaskedROIs,ranges,decDigits)
%ROIANALYSIS_COUNT Calculates information about # of voxel within several ROIs meeting the specified criteria
%
% This MAT... |
github | mccahill/docker-novnc-fmri-master | birn_qa.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/birn_qa.m | 16,239 | utf_8 | e55b9e29b90f68472c343a57ec1c1893 | function results=birn_qa(series_name, timepoints, slice)
% birn_qa(series_name, timepoints, slice)
%
% Performes quality assurance measures on phantom data
% series_name is the name of a bxh_file for the timeseries
% of data
% timepoints is an array of the timepoints on which to compute
% the statist... |
github | mccahill/docker-novnc-fmri-master | getzoom.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/getzoom.m | 8,726 | utf_8 | 6d9f842a44f2189017eab7995316761c | function srsZoom=getzoom(defZoom,fullZoom)
%GETZOOM Get MR series zoom parameters using GUI.
%
% srsZoom=getzoom(defZoom,fullZoom);
%
% defZoom is the default zoom.
% fullZoom is the full size of the images.
% srsZoom is the zoom parameters the user specified.
%
% For 2-dimensional zooming:
% zoom... |
github | mccahill/docker-novnc-fmri-master | addbxhhistory.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/addbxhhistory.m | 5,040 | utf_8 | 1d96020bcafc83c8c268600e42a090dc | function newmrstruct = addbxhhistory(mrstruct, historyMsg)
%ADDBXHHISTORY - Add BXH history entry to specified mrstruct
%
% newmrstruct = addbxhhistory(mrstruct, historyMsg);
% mrstruct - input mrstruct
% historyMsg - string to use as the history entry description
% newmrstruct - input mrstruct with the spe... |
github | mccahill/docker-novnc-fmri-master | showsrs2_cfgtrans.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/showsrs2_cfgtrans.m | 24,610 | utf_8 | 063687393e328c3a4d6ac8d1ca00ff90 | function outputFig_h=showsrs2_cfgtrans(varargin)
%SHOWSRS2_CFGTRANS - GUI to control transparency of each overlay in showsrs2
%
% gui_h = showsrs2_cfgtrans(h)
% Launch GUI for showsrs2 figure h. Or if GUI already exists, make
% it the current figure. gui_h is the handle of the transparency GUI.
%
... |
github | mccahill/docker-novnc-fmri-master | tstatprofile.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/tstatprofile.m | 42,742 | utf_8 | df62172ac4bd8c31c46540d5aa4565d2 | function Tout=tstatprofile(controlfname,flags)
%TSTATPROFILE Calculate statistics on functional, TRAligned data, with the
% baseline subtracted.
%
% USAGE
% tstatprofile;
% out=tstatprofile(controlfname);
% out=tstatprofile(flags);
% out=tstatprofile(controlfname,flags);
%
% INPUTS
% controlfna... |
github | mccahill/docker-novnc-fmri-master | showsrs2.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/showsrs2.m | 193,663 | utf_8 | b11283cd17070d0e8bcdea3080df8a8e | function figureh=showsrs2(varargin)
%SHOWSRS2 Display MR series in a window with a scroll bar.
%
% % Display with overlays
% h=showsrs2(baseSrs,overlaySrs, ...); % Uses default configuration.
% h=showsrs2(baseSrs,baseCfg,overlaySrs,overlayCfg, ...);
%
% % Display just a base image
% h=showsrs2(baseSrs,baseCf... |
github | mccahill/docker-novnc-fmri-master | reorient.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/reorient.m | 9,856 | utf_8 | abd62aed56abbd55e7f36a6af8a3caa9 | function [srsOut,flipMsg]=reorient(srs,outOrient,srsOrient)
%REORIENT Generate an different orthogonal orientation of specified image volume(s).
%
% Transform image volume(s) into a requested orthogonal orientation. This
% includes both permutation and flips in x, y, and z.
%
% srsOut=reorient(srs,outOrient);... |
github | mccahill/docker-novnc-fmri-master | readmrold.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/readmrold.m | 58,597 | utf_8 | 6f259eac76f12827a33fc2af5cb5b219 | function varargout=readmrold(fName,xSz,ySz,zSz,hdrSz,pixelType,byteOrder,allInOne,startExt,inGUI)
%READMROLD Read MR images from fName. Each of the zSz images is xSz by ySz pixels.
%
% [srs,name,params]=readmrold(fName,xSz,ySz,zSz,cannedFormat);
% [srs,name,params]=readmrold(fName,xSz,ySz,zSz,hdrSz,pixelType,b... |
github | mccahill/docker-novnc-fmri-master | roianalysis_timecourse.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/roianalysis_timecourse.m | 35,344 | utf_8 | 27844e23e017cc257596acdd53b9767e | function outputData=roianalysis_timecourse(dataPath,dataFileSpec,typeSpec,zoom,roiPath,roiFileSpec,...
studies,bins,gyri,sides,slices,outputExcelFileName, ...
preStimMeanSpecifier,tPoints,ranges,decDigits, ...
userStatFuncs,userHeaders,subBaselineForPerChange)
%ROIANALYSIS_TIMECOURSE Calculates statistics wit... |
github | mccahill/docker-novnc-fmri-master | readbxhhdr.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/readbxhhdr.m | 13,336 | utf_8 | 5384e150a515872022261db3870ec11e | function hdr=readbxhhdr(bxhfile)
% READBXHHDR - Read BXH header information
%
% hdr=readbxhhdr; % Choose bxhfile using GUI.
% hdr=readbxhhdr(bxhfile);
%
% bxhfile - filename of bxh header file
% hdr - Structure of header information.
% - Modifies field BASE to contain fully qualified URI ... |
github | mccahill/docker-novnc-fmri-master | showsrs2_cfg.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/showsrs2_cfg.m | 59,632 | utf_8 | b81ec06fcf33904550d8d91cafcbc754 | function outputFig_h = showsrs2_cfg(varargin)
%SHOWSRS2_CFG Application M-file for showsrs2_cfg.fig
% FIG = SHOWSRS2_CFG launch showsrs2_cfg GUI.
% SHOWSRS2_CFG('callback_name', ...) invoke the named callback.
% Last Modified by GUIDE v2.0 10-Jan-2002 15:19:20
% CVS ID and authorship of this code
% CVSI... |
github | mccahill/docker-novnc-fmri-master | readbxhdata.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/readbxhdata.m | 27,767 | utf_8 | d983ea2f2982224a25f268c810df6a67 | function data=readbxhdata(bxhref,recType,recSubType)
% READBXHDATA - Read data specified by BXH header file
%
% data=readbxhdata; % Choose bxhfile using GUI.
% data=readbxhdata(bxhfile); % Choose type & subtype using GUI.
% data=readbxhdata(bxhheader); % Choose type & subtype using GUI.
% data=re... |
github | mccahill/docker-novnc-fmri-master | showsrs2_goto.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/showsrs2_goto.m | 7,868 | utf_8 | 012f6b5235266b0bba866ef9821552a6 | function showsrs2_goto(fig1,currPoint)
%SHOWSRS2_GOTO Go to particular x,y,z coordinates in a showsrs2 window
% SHOWSRS2_GOTO(FIGURE1,COORDS) will move the cursors of a showsrs2
% window figure (FIGURE1) to the coordinates in the array COORDS.
% Any linked showsrs2 figures will also have the coordinates changed... |
github | mccahill/docker-novnc-fmri-master | overlay2_roitool.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/overlay2_roitool.m | 49,399 | utf_8 | 35197cbfd0198fb0fb717ecbf1ff34a3 | function gui_h = overlay2_roitool(varargin)
%OVERLAY2_ROITOOL - Tools for drawing and saving ROIs using OVERLAY2
%
% gui_h = overlay2_roitool(h)
% Launch roitool GUI for overlay2 figure h. Or if GUI already
% exists, make it the current figure. gui_h is the handle of
% the transparency GUI.
%... |
github | mccahill/docker-novnc-fmri-master | showsrs.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/showsrs.m | 48,565 | utf_8 | 02e60a4fa712835ef8f7804430aefb67 | function figureh=showsrs(srs,cmap)
%SHOWSRS Display MR series in a window with a scroll bar.
%
% h=showsrs(srs);
% h=showsrs(srs,cmap);
%
% srs is a 2, 3, or 4 dimensional series, where the fourth
% dimension is time. srs can either be the data array itself
% or a structure with the data array in... |
github | mccahill/docker-novnc-fmri-master | dmdata2bxh.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/dmdata2bxh.m | 11,860 | utf_8 | 6997c76138696d6eb5b58c41307ee6f8 | function dmdata2bxh(dmdatafile,bxhfile,typeformat)
%DMDATA2BXH - Generate BXH header for DMOD file.
%
% Generate BXH header for DMDATA files created by CIGAL, FSCAN, DMREAD,
% DMWRITE (Jim Voyvodic's suite of software)
%
% dmdata2bxh(dmdatafile)
% dmdata2bxh(dmdatafile,bxhfile)
% dmdata2bxh(dmdatafile,bxhfile,t... |
github | mccahill/docker-novnc-fmri-master | readmrgui.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/readmrgui.m | 65,960 | utf_8 | 6274eddfc3cb9846ddce3dfcbaa596b9 | function [args,workspaceVar]=readmrgui(varargin)
%READMRGUI Determine readmr arguments using a GUI
%
% Determine READMR arguments using a GUI
%
% [args,workspaceVar] = readmrgui(options);
% args - cell array of arguments to readmr
% empty cell array if the user cancels or a workspace variable.
% ... |
github | mccahill/docker-novnc-fmri-master | mrtest.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/mrtest.m | 49,143 | utf_8 | 01f07d94b7d7b86181c3e680b077fca0 | function Tout=mrtest(varargin)
%MRTEST Run T-Test or Epoch Average on MR series.
%
% out=mrtest;
% out=mrtest(controlFileName);
%
% Tmaps=mrtest(runNames,typeSpecs,paradigms,pCol,tests);
% epochAvgs=mrtest(runNames,typeSpecs,paradigms,pCol,bins,epoch,threshhold,template);
% Tmaps=mrtest(runNames,typeSpecs,para... |
github | mccahill/docker-novnc-fmri-master | roianalysis_peak.m | .m | docker-novnc-fmri-master/mri/BIAC/mr/roianalysis_peak.m | 33,131 | utf_8 | b1089d91b17922d0a4fe81cd6016c221 | function outputData=roianalysis_peak(dataPath,dataFileSpec,typeSpec,zoom,roiPath,roiFileSpec,...
studies,bins,gyri,sides,slices,outputExcelFileName,preStimMeanSpecifier,tPoints, ...
splineTR,tRanges,statFunc,limits,subBaselineForPerChange)
%ROIANALYSIS_PEAK Calculates peak value and time within several spline in... |
github | mccahill/docker-novnc-fmri-master | copyfile.m | .m | docker-novnc-fmri-master/mri/BIAC/fix/MATLAB61/copyfile.m | 5,259 | utf_8 | 75c78fc64d7bb7366f9f9a6bf222e429 | function varargout=copyfile(SourceFile,DestinationFile,flag)
%COPYFILE Copy file.
% COPYFILE(SOURCE,DEST) will copy the file SOURCE to the new file DEST.
% SOURCE and DEST may be an absolute pathname or a pathname relative to the
% current directory.
%
% COPYFILE(SOURCE,DEST,'writable') will make sure DE... |
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