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github | mccahill/docker-novnc-fmri-master | spm_eeg_montage_ui.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_montage_ui.m | 7,607 | utf_8 | 272f476d1f91d7a61972075e5c0aa796 | function montage = spm_eeg_montage_ui(montage)
% GUI for EEG montage (rereference EEG data to new reference channel(s))
% FORMAT montage = spm_eeg_montage_ui(montage)
%
% montage - structure with fields:
% tra - MxN matrix
% labelnew - Mx1 cell-array - new labels
% labelorg - Nx1 cell-array - original... |
github | mccahill/docker-novnc-fmri-master | spm_interp.m | .m | docker-novnc-fmri-master/mri/spm12/spm_interp.m | 1,108 | utf_8 | 5584ddb0b3ee14a9a9e3e5879056d7c1 | function [x] = spm_interp(x,r)
% 1 or 2-D array interpolation
% FORMAT [x] = spm_interp(x,r)
% x - array
% r - interpolation rate
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Karl Friston
% $Id: spm_interp.m 5219 2013-01-29 17... |
github | mccahill/docker-novnc-fmri-master | spm_transverse.m | .m | docker-novnc-fmri-master/mri/spm12/spm_transverse.m | 15,711 | utf_8 | 238cc1ba58179ed7881d989c691e24b1 | function spm_transverse(varargin)
% Rendering of regional effects [SPM{T/F}] on transverse sections
% FORMAT spm_transverse('set',SPM,hReg)
% FORMAT spm_transverse('setcoords',xyzmm)
% FORMAT spm_transverse('clear')
%
% SPM - structure containing SPM, distribution & filtering details
% about the excursion s... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_prep.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_prep.m | 20,375 | utf_8 | 3b8925b4697ec2a08ddd24e48e34630b | function D = spm_eeg_prep(S)
% Prepare converted M/EEG data for further analysis
% FORMAT D = spm_eeg_prep(S)
% S - configuration structure (optional)
% (optional) fields of S:
% S.D - MEEG object or filename of M/EEG mat-file
% S.task - action string. One of 'settype', 'default... |
github | mccahill/docker-novnc-fmri-master | spm_select.m | .m | docker-novnc-fmri-master/mri/spm12/spm_select.m | 11,088 | utf_8 | e6c3a9e24d374328156ef9cc65a02427 | function varargout = spm_select(varargin)
% File selector
% FORMAT [t,sts] = spm_select(n,typ,mesg,sel,wd,filt,frames)
% n - number of files [Default: Inf]
% A single value or a range. e.g.
% 1 - select one file
% Inf - select any number of files
% [1 Inf] - select 1 ... |
github | mccahill/docker-novnc-fmri-master | spm_results_nidm.m | .m | docker-novnc-fmri-master/mri/spm12/spm_results_nidm.m | 59,129 | utf_8 | 0e54d30b077c63e43b0842484f51ec21 | function [outdir, prov] = spm_results_nidm(SPM,xSPM,TabDat)
% Export SPM stats results using the Neuroimaging Data Model (NIDM)
% FORMAT [outdir, prov] = spm_results_nidm(SPM,xSPM,TabDat)
% SPM - structure containing analysis details (see spm_spm.m)
% xSPM - structure containing inference details (see spm_getSPM... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_invert_setuppatches.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_invert_setuppatches.m | 4,527 | utf_8 | 4edcc5fc42352d13bf27cc4addbf0fc6 | function [Qp,Qe,allpriornames] = spm_eeg_invert_setuppatches(allIp,mesh,base,priordir,Qe,UL)
% Set prior files for source inversion
% FORMAT [Qp,Qe,allpriornames] = spm_eeg_invert_setuppatches(allIp,mesh,base,priordir,Qe,UL)
% Each file contains number of smooth patches on cortical surface a
% allIp - each row deno... |
github | mccahill/docker-novnc-fmri-master | spm_mesh_render.m | .m | docker-novnc-fmri-master/mri/spm12/spm_mesh_render.m | 27,242 | utf_8 | cf18b4815a0d036856f8151825a71a3d | function varargout = spm_mesh_render(action,varargin)
% Display a surface mesh & various utilities
% FORMAT H = spm_mesh_render('Disp',M,'PropertyName',propertyvalue)
% M - a GIfTI filename/object or patch structure
% H - structure containing handles of various objects
% Opens a new figure unless a 'paren... |
github | mccahill/docker-novnc-fmri-master | spm_smooth.m | .m | docker-novnc-fmri-master/mri/spm12/spm_smooth.m | 3,785 | utf_8 | ce06f577ecb782c96f5821f143a7e48f | function spm_smooth(P,Q,s,dtype)
% 3 dimensional convolution of an image
% FORMAT spm_smooth(P,Q,s,dtype)
% P - image(s) to be smoothed (or 3D array)
% Q - filename for smoothed image (or 3D array)
% s - [sx sy sz] Gaussian filter width {FWHM} in mm (or edges)
% dtype - datatype [Default: 0 == same datatype... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_inv_imag_api.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_inv_imag_api.m | 15,977 | utf_8 | 2966e1060e2a747ebf45f00ff599e2ec | function varargout = spm_eeg_inv_imag_api(varargin)
% API for EEG/MEG source reconstruction interface
% FORMAT:
% FIG = SPM_EEG_INV_IMAG_API launch spm_eeg_inv_imag_api GUI.
% SPM_EEG_INV_IMAG_API('callback_name', ...) invoke the named callback.
%___________________________________________________________________... |
github | mccahill/docker-novnc-fmri-master | spm_smoothto8bit.m | .m | docker-novnc-fmri-master/mri/spm12/spm_smoothto8bit.m | 2,427 | utf_8 | d81ad311f697d9c9ad9899bd8115c3ce | function VO = spm_smoothto8bit(V,fwhm)
% 3 dimensional convolution of an image to 8bit data in memory
% FORMAT VO = spm_smoothto8bit(V,fwhm)
% V - mapped image to be smoothed
% fwhm - FWHM of Guassian filter width in mm
% VO - smoothed volume in a form that can be used by the
% spm_*_vol.mex* functions.... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_review_switchDisplay.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_review_switchDisplay.m | 27,990 | utf_8 | c75c19e8252d6ad20adb3e324da25288 | function [D] = spm_eeg_review_switchDisplay(D)
% Switch between displays in the M/EEG Review facility
%__________________________________________________________________________
% Copyright (C) 2008-2015 Wellcome Trust Centre for Neuroimaging
% Jean Daunizeau
% $Id: spm_eeg_review_switchDisplay.m 6405 2015-04-14 15:13... |
github | mccahill/docker-novnc-fmri-master | spm_dcm_bma_results.m | .m | docker-novnc-fmri-master/mri/spm12/spm_dcm_bma_results.m | 10,465 | utf_8 | 25c6ab0a494c7398738851e387fbe48b | function spm_dcm_bma_results(BMS,method)
% Plot histograms from BMA for selected modulatory and driving input
% FORMAT spm_dcm_bma_results(BMS,method)
% BMS - BMS.mat file
% method - inference method (FFX or RFX)
%__________________________________________________________________________
% Copyright (C) 2009... |
github | mccahill/docker-novnc-fmri-master | spm_check_filename.m | .m | docker-novnc-fmri-master/mri/spm12/spm_check_filename.m | 2,311 | utf_8 | b8de0a161ecbb9d70247bbf51873bb0e | function V = spm_check_filename(V)
% Checks paths are valid and tries to restore path names
% FORMAT V = spm_check_filename(V)
%
% V - struct array of file handles
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Karl Friston
% $I... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_read_bsa.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_read_bsa.m | 2,723 | utf_8 | cdc73e063e7cce45ce7704211f74f278 | function sconfounds = spm_eeg_read_bsa(bsa)
% This function reads a definition of spatial confounds from a BESA
% *.bsa file and returns an sconfounds struct with the following fields
% .label - labels of channels
% .coeff - matrix of coefficients (channels x components)
% .bad - logical vector - channels marked as bad... |
github | mccahill/docker-novnc-fmri-master | spm_sp.m | .m | docker-novnc-fmri-master/mri/spm12/spm_sp.m | 39,708 | utf_8 | 55e86396b4238aece69306350b6b624e | function varargout = spm_sp(varargin)
% Orthogonal (design) matrix space setting & manipulation
% FORMAT varargout = spm_spc(action,varargin)
%
% This function computes the different projectors related to the row
% and column spaces X. It should be used to avoid redundant computation
% of svd on large X matrix. It is ... |
github | mccahill/docker-novnc-fmri-master | spm_dicom_essentials.m | .m | docker-novnc-fmri-master/mri/spm12/spm_dicom_essentials.m | 3,630 | utf_8 | c3bde3ba3f51ca52c6a4187a09f074e2 | function hdr1 = spm_dicom_essentials(hdr0)
% Remove unused fields from DICOM header
% FORMAT hdr1 = spm_dicom_essentials(hdr0)
% hdr0 - original DICOM header
% hdr1 - Stripped down DICOM header
%
% With lots of DICOM files, the size of all the headers can become too
% big for all the fields to be saved. The idea here ... |
github | mccahill/docker-novnc-fmri-master | spm_dicom_text_to_dict.m | .m | docker-novnc-fmri-master/mri/spm12/spm_dicom_text_to_dict.m | 3,241 | utf_8 | 674a2029c1848a5c5f54603e8a1a6e68 | function dict = spm_dicom_text_to_dict(textfile)
% Create a DICOM dictionary .mat file from a text version
% FORMAT dict = spm_dicom_text_to_dict(textfile)
% OR spm_dicom_text_to_dict(textfile)
% textfile - the name of a suitable text version of the dictionary.
% With no output argument, the... |
github | mccahill/docker-novnc-fmri-master | spm_ecat2nifti.m | .m | docker-novnc-fmri-master/mri/spm12/spm_ecat2nifti.m | 16,716 | utf_8 | f0bc53aa3faadb3dbf33eaed3506a721 | function N = spm_ecat2nifti(fname,opts)
% Import ECAT 7 images from CTI PET scanners
% FORMAT N = spm_ecat2nifti(fname)
% fname - name of ECAT file
% opts - options structure
%
% N - NIfTI object (written in current directory)
%__________________________________________________________________________
% C... |
github | mccahill/docker-novnc-fmri-master | spm_platform.m | .m | docker-novnc-fmri-master/mri/spm12/spm_platform.m | 9,206 | utf_8 | 53549a4f6048166163ea4a80cd323ebc | function varargout=spm_platform(varargin)
% Platform specific configuration parameters for SPM
%
% FORMAT ans = spm_platform(arg)
% arg - optional string argument, can be
% - 'bigend' - return whether this architecture is bigendian
% - 0 - is little endian
% - 1 - ... |
github | mccahill/docker-novnc-fmri-master | spm_vb_graphcut.m | .m | docker-novnc-fmri-master/mri/spm12/spm_vb_graphcut.m | 6,187 | utf_8 | e66c1e4a9a6d484998db51df14cba084 | function labels = spm_vb_graphcut(labels,index,I,W,depth,grnd_type,CUTOFF,DIM)
% Recursive bi-partition of a graph using the isoperimetric algorithm
%
% FORMAT labels = spm_vb_graphcut(labels,index,I,W,depth,grnd_type,CUTOFF,DIM)
%
% labels each voxel is lableled depending on whihc segment is belongs
% index ... |
github | mccahill/docker-novnc-fmri-master | spm_preproc.m | .m | docker-novnc-fmri-master/mri/spm12/spm_preproc.m | 20,882 | utf_8 | c65d104206b34ac3e531fe38195ee5e6 | function results = spm_preproc(varargin)
% Combined Segmentation and Spatial Normalisation
%
% FORMAT results = spm_preproc(V,opts)
% V - image to work with
% opts - options
% opts.tpm - n tissue probability images for each class
% opts.ngaus - number of Gaussians per class (n+1 classes)
% opts.warpreg ... |
github | mccahill/docker-novnc-fmri-master | spm_DesRep.m | .m | docker-novnc-fmri-master/mri/spm12/spm_DesRep.m | 56,577 | utf_8 | 4c8d25f0dc5d35ae9adcd257d349b1fb | function varargout = spm_DesRep(varargin)
% Design reporting utilities
% FORMAT varargout = spm_DesRep(action,varargin)
%
% spm_DesRep (design reporting) is a suite of utility functions for various
% graphical reports on a given experimental design, embodied in the design
% matrix structure and other associated data st... |
github | mccahill/docker-novnc-fmri-master | spm_robust_glm.m | .m | docker-novnc-fmri-master/mri/spm12/spm_robust_glm.m | 3,455 | utf_8 | bcb212d68b21aa060a764bdf025894e1 | function [B, W] = spm_robust_glm(Y, X, dim, ks)
% Apply robust GLM
% FORMAT [B, W] = spm_robust_glm(Y, X, dim, ks)
% Y - data matrix
% X - design matrix
% dim - the dimension along which the function will work
% ks - offset of the weighting function (default: 3)
%
% OUTPUT:
% B - parameter estimat... |
github | mccahill/docker-novnc-fmri-master | spm_inv_spd.m | .m | docker-novnc-fmri-master/mri/spm12/spm_inv_spd.m | 2,156 | utf_8 | 5e0938822aa00e3cc5e2cab220731c81 | function X = spm_inv_spd(A, TOL)
% Inverse for symmetric positive (semi)definite matrices
% FORMAT X = spm_inv_spd(A,TOL)
%
% A - symmetric positive definite matrix (e.g. covariance or precision)
% X - inverse (should remain symmetric positive definite)
%
% TOL - tolerance: default = exp(-32)
%_____________________... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_invert_EBoptimise.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_invert_EBoptimise.m | 7,270 | utf_8 | 426d184cb36327567aac3b78676ac157 | function [F,M,Cq,Cp,QE,Qp] = spm_eeg_invert_EBoptimise(AY,UL,opttype,Qp,Qe,Qe0)
% Empirical Bayes optimization of priors Qp and Qe to fit data AY based on lead fields UL
% FORMAT [F,M,Cq,Cp,QE,Qp] = spm_eeg_invert_EBoptimise(AY,UL,opttype,Qp,Qe,Qe0)
% AY - concatenated dimension reduced trials of M/EEG data
% UL ... |
github | mccahill/docker-novnc-fmri-master | spm.m | .m | docker-novnc-fmri-master/mri/spm12/spm.m | 48,790 | utf_8 | d19ddd27875fd0274f2257c7122c703c | function varargout=spm(varargin)
% SPM: Statistical Parametric Mapping (startup function)
%_______________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/... |
github | mccahill/docker-novnc-fmri-master | spm_orthviews.m | .m | docker-novnc-fmri-master/mri/spm12/spm_orthviews.m | 88,556 | utf_8 | 443ae236b6d233d6f0f5549fb9296822 | function varargout = spm_orthviews(action,varargin)
% Display orthogonal views of a set of images
% FORMAT H = spm_orthviews('Image',filename[,position])
% filename - name of image to display
% area - position of image {relative}
% [left, bottom, width, height]
% H - handle for orthogonal sections... |
github | mccahill/docker-novnc-fmri-master | spm_FcUtil.m | .m | docker-novnc-fmri-master/mri/spm12/spm_FcUtil.m | 30,970 | utf_8 | 217241d0a5374e227e8d3d982b84a66c | function varargout = spm_FcUtil(varargin)
% Contrast utilities
% FORMAT varargout = spm_FcUtil(action,varargin)
%_______________________________________________________________________
%
% spm_FcUtil is a multi-function function containing various utilities
% for contrast construction and manipulation. In general, it a... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_inv_visu3D_api.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_inv_visu3D_api.m | 28,460 | utf_8 | ec63b3905839dd65ab8992fa513cc8e9 | function varargout = spm_eeg_inv_visu3D_api(varargin)
% SPM_EEG_INV_VISU3D_API M-file for spm_eeg_inv_visu3D_api.fig
% - FIG = SPM_EEG_INV_VISU3D_API launch spm_eeg_inv_visu3D_api GUI.
% - D = SPM_EEG_INV_VISU3D_API(D) open with D
% - SPM_EEG_INV_VISU3D_API(filename) where filename is the eeg/meg .mat file
% - SPM_EE... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_specest_mtmfft.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_specest_mtmfft.m | 4,092 | utf_8 | 484a60b9858fc75974ac12ab3e5cbfe4 | function res = spm_eeg_specest_mtmfft(S, data, time)
% Plugin for spm_eeg_tf implementing spectral estimation using Fieldtrip's freqanalysis_mtmconvol
% FORMAT res = spm_eeg_specest_mtmfft(S, data, time)
%
% S - input structure
% fields of S:
% S.taper - taper to use ('hanning', 'rectwin', ... |
github | mccahill/docker-novnc-fmri-master | spm_provenance.m | .m | docker-novnc-fmri-master/mri/spm12/spm_provenance.m | 33,118 | utf_8 | bee77abb7f291c846f7484bd755b1eb3 | classdef spm_provenance < handle
% Provenance using PROV Data Model
% http://www.w3.org/TR/prov-dm/
%
% p = spm_provenance;
% p.get_default_namespace
% p.set_default_namespace(uri)
% p.add_namespace(prefix,uri)
% p.get_namespace
% p.entity(id,attributes)
% p.activity(id,startTime,endTime,attributes)
% p.agent(id,attr... |
github | mccahill/docker-novnc-fmri-master | spm_load.m | .m | docker-novnc-fmri-master/mri/spm12/spm_load.m | 1,187 | utf_8 | 9e2a506bf52d19a51a627ece881f02b2 | function [x] = spm_load(f)
% function to load ascii file data as matrix
% FORMAT [x] = spm_load(f)
% f - file {ascii file containing a regular array of numbers
% x - corresponding data matrix
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroi... |
github | mccahill/docker-novnc-fmri-master | spm_toolbox.m | .m | docker-novnc-fmri-master/mri/spm12/spm_toolbox.m | 10,144 | utf_8 | b83235b2fcf42cb3ae3cb1dbe946422d | function varargout = spm_toolbox(action,varargin)
% Manage third-party SPM toolboxes
% FORMAT spm_toolbox
% FORMAT spm_toolbox install <tbxname>
%
% See http://www.fil.ion.ucl.ac.uk/spm/ext/
%__________________________________________________________________________
% Copyright (C) 2012-2014 Wellcome Trust Centre for N... |
github | mccahill/docker-novnc-fmri-master | spm_reslice.m | .m | docker-novnc-fmri-master/mri/spm12/spm_reslice.m | 14,072 | utf_8 | 9c1fbf6f105383b0160c76aff34016b2 | function spm_reslice(P,flags)
% Rigid body reslicing of images
% FORMAT spm_reslice(P,flags)
%
% P - matrix or cell array of filenames {one string per row}
% All operations are performed relative to the first image.
% ie. Coregistration is to the first image, and resampling
% of images i... |
github | mccahill/docker-novnc-fmri-master | spm_render.m | .m | docker-novnc-fmri-master/mri/spm12/spm_render.m | 14,735 | utf_8 | 492f25f3517d087ae1792839c81e286d | function varargout = spm_render(dat,brt,rendfile)
% Render blobs on surface of a 'standard' brain
% FORMAT spm_render(dat,brt,rendfile)
%
% dat - a struct array of length 1 to 3
% each element is a structure containing:
% - XYZ - the x, y & z coordinates of the transformed SPM{.}
% ... |
github | mccahill/docker-novnc-fmri-master | spm_uitable.m | .m | docker-novnc-fmri-master/mri/spm12/spm_uitable.m | 11,862 | utf_8 | df9da4e52bd155b7f62b3222a768741e | function [varargout] = spm_uitable(varargin)
% WARNING: This feature is not supported in MATLAB
% and the API and functionality may change in a future release.
% UITABLE creates a two dimensional graphic uitable component in a figure window.
% UITABLE creates a 1x1 uitable object using default property values in
%... |
github | mccahill/docker-novnc-fmri-master | spm_preproc_write8.m | .m | docker-novnc-fmri-master/mri/spm12/spm_preproc_write8.m | 20,747 | utf_8 | 654370ef507e0e547226af25b4c20525 | function [cls,M1] = spm_preproc_write8(res,tc,bf,df,mrf,cleanup,bb,vx)
% Write out VBM preprocessed data
% FORMAT [cls,M1] = spm_preproc_write8(res,tc,bf,df,mrf,cleanup,bb,vx)
%__________________________________________________________________________
% Copyright (C) 2008-2014 Wellcome Trust Centre for Neuroimaging
% ... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_convert.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_convert.m | 19,723 | utf_8 | 4fd390d7d34b24030720b9e460258658 | function D = spm_eeg_convert(S)
% Convert various M/EEG formats to SPM12 format
% FORMAT D = spm_eeg_convert(S)
% S - string (filename) or struct (see below)
%
% If S is a struct it can have the optional following fields:
% S.dataset - file name
% S.mode - 'header' - only convert the... |
github | mccahill/docker-novnc-fmri-master | spm_est_V.m | .m | docker-novnc-fmri-master/mri/spm12/spm_est_V.m | 6,746 | utf_8 | 178b66a5ac59482231b4ffd1a823a6b2 | function [h] = spm_est_V(SPM,c)
% Test routine to evaluate non-sphericity correction (ReML Whitening)
% FORMAT [h] = spm_est_V(SPM,c)
% SPM - structure containing generic analysis details
% c - number of contrasts to simulate (default = 4)
%
% h - hyperparameter estimates
%_________________________________... |
github | mccahill/docker-novnc-fmri-master | spm_data_read.m | .m | docker-novnc-fmri-master/mri/spm12/spm_data_read.m | 3,297 | utf_8 | 1b550cecf27e5a0864c1978b02b5276d | function Y = spm_data_read(V,varargin)
% Read data from disk [Y = V(I)]
% FORMAT Y = spm_data_read(V)
% V - a structure array (see spm_data_hdr_read)
% Y - an array of data values; the last dimension indexes numel(V)
%
% FORMAT Y = spm_data_read(V,'slice',S)
% V - a structure array of image volumes... |
github | mccahill/docker-novnc-fmri-master | spm_diff.m | .m | docker-novnc-fmri-master/mri/spm12/spm_diff.m | 4,409 | utf_8 | 5b7b6e665bfb7610fa3558e4aa4613d1 | function [varargout] = spm_diff(varargin)
% matrix high-order numerical differentiation
% FORMAT [dfdx] = spm_diff(f,x,...,n)
% FORMAT [dfdx] = spm_diff(f,x,...,n,V)
% FORMAT [dfdx] = spm_diff(f,x,...,n,'q')
%
% f - [inline] function f(x{1},...)
% x - input argument[s]
% n - arguments to differentiate w.... |
github | mccahill/docker-novnc-fmri-master | spm_DisplayTimeSeries.m | .m | docker-novnc-fmri-master/mri/spm12/spm_DisplayTimeSeries.m | 14,423 | utf_8 | 4d780e2231301bec7a83c2e48efc4d0c | function [ud] = spm_DisplayTimeSeries(y,options)
% Build a GUI for 'smart' time series display
% FORMAT [ud] = spm_DisplayTimeSeries(y,options)
% IN:
% - y: the txn data, where t is the number of time sample, and p the
% number of 'channels'
% - options: a structure (default is empty), which allows to adapt ... |
github | mccahill/docker-novnc-fmri-master | spm_browser.m | .m | docker-novnc-fmri-master/mri/spm12/spm_browser.m | 4,521 | utf_8 | 42b14a124bfa86885245a86796f31d36 | function [H, HC] = spm_browser(url,F,pos,format)
% Display an HTML document within a MATLAB figure
% FORMAT H = spm_browser(url,F,pos,[format])
%
% url - string containing URL (e.g. 'http://...' or 'file://...')
% F - figure handle or Tag [Default: Graphics]
% pos - position within figure in pixel units with... |
github | mccahill/docker-novnc-fmri-master | loadxml.m | .m | docker-novnc-fmri-master/mri/spm12/loadxml.m | 4,985 | utf_8 | 9429ec4334b8abc0ff9910e7c9019fdc | function varargout = loadxml(filename,varargin)
%LOADXML Load workspace variables from disk (XML file).
% LOADXML FILENAME retrieves all variables from a file given a full
% pathname or a MATLABPATH relative partial pathname (see PARTIALPATH).
% If FILENAME has no extension LOAD looks for FILENAME and FILENAME.xml ... |
github | mccahill/docker-novnc-fmri-master | spm_robust_average.m | .m | docker-novnc-fmri-master/mri/spm12/spm_robust_average.m | 3,558 | utf_8 | 54b6ccfc9f894d7b58c8222146712590 | function [Y,W] = spm_robust_average(X, dim, ks)
% Apply robust averaging routine to X sets
% FORMAT [Y,W] = spm_robust_averaget(X, dim, ks)
% X - data matrix to be averaged
% dim - the dimension along which the function will work
% ks - offset of the weighting function (default: 3)
%
% W - estimated we... |
github | mccahill/docker-novnc-fmri-master | spm_peb_ppi.m | .m | docker-novnc-fmri-master/mri/spm12/spm_peb_ppi.m | 21,420 | utf_8 | 234a7aa77560d35a0bb109cc8b59c4b2 | function PPI = spm_peb_ppi(varargin)
% Bold deconvolution to create physio- or psycho-physiologic interactions
% FORMAT PPI = spm_peb_ppi(SPMname,ppiflag,VOI,Uu,ppiname,showGraphics)
%
% SPM - Structure containing generic details about the analysis or
% the fully qualified filename of such a str... |
github | mccahill/docker-novnc-fmri-master | spm_BMS_F_smpl.m | .m | docker-novnc-fmri-master/mri/spm12/spm_BMS_F_smpl.m | 1,628 | utf_8 | ee07ac8baecef03c27abc7bbde7c2ebe | function [s_samp,s_bound] = spm_BMS_F_smpl (alpha,lme,alpha0)
% Get sample and lower bound approx. for model evidence p(y|r)
% in group BMS; see spm_BMS_F.
%
% FORMAT [s_samp,s_bound] = spm_BMS_F_smpl (alpha,lme,alpha0)
%
% REFERENCE: See appendix in
% Stephan KE, Penny WD, Daunizeau J, Moran RJ, Friston KJ
% Bayesia... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_ft2spm.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_ft2spm.m | 5,773 | utf_8 | cfa39b2a8583f3be7d6253a1a3fedb90 | function D = spm_eeg_ft2spm(ftdata, filename)
% Converter from Fieldtrip (http://www.ru.nl/fcdonders/fieldtrip/)
% data structures to SPM file format
%_______________________________________________________________________
% Copyright (C) 2008-2013 Wellcome Trust Centre for Neuroimaging
% Vladimir Litvak
% $Id: spm_ee... |
github | mccahill/docker-novnc-fmri-master | spm_deformations.m | .m | docker-novnc-fmri-master/mri/spm12/spm_deformations.m | 24,675 | utf_8 | 0fc60981840e1fa30d81d18c4ee98f7b | function out = spm_deformations(job)
% Various deformation field utilities.
% FORMAT out = spm_deformations(job)
% job - a job created via spm_cfg_deformations.m
% out - a struct with fields
% .def - file name of created deformation field
% .warped - file names of warped images
%
% See spm_cfg_deformatio... |
github | mccahill/docker-novnc-fmri-master | spm_pf.m | .m | docker-novnc-fmri-master/mri/spm12/spm_pf.m | 6,768 | utf_8 | 7a122bb3a5c25e63f4470b6ba52cdb54 | function [qx,qP,qD,xhist] = spm_pf(M,y,U)
% Particle Filtering for dynamic models
% FORMAT [qx,qP,qD,xhist] = spm_pf(M,y)
% M - model specification structure
% y - output or data (N x T)
% U - exogenous input
%
% M(1).x % initial states
% M(1).f = inline(f,'x','v','P') % state equation
% M... |
github | mccahill/docker-novnc-fmri-master | spm_atlas.m | .m | docker-novnc-fmri-master/mri/spm12/spm_atlas.m | 30,808 | utf_8 | 7f351435d79d415e067eb21ef7386a2c | function varargout = spm_atlas(action,varargin)
% Atlas multi-function
% FORMAT xA = spm_atlas('load',atlas)
% FORMAT L = spm_atlas('list')
% FORMAT [S,sts] = spm_atlas('select',xA,label)
% FORMAT Q = spm_atlas('query',xA,XYZmm)
% FORMAT [Q,P] = spm_atlas('query',xA,xY)
% FORMAT VM = spm_atlas('mask',xA,label)
% FORMAT... |
github | mccahill/docker-novnc-fmri-master | spm_SpUtil.m | .m | docker-novnc-fmri-master/mri/spm12/spm_SpUtil.m | 27,031 | utf_8 | 52ecc1ec2086a8b82b6e6192fd8f435a | function varargout = spm_SpUtil(varargin)
% Space matrix utilities
% FORMAT varargout = spm_SpUtil(action,varargin)
%
%_______________________________________________________________________
%
% spm_SpUtil is a multi-function function containing various utilities
% for Design matrix and contrast construction and manipu... |
github | mccahill/docker-novnc-fmri-master | spm_vb_regionF.m | .m | docker-novnc-fmri-master/mri/spm12/spm_vb_regionF.m | 2,449 | utf_8 | 86ac2edd67423fcb962720651982e2c1 | function [F] = spm_vb_regionF (Y,xY,SPM)
% Get log model evidence over a region of data for a GLM
% FORMAT [F] = spm_vb_regionF (Y,xY,SPM)
%
% Y Matrix of fMRI data (eg. from spm_summarise.m)
% xY Coordinates etc from region (eg. from spm_voi.m)
% SPM SPM data structure (this must be loaded in from an
% ... |
github | mccahill/docker-novnc-fmri-master | spm_dicom_convert.m | .m | docker-novnc-fmri-master/mri/spm12/spm_dicom_convert.m | 69,051 | utf_8 | 11e72bb7edde3955b1ad5bed2afcf530 | function out = spm_dicom_convert(hdr,opts,root_dir,format,out_dir)
% Convert DICOM images into something that SPM can use (e.g. NIfTI)
% FORMAT spm_dicom_convert(hdr,opts,root_dir,format,out_dir)
% Inputs:
% hdr - a cell array of DICOM headers from spm_dicom_headers
% opts - options:
% 'all' ... |
github | mccahill/docker-novnc-fmri-master | spm_bms_ttest.m | .m | docker-novnc-fmri-master/mri/spm12/spm_bms_ttest.m | 2,137 | utf_8 | 40afca90e274fb2978edc3b69a2d8740 | function [logbf,t] = spm_bms_ttest (y,prior)
% Log Bayes Factor against null for one sample t-test
% FORMAT [logbf,t] = spm_bms_ttest (y,prior)
%
% y [N x 1] data vector
% prior 'jzs' (default), 'unit'
%
% logbf Log Bayes Factor
% t t-statistic
%
% Default prior is 'jzs'. The different priors ... |
github | mccahill/docker-novnc-fmri-master | spm_minmax.m | .m | docker-novnc-fmri-master/mri/spm12/spm_minmax.m | 3,751 | utf_8 | 1a7267151fb6239e66dbd59584c49bea | function [mnv,mxv] = spm_minmax(g)
% Compute a suitable range of intensities for VBM preprocessing stuff
% FORMAT [mnv,mxv] = spm_minmax(g)
% g - array of data
% mnv - minimum value
% mxv - maximum value
%
% A MOG with two Gaussians is fitted to the intensities. The lower
% Gaussian is assumed to represent backgr... |
github | mccahill/docker-novnc-fmri-master | spm_create_vol.m | .m | docker-novnc-fmri-master/mri/spm12/spm_create_vol.m | 5,621 | utf_8 | 47b07a38aec31f2181cc87575abdd92c | function V = spm_create_vol(V)
% Create a NIfTI image volume
% FORMAT V = spm_create_vol(V)
% V - image volume information (see spm_vol.m)
%__________________________________________________________________________
% Copyright (C) 2005-2014 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: spm_crea... |
github | mccahill/docker-novnc-fmri-master | spm_check_results.m | .m | docker-novnc-fmri-master/mri/spm12/spm_check_results.m | 2,501 | utf_8 | ad3b39a63d2fae76927b5a4520d78736 | function spm_check_results(SPMs,xSPM)
% Display several MIPs in the same figure
% FORMAT spm_check_results(SPMs,xSPM)
% SPMs - char or cell array of paths to SPM.mat[s]
% xSPM - structure containing thresholding details, see spm_getSPM.m
%
% Beware: syntax and features of this function are likely to change.
%____... |
github | mccahill/docker-novnc-fmri-master | spm_preproc_run.m | .m | docker-novnc-fmri-master/mri/spm12/spm_preproc_run.m | 10,577 | utf_8 | a29f32c6da0c3ad98ada237fb870dabd | function varargout = spm_preproc_run(job,action)
% Segment a bunch of images
% FORMAT spm_preproc_run(job)
% job.channel(n).vols{m}
% job.channel(n).biasreg
% job.channel(n).biasfwhm
% job.channel(n).write
% job.tissue(k).tpm
% job.tissue(k).ngaus
% job.tissue(k).native
% job.tissue(k).warped
% job.warp.mrf
% job.warp.... |
github | mccahill/docker-novnc-fmri-master | spm_get_bf.m | .m | docker-novnc-fmri-master/mri/spm12/spm_get_bf.m | 5,922 | utf_8 | 315223f533f29c0ae12796af47fc955b | function [xBF] = spm_get_bf(xBF)
% Fill in basis function structure
% FORMAT [xBF] = spm_get_bf(xBF)
%
% xBF.dt - time bin length {seconds}
% xBF.name - description of basis functions specified
% 'hrf'
% 'hrf (with time derivative)'
% 'hrf (with time and dispersion deri... |
github | mccahill/docker-novnc-fmri-master | spm_dcm_connectivity_ui.m | .m | docker-novnc-fmri-master/mri/spm12/spm_dcm_connectivity_ui.m | 10,151 | utf_8 | e6dea196c6106078e1cb8558cb175b6a | function con = spm_dcm_connectivity_ui(DCM,D,title_text,defaults,enabled)
% GUI for manually specifying connection values in a DCM
% FORMAT [con] = spm_dcm_connectivity_ui(DCM,D)
%
% DCM - DCM structure
% D - 'A','B' or 'C' i.e. connectivity matrix of interest
% title_text - Text to display above the ma... |
github | mccahill/docker-novnc-fmri-master | spm_dicom_header.m | .m | docker-novnc-fmri-master/mri/spm12/spm_dicom_header.m | 18,781 | utf_8 | 0f1ee5cb85d233f04e9f6b0d44a260cc | function hdr = spm_dicom_header(P, dict)
% Read header information from a DICOM file
% FORMAT hdr = spm_dicom_header(P,dict)
% P - array of filenames
% dict - DICOM dictionary loaded from file
%
% hdr - a header.
%
% Contents of headers are approximately explained in:
% http://medical.nema.org/sta... |
github | mccahill/docker-novnc-fmri-master | spm_check_installation.m | .m | docker-novnc-fmri-master/mri/spm12/spm_check_installation.m | 20,440 | utf_8 | 04eb219daa39157fac725014a94aa8c9 | function varargout = spm_check_installation(action)
% Check SPM installation
% FORMAT spm_check_installation('basic')
% Perform a superficial check of SPM installation [default].
%
% FORMAT spm_check_installation('full')
% Perform an in-depth diagnostic of SPM installation.
%
% FORMAT rev = spm_check_installation('rev'... |
github | mccahill/docker-novnc-fmri-master | spm_BMS_bor.m | .m | docker-novnc-fmri-master/mri/spm12/spm_BMS_bor.m | 2,975 | utf_8 | d113d145b80da7ff02f75c0bf6b68d56 | function [bor,F0,F1] = spm_BMS_bor(L,posterior,priors,C)
% Compute Bayes Omnibus Risk
% FORMAT [bor,F0,F1] = spm_BMS_bor(L,posterior,priors,C)
%
% L Log model evidence table (models x subjects)
% posterior .a model counts, .r model-subject probs
% priors .a model counts
% C if this field is specifie... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_history.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_history.m | 7,785 | utf_8 | ddbe2f7ffb1d58ae0f037096df50c137 | function H = spm_eeg_history(S)
% Generate a MATLAB script from the history of an M/EEG SPM data file
% FORMAT H = spm_eeg_history(S)
%
% S - filename or input struct (optional)
% (optional) fields of S:
% history - history of M/EEG object (D.history)
% sname - filename of the MATLAB script to genera... |
github | mccahill/docker-novnc-fmri-master | spm_regions.m | .m | docker-novnc-fmri-master/mri/spm12/spm_regions.m | 10,277 | utf_8 | 917d69984ea377744ce8f98bc8fb9b48 | function [Y,xY] = spm_regions(xSPM,SPM,hReg,xY)
% VOI time-series extraction of adjusted data (& local eigenimage analysis)
% FORMAT [Y,xY] = spm_regions(xSPM,SPM,hReg,[xY])
%
% xSPM - structure containing specific SPM, distribution & filtering details
% SPM - structure containing generic analysis details
% hReg ... |
github | mccahill/docker-novnc-fmri-master | spm_file_template.m | .m | docker-novnc-fmri-master/mri/spm12/spm_file_template.m | 6,031 | utf_8 | 11aef24c0eaf739a633c25da3050baf9 | classdef spm_file_template
% Text file template engine
%
% Example:
% >> tpl = spm_file_template;
% >> tpl = file(tpl,'myfile','template.txt');
% >> tpl = var(tpl,'TITLE',spm('Ver'));
% >> tpl = var(tpl,'DATE',date);
% >> tpl = parse(tpl,'OUT','myfile');
% >> get(tpl,'OUT')
%____________________________________________... |
github | mccahill/docker-novnc-fmri-master | spm_results_ui.m | .m | docker-novnc-fmri-master/mri/spm12/spm_results_ui.m | 62,695 | utf_8 | 52e7fb3aab67932707418c808db8ec6b | function varargout = spm_results_ui(varargin)
% User interface for SPM/PPM results: Display and analysis of regional effects
% FORMAT [hReg,xSPM,SPM] = spm_results_ui('Setup',[xSPM])
%
% hReg - handle of MIP XYZ registry object
% (see spm_XYZreg.m for details)
% xSPM - structure containing specific SPM, di... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_review.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_review.m | 9,773 | utf_8 | 0e8feb9855f80304a42069281aa0b3d6 | function spm_eeg_review(D,flag,inv)
% General review (display) of SPM meeg object
% FORMAT spm_eeg_review(D,flags,inv)
%
% INPUT:
% D - meeg object
% flag - switch to any of the displays (optional)
% inv - which source reconstruction to display (when called from
% spm_eeg_inv_imag_api.m)
%____________________... |
github | mccahill/docker-novnc-fmri-master | spm_coreg.m | .m | docker-novnc-fmri-master/mri/spm12/spm_coreg.m | 14,221 | utf_8 | 57edbfddf8cb9a3ed5e3cc64e3696cf0 | function x = spm_coreg(varargin)
% Between modality coregistration using information theory
% FORMAT x = spm_coreg(VG,VF,flags)
% VG - handle for reference image (see spm_vol).
% VF - handle for source (moved) image.
% flags - a structure containing the following elements:
% sep - optimisation sampl... |
github | mccahill/docker-novnc-fmri-master | spm_axis.m | .m | docker-novnc-fmri-master/mri/spm12/spm_axis.m | 906 | utf_8 | 7151ac1eea99c4f1ba40be428746c6a2 | function varargout = spm_axis(varargin)
% AXIS Control axis scaling and appearance.
if nargout
[varargout{1:nargout}] = axis(varargin{:});
else
try
axis(varargin{:});
end
end
if nargin == 1 && any(strcmpi(varargin{1},{'tight','scale'}))
spm_axis(gca,varargin{1});
elseif nargin == 2 && allAxes... |
github | mccahill/docker-novnc-fmri-master | spm_uw_estimate.m | .m | docker-novnc-fmri-master/mri/spm12/spm_uw_estimate.m | 33,583 | utf_8 | 2dfbce5635876b2dc1527ff4742aa23a | function ds = spm_uw_estimate(P,par)
% Estimation of partial derivatives of EPI deformation fields
%
% FORMAT [ds] = spm_uw_estimate((P),(par))
%
% P - List of file names or headers.
% par - Structure containing parameters governing the specifics
% of how to estimate the fields.
% .M ... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_specest_mtmconvol.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_specest_mtmconvol.m | 5,316 | utf_8 | 60838379126832234202a1071a12eeb3 | function res = spm_eeg_specest_mtmconvol(S, data, time)
% Plugin for spm_eeg_tf implementing spectral estimation using Fieldtrip's freqanalysis_mtmconvol
% FORMAT res = spm_eeg_specest_ft_mtmconvol(S, data, time)
%
% S - input structure
% fields of S:
% S.taper - taper to use ('hanning', 'r... |
github | mccahill/docker-novnc-fmri-master | spm_eeg_inv_vbecd_gui.m | .m | docker-novnc-fmri-master/mri/spm12/spm_eeg_inv_vbecd_gui.m | 27,952 | utf_8 | 14da72f11767dff271d6113b58cd81da | function D = spm_eeg_inv_vbecd_gui(D,val)
% GUI function for Bayesian ECD inversion
% - load the necessary data, if not provided
% - fill in all the necessary bits for the VB-ECD inversion routine,
% - launch the B_ECD routine, aka. spm_eeg_inv_vbecd
% - displays the results.
%__________________________________________... |
github | mccahill/docker-novnc-fmri-master | spm_changepath.m | .m | docker-novnc-fmri-master/mri/spm12/spm_changepath.m | 3,869 | utf_8 | ba43d18fcb193c2bafae0a418452b537 | function varargout = spm_changepath(Sf, oldp, newp)
% Recursively replace all occurences of a text pattern in a MATLAB variable.
% FORMAT S = spm_changepath(Sf, oldp, newp)
%
% Sf - MATLAB variable to fix, or char array of MAT filenames,
% or directory name (all found MAT files will be analysed)
% oldp... |
github | mccahill/docker-novnc-fmri-master | cfg_util.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_util.m | 77,581 | utf_8 | bd195e1a657c581a2ccadd24db9a7f8d | function varargout = cfg_util(cmd, varargin)
% This is the command line interface to the batch system. It manages the
% following structures:
% * Generic configuration structure c0. This structure will be initialised
% to an cfg_repeat with empty .values list. Each application should
% provide an application-speci... |
github | mccahill/docker-novnc-fmri-master | cfg_load_jobs.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_load_jobs.m | 1,975 | utf_8 | 24d57ef2c0762a668e5dee87c6319ce7 | function [newjobs, uind] = cfg_load_jobs(job)
% function newjobs = cfg_load_jobs(job)
%
% Load a list of possible job files, return a cell list of jobs.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%________________________________________... |
github | mccahill/docker-novnc-fmri-master | cfg_ui.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_ui.m | 40,936 | utf_8 | d58887a92b0740f36e6dfb2de02176b3 | function varargout = cfg_ui(varargin)
% CFG_UI M-File for cfg_ui.fig
% CFG_UI, by itself, creates a new CFG_UI or raises the existing
% singleton*.
%
% H = CFG_UI returns the handle to a new CFG_UI or the handle to
% the existing singleton*.
%
% CFG_UI('CALLBACK',hObject,eventData,handles,...) ... |
github | mccahill/docker-novnc-fmri-master | gencode_rvalue.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/gencode_rvalue.m | 6,198 | utf_8 | c5e0af86f39322a8d0fe0517e1f9d8c4 | function [str, sts] = gencode_rvalue(item, cflag)
% GENCODE_RVALUE Code for right hand side of MATLAB assignment
% Generate the right hand side for a valid MATLAB variable
% assignment. This function is a helper to GENCODE, but can be used on
% its own to generate code for the following types of variables:
% * scalar... |
github | mccahill/docker-novnc-fmri-master | cfg_getfile.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_getfile.m | 51,231 | utf_8 | 2b8227dc8614e49e7c17ac2771988a19 | function [t,sts] = cfg_getfile(varargin)
% File selector
% FORMAT [t,sts] = cfg_getfile(n,typ,mesg,sel,wd,filt,prms)
% n - Number of files
% A single value or a range. e.g.
% 1 - Select one file
% Inf - Select any number of files
% [1 Inf] - Select 1 to Inf ... |
github | mccahill/docker-novnc-fmri-master | cfg_ui_multibatch.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_ui_multibatch.m | 18,628 | utf_8 | 994a2831892bccad99c5364ef85b8fc6 | function varargout = cfg_ui_multibatch(varargin)
% CFG_UI_MULTIBATCH MATLAB code for cfg_ui_multibatch.fig
% CFG_UI_MULTIBATCH, by itself, creates a new CFG_UI_MULTIBATCH or raises the existing
% singleton*.
%
% H = CFG_UI_MULTIBATCH returns the handle to a new CFG_UI_MULTIBATCH or the handle to
% t... |
github | mccahill/docker-novnc-fmri-master | cfg_struct2cfg.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_struct2cfg.m | 4,221 | utf_8 | 528320103babd350c9b0d18dcd1ac728 | function cc = cfg_struct2cfg(co, indent)
% Import a config structure into a matlabbatch class tree. Input structures
% are those generated from the configuration editor, cfg2struct methods or
% spm_jobman config structures.
%
% The layout of the configuration tree and the types of configuration items
% have been kept ... |
github | mccahill/docker-novnc-fmri-master | cfg_serial.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_serial.m | 10,187 | utf_8 | 02ee496b3800b2d190cd80be5e683b05 | function cfg_serial(guifcn, job, varargin)
% This function is deprecated.
% The functionality should replaced by the following sequence of calls:
%
% Instead of
% cfg_serial(guifcn, job, varargin)
% use
% cjob = cfg_util('initjob', job);
% sts = cfg_util('filljobui', cjob, guifcn, varargin);
% if sts
% cfg_util(... |
github | mccahill/docker-novnc-fmri-master | gencode.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/gencode.m | 8,379 | utf_8 | b4207998f286a5119f60030d9dc208f7 | function [str, tag, cind] = gencode(item, tag, tagctx)
% GENCODE Generate code to recreate any MATLAB struct/cell variable.
% For any MATLAB variable, this function generates a .m file that
% can be run to recreate it. Classes can implement their class specific
% equivalent of gencode with the same calling syntax. By... |
github | mccahill/docker-novnc-fmri-master | cfg_message.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_message.m | 9,858 | utf_8 | 54e948d224ffc77bbc5a4c740e3ebaa2 | function varargout = cfg_message(varargin)
% function cfg_message(msgid, msgfmt, varargin)
% Display a message. The message identifier msgid will be looked up in a
% message database to decide how to treat this message. This database is
% a struct array with fields:
% .identifier - message id
% .level - message... |
github | mccahill/docker-novnc-fmri-master | cfg_ui_util.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_ui_util.m | 28,599 | utf_8 | aa0cf5c5a74c48c2a2461a50fe328a4a | function varargout = cfg_ui_util(cmd, varargin)
%CFG_UI_UTIL utility functions for displaying job, module and item values
% This function is a collection of utility functions to display a job,
% module or data summary. It also handles all value display and editing for
% a particular item.
%
% This code is part of a bat... |
github | mccahill/docker-novnc-fmri-master | initialise.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/@cfg_branch/initialise.m | 2,320 | utf_8 | e33a8c7707d19f85627dd03955ff79cb | function item = initialise(item, val, dflag)
% function item = initialise(item, val, dflag)
% Initialise a configuration tree with values. If val is a job
% struct/cell, only the parts of the configuration that are present in
% this job will be initialised.
% If val has the special value '<DEFAULTS>', the entire confi... |
github | mccahill/docker-novnc-fmri-master | cfg_run_subsrefvar.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_basicio/cfg_run_subsrefvar.m | 6,686 | utf_8 | daad846e0faec15f03788c48065c474d | function varargout = cfg_run_subsrefvar(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = cfg_run_subsrefvar(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_run_subsrefvar('run', job)
% Run a job, and return its output argumen... |
github | mccahill/docker-novnc-fmri-master | cfg_run_call_matlab.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_basicio/cfg_run_call_matlab.m | 5,995 | utf_8 | afc10d877d7bb3f52c6f308ede6c4707 | function varargout = cfg_run_call_matlab(cmd, varargin)
% A generic interface to call any MATLAB function through the batch system
% and make its output arguments available as dependencies.
% varargout = cfg_run_call_matlab(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_run_call_matlab('run', job)
% ... |
github | mccahill/docker-novnc-fmri-master | cfg_load_vars.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_basicio/cfg_load_vars.m | 5,292 | utf_8 | f097076d4059331911b30b3a67a48c3d | function varargout = cfg_load_vars(cmd, varargin)
% Load a .mat file, and return its contents via output dependencies.
% varargout = cfg_load_vars(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_load_vars('run', job)
% Run a job, and return its output argument
% 'vout' - dep = cfg_load_va... |
github | mccahill/docker-novnc-fmri-master | create_cfg_cfg_basicio.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/cfg_basicio/src/create_cfg_cfg_basicio.m | 1,490 | utf_8 | 1ab27a6291fa156177f78a5515a2624d | function create_cfg_cfg_basicio
src_dir = fileparts(mfilename('fullpath'));
cfg_dir = fileparts(src_dir);
out = process_dir(src_dir);
%% Code Generator batch
codegen = fullfile(src_dir,'batch_basicio_codegen.m');
id = cfg_util('initjob',codegen);
cfg_util('filljob',id,{cfg_dir},out);
cfg_util('run',id);
cfg_util('deljo... |
github | mccahill/docker-novnc-fmri-master | initialise.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/@cfg_choice/initialise.m | 3,476 | utf_8 | 442ecd7195dc341fda468e000d6b5854 | function item = initialise(item, val, dflag)
% function item = initialise(item, val, dflag)
% Initialise a configuration tree with values. If val is a job
% struct/cell, only the parts of the configuration that are present in
% this job will be initialised. If dflag is true, then matching items
% from item.values will... |
github | mccahill/docker-novnc-fmri-master | subsasgn.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/@cfg_dep/subsasgn.m | 4,224 | utf_8 | 98a5acff1bf7803cc4bd59cd0930ca31 | function dep = subsasgn(dep, subs, varargin)
% function dep = subsasgn(dep, subs, varargin)
% subscript references we have to deal with are:
% one level
% dep.(field) - i.e. struct('type',{'.'} ,'subs',{field})
% dep(idx) - i.e. struct('type',{'()'},'subs',{idx})
% two levels
% dep(idx).(field)
%
% to be dealt ... |
github | mccahill/docker-novnc-fmri-master | cfg_example_cumsum1.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/examples/cfg_example_cumsum1.m | 2,891 | utf_8 | 23f6fba4270a8acd77c9324318e47a05 | function cumsum = cfg_example_cumsum1
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as vector, the output is a vector containing the
% cumulative sums. This function differs from cfg_example_sum (except from
% names) only in the specification of the output subscript.
%
% Thi... |
github | mccahill/docker-novnc-fmri-master | cfg_example_div.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/examples/cfg_example_div.m | 3,312 | utf_8 | 0b78f049e9e37d5746c7afc33384510b | function div = cfg_example_div
% Example script that creates an cfg_exbranch to compute mod and rem of two
% natural numbers. The inputs are entered as two single numbers, the output
% is a struct with two fields 'mod' and 'rem'.
%
% This code is part of a batch job configuration system for MATLAB. See
% help mat... |
github | mccahill/docker-novnc-fmri-master | cfg_example_add2.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/examples/cfg_example_add2.m | 2,622 | utf_8 | 1f1af41a7da0e1e6bd9839d66705b0ed | function add2 = cfg_example_add2
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as 2-vector, the output is just a single
% number.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%___________________... |
github | mccahill/docker-novnc-fmri-master | cfg_example_add1.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/examples/cfg_example_add1.m | 3,291 | utf_8 | ea93e248b0ce90d87b6616e927d55829 | function add1 = cfg_example_add1
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as two single numbers, the output is just a single
% number.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%_________... |
github | mccahill/docker-novnc-fmri-master | cfg_example_cumsum2.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/examples/cfg_example_cumsum2.m | 3,392 | utf_8 | db5b5ac94fe794d4450fecbf07fe0c63 | function cumsum = cfg_example_cumsum2
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as vector, the output is a vector containing the
% cumulative sums. This function differs from cfg_example_sum (except from
% names) only in the specification of the output subscript.
%
% Thi... |
github | mccahill/docker-novnc-fmri-master | cfg_example_sum.m | .m | docker-novnc-fmri-master/mri/spm12/matlabbatch/examples/cfg_example_sum.m | 2,706 | utf_8 | 2dcd9f8e452fa818b4d3aaee964921d5 | function sum = cfg_example_sum
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as vector, the output is just a single
% number. This function differs from cfg_example_add2 (except from names)
% only in the specification of input1.num.
%
% This code is part of a batch job confi... |
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