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github | philippboehmsturm/antx-master | flip_lr.m | .m | antx-master/mritools/others/nii/flip_lr.m | 3,568 | utf_8 | d95b62698d44a65a3c2f02fbabc632ac | % When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
% it with 'view_nii.m', you may find that the image is L-R flipped.
% This is because of the confusion of radiological and neurological
% convention in the medical image before NIfTI format is adopted. You
% can find more details from:
%
%... |
github | philippboehmsturm/antx-master | save_nii.m | .m | antx-master/mritools/others/nii/save_nii.m | 9,690 | utf_8 | ed292054cab74afaf953455bfbc200aa | % Save NIFTI dataset. Support both *.nii and *.hdr/*.img file extension.
% If file extension is not provided, *.hdr/*.img will be used as default.
%
% Usage: save_nii(nii, filename, [old_RGB])
%
% nii.hdr - struct with NIFTI header fields (from load_nii.m or make_nii.m)
%
% nii.img - 3D (or 4D) matrix o... |
github | philippboehmsturm/antx-master | rri_file_menu.m | .m | antx-master/mritools/others/nii/rri_file_menu.m | 4,153 | utf_8 | c9faa3905c642854eeed98ab8b02998e | % Imbed a file menu to any figure. If file menu exist, it will append
% to the existing file menu. This file menu includes: Copy to clipboard,
% print, save, close etc.
%
% Usage: rri_file_menu(fig);
%
% rri_file_menu(fig,0) means no 'Close' menu.
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
... |
github | philippboehmsturm/antx-master | reslice_nii.m | .m | antx-master/mritools/others/nii/reslice_nii.m | 10,138 | utf_8 | ea18d2f994fd5d9989449feaced1e4dd | % The basic application of the 'reslice_nii.m' program is to perform
% any 3D affine transform defined by a NIfTI format image.
%
% In addition, the 'reslice_nii.m' program can also be applied to
% generate an isotropic image from either a NIfTI format image or
% an ANALYZE format image.
%
% The resliced N... |
github | philippboehmsturm/antx-master | save_untouch_nii.m | .m | antx-master/mritools/others/nii/save_untouch_nii.m | 6,726 | utf_8 | cb98e2799abc112dca5b10078bde09bf | % Save NIFTI or ANALYZE dataset that is loaded by "load_untouch_nii.m".
% The output image format and file extension will be the same as the
% input one (NIFTI.nii, NIFTI.img or ANALYZE.img). Therefore, any file
% extension that you specified will be ignored.
%
% Usage: save_untouch_nii(nii, filename)
%
%... |
github | philippboehmsturm/antx-master | view_nii.m | .m | antx-master/mritools/others/nii/view_nii.m | 144,481 | utf_8 | 8ea68ec34d3a6bec721497afb56cfb54 | % VIEW_NII: Create or update a 3-View (Front, Top, Side) of the
% brain data that is specified by nii structure
%
% Usage: status = view_nii([h], nii, [option]) or
% status = view_nii(h, [option])
%
% Where, h is the figure on which the 3-View will be plotted;
% nii is the brain data in NIFTI format;
% o... |
github | philippboehmsturm/antx-master | mat_into_hdr.m | .m | antx-master/mritools/others/nii/mat_into_hdr.m | 2,691 | utf_8 | 847d96698f45f7c5e7decbb3a0c3187f | %MAT_INTO_HDR The old versions of SPM (any version before SPM5) store
% an affine matrix of the SPM Reoriented image into a matlab file
% (.mat extension). The file name of this SPM matlab file is the
% same as the SPM Reoriented image file (.img/.hdr extension).
%
% This program will convert the ANALYZE 7.5 SPM... |
github | philippboehmsturm/antx-master | xform_nii.m | .m | antx-master/mritools/others/nii/xform_nii.m | 18,628 | utf_8 | e39c421e7f117cbc81c56e9d023774a3 | % internal function
% 'xform_nii.m' is an internal function called by "load_nii.m", so
% you do not need run this program by yourself. It does simplified
% NIfTI sform/qform affine transform, and supports some of the
% affine transforms, including translation, reflection, and
% orthogonal rotation (N*90 ... |
github | philippboehmsturm/antx-master | make_ana.m | .m | antx-master/mritools/others/nii/make_ana.m | 5,665 | utf_8 | 37d574b277823f941138c9548127d720 | % Make ANALYZE 7.5 data structure specified by a 3D or 4D matrix.
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the ANALYZE structure is made, it can be saved into ANALYZE 7.5
% format data file using "save_untouch_nii" command (for more de... |
github | philippboehmsturm/antx-master | extra_nii_hdr.m | .m | antx-master/mritools/others/nii/extra_nii_hdr.m | 8,085 | utf_8 | 4f76a8a66736025a0acf3efa15a2d2aa | % Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.da... |
github | philippboehmsturm/antx-master | rri_xhair.m | .m | antx-master/mritools/others/nii/rri_xhair.m | 2,300 | utf_8 | 95954b8cd43e01fba5c4b2f335be1780 | % rri_xhair: create a pair of full_cross_hair at point [x y] in
% axes h_ax, and return xhair struct
%
% Usage: xhair = rri_xhair([x y], xhair, h_ax);
%
% If omit xhair, rri_xhair will create a pair of xhair; otherwise,
% rri_xhair will update the xhair. If omit h_ax, current axes will
% b... |
github | philippboehmsturm/antx-master | save_untouch_nii_hdr.m | .m | antx-master/mritools/others/nii/save_untouch_nii_hdr.m | 8,721 | utf_8 | 0d396eaeebb6114f24d56ab74a8299cf | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%------------------------------------------------... |
github | philippboehmsturm/antx-master | expand_nii_scan.m | .m | antx-master/mritools/others/nii/expand_nii_scan.m | 1,381 | utf_8 | 0715d668d046bcc608ea78cd0c2089bd | % Expand a multiple-scan NIFTI file into multiple single-scan NIFTI files
%
% Usage: expand_nii_scan(multi_scan_filename, [img_idx], [path_to_save])
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function expand_nii_scan(filename, img_idx, n... |
github | philippboehmsturm/antx-master | load_untouch_header_only.m | .m | antx-master/mritools/others/nii/load_untouch_header_only.m | 7,255 | utf_8 | f1210f851ab6610e7656121194cb5c8b | % Load NIfTI / Analyze header without applying any appropriate affine
% geometric transform or voxel intensity scaling. It is equivalent to
% hdr field when using load_untouch_nii to load dataset. Support both
% *.nii and *.hdr file extension. If file extension is not provided,
% *.hdr will be used as default.... |
github | philippboehmsturm/antx-master | bipolar.m | .m | antx-master/mritools/others/nii/bipolar.m | 2,239 | utf_8 | c860ec93d96b6ab636c985280d79958d | %BIPOLAR returns an M-by-3 matrix containing a blue-red colormap, in
% in which red stands for positive, blue stands for negative,
% and white stands for 0.
%
% Usage: cmap = bipolar(M, lo, hi, contrast); or cmap = bipolar;
%
% cmap: output M-by-3 matrix for BIPOLAR colormap.
% M: number of shades in th... |
github | philippboehmsturm/antx-master | save_nii_hdr.m | .m | antx-master/mritools/others/nii/save_nii_hdr.m | 9,497 | utf_8 | 66a99df0cb0f3c1f44c6e36dcd13cddf | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~exist('hdr','var') | ~exist('fid','var')
error('Usage: save_nii_hdr(hdr, fid)');
end
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
... |
github | philippboehmsturm/antx-master | skullstrip_pcnn3d.m | .m | antx-master/mritools/others/PCNN3D/skullstrip_pcnn3d.m | 1,473 | utf_8 | 9caa6079dcad36d4cb8d74d33386ce79 |
function skullstrip_pcnn3d(t2file, fileout, mode )
if 0
skullstrip_pcnn3d(fullfile(pwd,'t2_aa.nii'), fullfile(pwd, '_test1.nii' ), 'mask' )
skullstrip_pcnn3d(fullfile(pwd,'t2_aa.nii'), fullfile(pwd, '_test2.nii' ), 'skullstrip' )
end
warning off;
% tmpfile=fullfile(fileparts(t2fi... |
github | philippboehmsturm/antx-master | screencapture.m | .m | antx-master/mritools/others/ScreenCapture/screencapture.m | 37,131 | utf_8 | 221211bbef30a51283574e24a0c5fb2a | function imageData = screencapture(varargin)
% screencapture - get a screen-capture of a figure frame, component handle, or screen area rectangle
%
% ScreenCapture gets a screen-capture of any Matlab GUI handle (including desktop,
% figure, axes, image or uicontrol), or a specified area rectangle located relative ... |
github | philippboehmsturm/antx-master | demo_WindowAPI.m | .m | antx-master/mritools/others/windowapi/demo_WindowAPI.m | 7,664 | utf_8 | 4521f3e55d6634de6a8e4bf7fa63ced1 | function demo_WindowAPI
% Demo for WindowAPI
% The function WindowAPI has grown to an universal super tool. Unfortunately
% this reduces the readability of the help section. Therefore I've created this
% function to demonstrate the usage of all features.
%
% Author: Jan Simon, Heidelberg, (C) 2008-2016 matlab.THISYEAR(... |
github | philippboehmsturm/antx-master | spm_uitab.m | .m | antx-master/xspm8/spm_uitab.m | 7,695 | utf_8 | e80b69279b276644a59f0e838bc07817 | function [handles] = spm_uitab(hparent,labels,callbacks,...
tag,active,height,tab_height)
% Create tabs in the SPM Graphics window
% FORMAT [handles] = spm_uitab(hfig,labels,callbacks,...
% tag,active,height,tab_height)
% This functiuon creates tabs in the SPM graphics window.
% These tabs may be associated with... |
github | philippboehmsturm/antx-master | spm_vb_ppm_anova.m | .m | antx-master/xspm8/spm_vb_ppm_anova.m | 3,873 | utf_8 | 5360b2f4d1d7fe1f61c455b53a468fd5 | function spm_vb_ppm_anova(SPM)
% Bayesian ANOVA using model comparison
% FORMAT spm_vb_ppm_anova(SPM)
%
% SPM - Data structure corresponding to a full model (ie. one
% containing all experimental conditions).
%
% This function creates images of differences in log evidence
% which characterise t... |
github | philippboehmsturm/antx-master | spm_fmri_spm_ui.m | .m | antx-master/xspm8/spm_fmri_spm_ui.m | 19,258 | utf_8 | 8205c5db88ee6848b51de86102b8b0d0 | function [SPM] = spm_fmri_spm_ui(SPM)
% Setting up the general linear model for fMRI time-series
% FORMAT [SPM] = spm_fmri_spm_ui(SPM)
%
% creates SPM with the following fields
%
% xY: [1x1 struct] - data structure
% nscan: [double] - vector of scans per session
% xBF: [1x1 struct] - Basis function st... |
github | philippboehmsturm/antx-master | spm_input.m | .m | antx-master/xspm8/spm_input.m | 89,733 | utf_8 | 57a58b73c9dcef093e755ad4051efd65 | function varargout = spm_input(varargin)
% Comprehensive graphical and command line input function
% FORMATs (given in Programmers Help)
%_______________________________________________________________________
%
% spm_input handles most forms of interactive user input for SPM.
% (File selection is handled by spm_select... |
github | philippboehmsturm/antx-master | spm_realign.m | .m | antx-master/xspm8/spm_realign.m | 18,390 | utf_8 | 40c5bf8bb41fe8dfc414a2afccf6270d | function P = spm_realign(P,flags)
% Estimation of within modality rigid body movement parameters
% FORMAT P = spm_realign(P,flags)
%
% P - matrix of filenames {one string per row}
% All operations are performed relative to the first image.
% ie. Coregistration is to the first image, and resampling
%... |
github | philippboehmsturm/antx-master | spm_surf.m | .m | antx-master/xspm8/spm_surf.m | 9,740 | utf_8 | aa92ddde8b875463a0fefee45e0a1d79 | function varargout = spm_surf(P,mode,thresh)
% Surface extraction
% FORMAT spm_surf(P,mode,thresh)
%
% P - char array of filenames
% Usually, this will be c1xxx.img & c2xxx.img - grey and white
% matter segments created using the segmentation routine.
% mode - operation mode [1: rendering, 2: s... |
github | philippboehmsturm/antx-master | spm_eeg_plotScalpData.m | .m | antx-master/xspm8/spm_eeg_plotScalpData.m | 11,761 | utf_8 | 47767f883d6ed147946a3f14900db01d | function [ZI,f] = spm_eeg_plotScalpData(Z,pos,ChanLabel,in)
% Display interpolated sensor data on the scalp in a new figure
% FORMAT [ZI,f] = spm_eeg_plotScalpData(Z,pos,ChanLabel,in)
%
% INPUT:
% Z - the data matrix at the sensors
% pos - the positions of the sensors
% ChanLabel - the names of t... |
github | philippboehmsturm/antx-master | spm_eeg_render.m | .m | antx-master/xspm8/spm_eeg_render.m | 10,872 | utf_8 | 52b7ba99932d4227bf2efefcc8766540 | function [out] = spm_eeg_render(m,options)
% Visualisation routine for the cortical surface
% FORMAT [out] = spm_eeg_render(m,options)
%
% INPUT:
% - m = MATLAB mesh (containing the fields .faces et .vertices) or GIFTI
% format file.
% - options = structure variable:
% .texture = texture to be projected onto the... |
github | philippboehmsturm/antx-master | spm_write_sn.m | .m | antx-master/xspm8/spm_write_sn.m | 19,859 | utf_8 | 0ea1c7ae2ba1644c71deaf8ae1518452 | function VO = spm_write_sn(V,prm,flags,extras)
% Write out warped images
% FORMAT VO = spm_write_sn(V,prm,flags,msk)
% V - Images to transform (filenames or volume structure).
% prm - Transformation information (filename or structure).
% flags - flags structure, with fields...
% interp - i... |
github | philippboehmsturm/antx-master | spm_DesMtx.m | .m | antx-master/xspm8/spm_DesMtx.m | 32,503 | utf_8 | 3378b7ab974fe4c63802be7041a77998 | function [X,Pnames,Index,idx,jdx,kdx]=spm_DesMtx(varargin)
% Design matrix construction from factor level and covariate vectors
% FORMAT [X,Pnames] = spm_DesMtx(<FCLevels-Constraint-FCnames> list)
% FORMAT [X,Pnames,Index,idx,jdx,kdx] = spm_DesMtx(FCLevels,Constraint,FCnames)
%
% <FCLevels-Constraints-FCnames>
% ... |
github | philippboehmsturm/antx-master | spm_eeg_review_callbacks.m | .m | antx-master/xspm8/spm_eeg_review_callbacks.m | 76,846 | utf_8 | 4bf26af64c0f704d189a16b6116cf1fb | function [varargout] = spm_eeg_review_callbacks(varargin)
% Callbacks of the M/EEG Review facility
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Jean Daunizeau
% $Id: spm_eeg_review_callbacks.m 6071 2014-06-27 12:52:33Z guillau... |
github | philippboehmsturm/antx-master | spm_imatrix.m | .m | antx-master/xspm8/spm_imatrix.m | 1,545 | utf_8 | 6bd968e6c68acf278802d6e9a58610fa | function P = spm_imatrix(M)
% returns the parameters for creating an affine transformation
% FORMAT P = spm_imatrix(M)
% M - Affine transformation matrix
% P - Parameters (see spm_matrix for definitions)
%___________________________________________________________________________
% Copyright (C) 2008 Wellcome... |
github | philippboehmsturm/antx-master | spm_affreg.m | .m | antx-master/xspm8/spm_affreg.m | 18,516 | utf_8 | 0861aa4a29a7aac70856750d2c0af6ff | function [M,scal] = spm_affreg(VG,VF,flags,M,scal)
% Affine registration using least squares.
% FORMAT [M,scal] = spm_affreg(VG,VF,flags,M0,scal0)
%
% VG - Vector of template volumes.
% VF - Source volume.
% flags - a structure containing various options. The fields are:
% WG - Weig... |
github | philippboehmsturm/antx-master | spm_eeg_locate_channels.m | .m | antx-master/xspm8/spm_eeg_locate_channels.m | 2,870 | utf_8 | 5c2b41cee32e14bd2f6b0d7565ddd0fb | function [Cel, Cind, x, y] = spm_eeg_locate_channels(D, n, interpolate_bad)
% Locate channels and generate mask for converting M/EEG data into images
% FORMAT [Cel, Cind, x, y] = spm_eeg_locate_channels(D, n, interpolate_bad)
%
% D - M/EEG object
% n - number of voxels in each direction
% in... |
github | philippboehmsturm/antx-master | spm_eeg_filter.m | .m | antx-master/xspm8/spm_eeg_filter.m | 6,617 | utf_8 | 38ceb423092384f9bf967a6534b6484e | function D = spm_eeg_filter(S)
% Filter M/EEG data
% FORMAT D = spm_eeg_filter(S)
%
% S - input structure (optional)
% (optional) fields of S:
% S.D - MEEG object or filename of M/EEG mat-file
% S.filter - struct with the following fields:
% type - optional filter type, can be
% ... |
github | philippboehmsturm/antx-master | savexml.m | .m | antx-master/xspm8/savexml.m | 5,240 | utf_8 | 575501e05a68903f8f5a2db4cb6a18e9 | function savexml(filename, varargin)
%SAVEXML Save workspace variables to disk in XML.
% SAVEXML FILENAME saves all workspace variables to the XML-file
% named FILENAME.xml. The data may be retrieved with LOADXML. if
% FILENAME has no extension, .xml is assumed.
%
% SAVE, by itself, creates the XML-file named 'ma... |
github | philippboehmsturm/antx-master | spm_bilinear.m | .m | antx-master/xspm8/spm_bilinear.m | 3,787 | utf_8 | 37e6b8a17a436698a9c87c2c7e5235be | function [H0,H1,H2] = spm_bilinear(A,B,C,D,x0,N,dt)
% returns global Volterra kernels for a MIMO Bilinear system
% FORMAT [H0,H1,H2] = spm_bilinear(A,B,C,D,x0,N,dt)
% A - (n x n) df(x(0),0)/dx - n states
% B - (n x n x m) d2f(x(0),0)/dxdu - m inputs
% C - (n x m) d... |
github | philippboehmsturm/antx-master | spm_powell.m | .m | antx-master/xspm8/spm_powell.m | 8,945 | utf_8 | 5c2706664704f8db313454deb4e1b755 | function [p,f] = spm_powell(p,xi,tolsc,func,varargin)
% Powell optimisation method
% FORMAT [p,f] = spm_powell(p,xi,tolsc,func,varargin)
% p - Starting parameter values
% xi - columns containing directions in which to begin
% searching.
% tolsc - stopping criteria
% - opt... |
github | philippboehmsturm/antx-master | spm_vol.m | .m | antx-master/xspm8/spm_vol.m | 4,687 | utf_8 | 2066ba9cc72b0c288e592c2871538689 | function V = spm_vol(P)
% Get header information for images.
% FORMAT V = spm_vol(P)
% P - a matrix of filenames.
% V - a vector of structures containing image volume information.
% The elements of the structures are:
% V.fname - the filename of the image.
% V.dim - the x, y and z dimensions of the volume... |
github | philippboehmsturm/antx-master | spm_eeg_epochs.m | .m | antx-master/xspm8/spm_eeg_epochs.m | 7,801 | utf_8 | 4fabb15c82422268deb9dca5b1a0ea6b | function D = spm_eeg_epochs(S)
% Epoching continuous M/EEG data
% FORMAT D = spm_eeg_epochs(S)
%
% S - input structure (optional)
% (optional) fields of S:
% S.D - MEEG object or filename of M/EEG mat-file with
% continuous data
% S.bc - bas... |
github | philippboehmsturm/antx-master | spm_jobman.m | .m | antx-master/xspm8/spm_jobman.m | 21,770 | utf_8 | 10c04d4d60570a5fff732bdebb4a6482 | function varargout = spm_jobman(varargin)
% Main interface for SPM Batch System
% This function provides a compatibility layer between SPM and matlabbatch.
% It translates spm_jobman callbacks into matlabbatch callbacks and allows
% to edit and run SPM5 style batch jobs.
%
% FORMAT spm_jobman('initcfg')
% Initialise jo... |
github | philippboehmsturm/antx-master | spm_bms_partition.m | .m | antx-master/xspm8/spm_bms_partition.m | 4,648 | utf_8 | 0b0d4cfa175b9620fe86629a8490391c | function spm_bms_partition(BMS)
% Compute model partitioning for BMS
% FORMAT spm_bms_partition(BMS)
%
% Input:
% BMS structure (BMS.mat)
%
% Output:
% PPM (images) for each of the subsets defined
% xppm_subsetn.img (RFX) and ppm_subsetn.img (FFX)
%_______________________________________________________________________... |
github | philippboehmsturm/antx-master | spm_eeg_inv_vbecd_disp.m | .m | antx-master/xspm8/spm_eeg_inv_vbecd_disp.m | 23,018 | UNKNOWN | 5277a06e987a0014165d867f7c51bb1b | function spm_eeg_inv_vbecd_disp(action,varargin)
% Display the dipoles as obtained from VB-ECD
%
% FORMAT spm_eeg_inv_vbecd_disp('Init',D)
% Display the latest VB-ECD solution saved in the .inv{} field of the
% data structure D.
%
% FORMAT spm_eeg_inv_vbecd_disp('Init',D, ind)
% Display the ind^th .inv{} cell element, ... |
github | philippboehmsturm/antx-master | spm_eeg_definetrial.m | .m | antx-master/xspm8/spm_eeg_definetrial.m | 11,429 | utf_8 | 56a6ae7de86bca4e155843aa0d2f736f | function [trl, conditionlabels, S] = spm_eeg_definetrial(S)
% Definition of trials based on events
% FORMAT[trl, conditionlabels, S] = spm_eeg_definetrial(S)
% S - input structure (optional)
% (optional) fields of S:
% S.event - event struct (optional)
% S.fsample - sampling rate
% S.... |
github | philippboehmsturm/antx-master | spm_mvb_cvk2.m | .m | antx-master/xspm8/spm_mvb_cvk2.m | 5,093 | utf_8 | 751f7db1cea711d16bdb424252c3e636 | function [p,pc,R2] = spm_mvb_cvk2(MVB,k)
% k-fold cross validation of a multivariate Bayesian model
% FORMAT [p_value,percent,R2] = spm_mvb_cvk(MVB,k)
%
% MVB - Multivariate Bayes structure
% k - k-fold cross-validation ('0' implies a leave-one-out scheme)
%
% p - p-value: under a null GLM
% percent: proportion cor... |
github | philippboehmsturm/antx-master | spm_eeg_displayECD.m | .m | antx-master/xspm8/spm_eeg_displayECD.m | 8,250 | utf_8 | 471c105bf4bbbec394478ff1a280b571 | function [out] = spm_eeg_displayECD(Pos,Orient,Var,Names,options)
% Plot dipole positions onto the SPM canonical mesh
% FORMAT [out] = spm_eeg_displayDipoles(Pos,Orient,Var,Names,options)
%
% IN (admissible choices):
% - Pos: a 3xndip matrix containing the positions of the dipoles in
% the canonical frame of refere... |
github | philippboehmsturm/antx-master | spm_uw_apply.m | .m | antx-master/xspm8/spm_uw_apply.m | 14,676 | utf_8 | 79e215c42faaa2e17fc6bae5cea47179 | function varargout = spm_uw_apply(ds,flags)
% Reslices images volume by volume
% FORMAT spm_uw_apply(ds,[flags])
% or
% FORMAT P = spm_uw_apply(ds,[flags])
%
%
% ds - a structure created by spm_uw_estimate.m containing the fields:
% ds can also be an array of structures, each struct corr... |
github | philippboehmsturm/antx-master | spm_eeg_prep_ui.m | .m | antx-master/xspm8/spm_eeg_prep_ui.m | 29,442 | utf_8 | 80bb3efbe6195079a20c2e95d5a38104 | function spm_eeg_prep_ui(callback)
% User interface for spm_eeg_prep function performing several tasks
% for preparation of converted MEEG data for further analysis
% FORMAT spm_eeg_prep_ui(callback)
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre f... |
github | philippboehmsturm/antx-master | spm_read_netcdf.m | .m | antx-master/xspm8/spm_read_netcdf.m | 4,350 | utf_8 | 1cd1b0f7f4b4349d963028c168cd4f2d | function cdf = spm_read_netcdf(fname)
% Read the header information from a NetCDF file into a data structure.
% FORMAT cdf = spm_read_netcdf(fname)
% fname - name of NetCDF file
% cdf - data structure
%
% See: http://www.unidata.ucar.edu/packages/netcdf/
% _____________________________________________________________... |
github | philippboehmsturm/antx-master | spm_figure.m | .m | antx-master/xspm8/spm_figure.m | 38,709 | utf_8 | 4197abc8004aba283a121158d6f42aa7 | function varargout=spm_figure(varargin)
% Setup and callback functions for Graphics window
% FORMAT varargout=spm_figure(varargin)
%
% spm_figure provides utility routines for using the SPM Graphics
% interface. Most used syntaxes are listed here, see the embedded callback
% reference in the main body of this function... |
github | philippboehmsturm/antx-master | spm_P_RF.m | .m | antx-master/xspm8/spm_P_RF.m | 6,258 | utf_8 | 12cabbf3a8ca0c5e43a3fd4025db3e69 | function [P,p,Ec,Ek] = spm_P_RF(c,k,Z,df,STAT,R,n)
% Returns the [un]corrected P value using unifed EC theory
% FORMAT [P p Ec Ek] = spm_P_RF(c,k,z,df,STAT,R,n)
%
% c - cluster number
% k - extent {RESELS}
% z - height {minimum over n values}
% df - [df{interest} df{error}]
% STAT - Statistical field
%... |
github | philippboehmsturm/antx-master | spm_dicom_headers.m | .m | antx-master/xspm8/spm_dicom_headers.m | 20,594 | utf_8 | 1383d5701aed00742ecf464bb28923b6 | function hdr = spm_dicom_headers(P, essentials)
% Read header information from DICOM files
% FORMAT hdr = spm_dicom_headers(P [,essentials])
% P - array of filenames
% essentials - if true, then only save the essential parts of the header
% hdr - cell array of headers, one element for each file.
%
% Contents of heade... |
github | philippboehmsturm/antx-master | spm_eeg_inv_mesh_spherify.m | .m | antx-master/xspm8/spm_eeg_inv_mesh_spherify.m | 5,338 | utf_8 | 95d0130b96a9bec003e301440cfd4caa | function [pnt, tri] = spm_eeg_inv_mesh_spherify(pnt, tri, varargin)
% Takes a cortical mesh and scales it so that it fits into a
% unit sphere.
%
% This function determines the points of the original mesh that support a
% convex hull and determines the radius of those points. Subsequently the
% radius of the support po... |
github | philippboehmsturm/antx-master | spm_image.m | .m | antx-master/xspm8/spm_image.m | 20,761 | utf_8 | a7e827e9560894219b55572753d8dde4 | function spm_image(action,varargin)
% Image and header display
% FORMAT spm_image
%__________________________________________________________________________
%
% spm_image is an interactive facility that allows orthogonal sections
% from an image volume to be displayed. Clicking the cursor on either
% of the three ima... |
github | philippboehmsturm/antx-master | spm_eeg_montage_ui.m | .m | antx-master/xspm8/spm_eeg_montage_ui.m | 7,209 | utf_8 | 81b00840683562c05ad7e333633cbfb5 | 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 | philippboehmsturm/antx-master | spm_interp.m | .m | antx-master/xspm8/spm_interp.m | 1,111 | utf_8 | 5f0170891b0600c4824810d278725d9f | 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 3733 2010-02-18 17... |
github | philippboehmsturm/antx-master | spm_transverse.m | .m | antx-master/xspm8/spm_transverse.m | 15,678 | utf_8 | 22c28b8cda464e1764eee552402294ab | 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 | philippboehmsturm/antx-master | spm_eeg_prep.m | .m | antx-master/xspm8/spm_eeg_prep.m | 17,655 | utf_8 | d0182fc86adc8bc7eba089ae3f0dab97 | 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 | philippboehmsturm/antx-master | spm_bias_ui.m | .m | antx-master/xspm8/spm_bias_ui.m | 5,624 | utf_8 | bf36e864bf3d49ba97e9bc133ecb84c2 | function spm_bias_ui(P)
% Non-uniformity correct images.
%
% The objective function is related to minimising the entropy of
% the image histogram, but is modified slightly.
% This fixes the problem with the SPM99 non-uniformity correction
% algorithm, which tends to try to reduce the image intensities. As
% the field w... |
github | philippboehmsturm/antx-master | spm_mesh_render.m | .m | antx-master/xspm8/spm_mesh_render.m | 26,531 | utf_8 | 8b3c350d44240000e9ceec7b0d41cdc9 | 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 | philippboehmsturm/antx-master | spm_smooth.m | .m | antx-master/xspm8/spm_smooth.m | 3,746 | utf_8 | 641f9055c7e9c0b87c38737330881a53 | function spm_smooth(P,Q,s,dtype)
% 3 dimensional convolution of an image
% FORMAT spm_smooth(P,Q,S,dtype)
% P - image 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 as... |
github | philippboehmsturm/antx-master | spm_eeg_inv_imag_api.m | .m | antx-master/xspm8/spm_eeg_inv_imag_api.m | 15,840 | utf_8 | 169f5a7cb18e2a5ae436135b1c16203c | 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 | philippboehmsturm/antx-master | spm_smoothto8bit.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_eeg_review_switchDisplay.m | .m | antx-master/xspm8/spm_eeg_review_switchDisplay.m | 26,701 | utf_8 | a75c0568a1bf5e7efc01a71adf3e3e20 | function [D] = spm_eeg_review_switchDisplay(D)
% Switch between displays in the M/EEG Review facility
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Jean Daunizeau
% $Id: spm_eeg_review_switchDisplay.m 4136 2010-12-09 22:22:28Z ... |
github | philippboehmsturm/antx-master | spm_dcm_bma_results.m | .m | antx-master/xspm8/spm_dcm_bma_results.m | 10,490 | utf_8 | cfe23c82927c89ef91f7d28a226bff0e | function spm_dcm_bma_results(BMS,method)
% Plot histograms from BMA for selected modulatory and driving input
% FORMAT spm_dcm_bma_results(BMS,mod_in,drive_in,method)
%
% Input:
% BMS - BMS.mat file
% method - inference method (FFX or RFX)
%____________________________________________________________________... |
github | philippboehmsturm/antx-master | spm_check_filename.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_defs.m | .m | antx-master/xspm8/spm_defs.m | 11,688 | utf_8 | 217cf06b73a160542c57789ec5490b4f | function out = spm_defs(job)
% Various deformation field utilities.
% FORMAT out = spm_defs(job)
% job - a job created via spm_config_defs.m and spm_jobman.m
% out - a struct with fields
% .def - file name of created deformation field
% .warped - file names of warped images
%
% See spm_config_defs.m for ... |
github | philippboehmsturm/antx-master | spm_sp.m | .m | antx-master/xspm8/spm_sp.m | 39,708 | utf_8 | 180830974ed2715dc2f976a356081a60 | 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 | philippboehmsturm/antx-master | spm_dicom_essentials.m | .m | antx-master/xspm8/spm_dicom_essentials.m | 3,266 | utf_8 | 586ff55f155ffdd002e53be7402aa26f | 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 | philippboehmsturm/antx-master | spm_ecat2nifti.m | .m | antx-master/xspm8/spm_ecat2nifti.m | 16,572 | utf_8 | 753e9a7e6e367abce74e0a0c4878f6c5 | function N = spm_ecat2nifti(fname,opts)
% Import ECAT 7 images from CTI PET scanners.
% FORMAT N = spm_ecat2nifti(fname)
% fname - name of ECAT file
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner & Roger Gunn
%... |
github | philippboehmsturm/antx-master | spm_platform.m | .m | antx-master/xspm8/spm_platform.m | 8,916 | utf_8 | 1ead463af23059fb998f62b124a12a6d | 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 | philippboehmsturm/antx-master | spm_vb_graphcut.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_preproc.m | .m | antx-master/xspm8/spm_preproc.m | 20,562 | utf_8 | 4fb344b9d6037ec12448af8a5f36eaff | 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 | philippboehmsturm/antx-master | spm_preproc_write.m | .m | antx-master/xspm8/spm_preproc_write.m | 8,906 | utf_8 | 6313e4e753e749911aac1143ba425149 | function spm_preproc_write(p,opts)
% Write out VBM preprocessed data
% FORMAT spm_preproc_write(p,opts)
% p - results from spm_prep2sn
% opts - writing options. A struct containing these fields:
% biascor - write bias corrected image
% GM - flags for which images should be written
% WM ... |
github | philippboehmsturm/antx-master | spm_robust_glm.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_inv_spd.m | .m | antx-master/xspm8/spm_inv_spd.m | 2,156 | utf_8 | cd4bba226b2f3ecf23302491c65f9bfe | 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 | philippboehmsturm/antx-master | spm.m | .m | antx-master/xspm8/spm.m | 49,057 | utf_8 | 98c0598c63fb03fb76fb44b4320b9c53 | function varargout=spm(varargin)
% SPM: Statistical Parametric Mapping (startup function)
%_______________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/... |
github | philippboehmsturm/antx-master | spm_orthviews.m | .m | antx-master/xspm8/spm_orthviews.m | 84,666 | utf_8 | 4edf17c77a1c5d30eb009dd4cd64b24b | 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}
% - area(1) - position x
% - area(2) - position y
% ... |
github | philippboehmsturm/antx-master | spm_FcUtil.m | .m | antx-master/xspm8/spm_FcUtil.m | 30,975 | utf_8 | 0d64cc7e875dbb54242a27a69ebaee99 | 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 | philippboehmsturm/antx-master | spm_read_hdr.m | .m | antx-master/xspm8/spm_read_hdr.m | 5,627 | utf_8 | 785bdd356119ce704a546f3774cd819e | function [hdr,otherendian] = spm_read_hdr(fname)
% Read (SPM customised) Analyze header
% FORMAT [hdr,otherendian] = spm_read_hdr(fname)
% fname - .hdr filename
% hdr - structure containing Analyze header
% otherendian - byte swapping necessary flag
%_______________________________________________________... |
github | philippboehmsturm/antx-master | spm_eeg_inv_visu3D_api.m | .m | antx-master/xspm8/spm_eeg_inv_visu3D_api.m | 28,460 | utf_8 | 31ed5e0329581a73574a4b7986a89440 | 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 | philippboehmsturm/antx-master | spm_load.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_reslice.m | .m | antx-master/xspm8/spm_reslice.m | 13,297 | utf_8 | 831352bc3482e5f11321a4d86aac663d | 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 | philippboehmsturm/antx-master | spm_render.m | .m | antx-master/xspm8/spm_render.m | 13,308 | utf_8 | 8570c1025420d1ad7f3d512eeee07ddc | function 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{.}
% val... |
github | philippboehmsturm/antx-master | spm_uitable.m | .m | antx-master/xspm8/spm_uitable.m | 12,089 | utf_8 | d558e960781ada6e23daad2fcf5012c3 | 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 | philippboehmsturm/antx-master | spm_eeg_convert.m | .m | antx-master/xspm8/spm_eeg_convert.m | 16,945 | utf_8 | a71c71902f215e5d6bfa54b043e525d8 | function D = spm_eeg_convert(S)
% Main function for converting different M/EEG formats to SPM8 format.
% FORMAT D = spm_eeg_convert(S)
% S - can be string (file name) or struct (see below)
%
% If S is a struct it can have the optional following fields:
% S.dataset - file name
% S.continuous - ... |
github | philippboehmsturm/antx-master | spm_maff.m | .m | antx-master/xspm8/spm_maff.m | 8,022 | utf_8 | 33d6a7e3d4b7305bf9bd04c4ffb4eef5 | function M = spm_maff(varargin)
% Affine registration to MNI space using mutual information
% FORMAT M = spm_maff(P,samp,x,b0,MF,M,regtyp,ff)
% P - filename or structure handle of image
% x - cell array of {x1,x2,x3}, where x1 and x2 are
% co-ordinates (from ndgrid), and x3 is a list of
% ... |
github | philippboehmsturm/antx-master | spm_diff.m | .m | antx-master/xspm8/spm_diff.m | 4,795 | utf_8 | ad03f0b9baf443336e6690d292b28a58 | 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 | philippboehmsturm/antx-master | spm_DisplayTimeSeries.m | .m | antx-master/xspm8/spm_DisplayTimeSeries.m | 14,418 | utf_8 | 16a41e1bf873e9a548085da219e4b413 | function [ud] = spm_DisplayTimeSeries(y,options)
% This function builds a GUI for 'smart' time series display.
% FORMAT function [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), wh... |
github | philippboehmsturm/antx-master | loadxml.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_robust_average.m | .m | antx-master/xspm8/spm_robust_average.m | 3,381 | utf_8 | 8a8769e0ba80b51f950c5472f6f79613 | 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 | philippboehmsturm/antx-master | spm_BMS_F_smpl.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_normalise.m | .m | antx-master/xspm8/spm_normalise.m | 12,919 | utf_8 | 716d6de42742658332dc1d1712f9738f | function params = spm_normalise(VG,VF,matname,VWG,VWF,flags)
% Spatial (stereotactic) normalisation
%
% FORMAT params = spm_normalise(VG,VF,matname,VWG,VWF,flags)
% VG - template handle(s)
% VF - handle of image to estimate params from
% matname - name of file to store deformation definitions
% VWG ... |
github | philippboehmsturm/antx-master | spm_eeg_ft2spm.m | .m | antx-master/xspm8/spm_eeg_ft2spm.m | 6,129 | utf_8 | a5369fdb03fab87d6f33d7a88c8bbac1 | function D = spm_eeg_ft2spm(ftdata, filename)
% Converter from Fieldtrip (http://www.ru.nl/fcdonders/fieldtrip/)
% data structures to SPM8 file format
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Vladimir Litvak
% $Id: spm_eeg_ft... |
github | philippboehmsturm/antx-master | spm_pf.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_SpUtil.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_dicom_convert.m | .m | antx-master/xspm8/spm_dicom_convert.m | 45,741 | utf_8 | 3053cf7d299fcdf734d63ad35fd14602 | function out = spm_dicom_convert(hdr,opts,root_dir,format)
% Convert DICOM images into something that SPM can use
% FORMAT spm_dicom_convert(hdr,opts,root_dir,format)
% Inputs:
% hdr - a cell array of DICOM headers from spm_dicom_headers
% opts - options
% 'all' - all DICOM files [default]
% 'mosaic... |
github | philippboehmsturm/antx-master | spm_spm_ui.m | .m | antx-master/xspm8/spm_spm_ui.m | 98,074 | utf_8 | dfdd679af4a4b15272726dcb46e888fe | function varargout = spm_spm_ui(varargin)
% Setting up the general linear model for independent data
% FORMATs (given in Programmers Help)
%_______________________________________________________________________
%
% spm_spm_ui.m configures the design matrix (describing the general
% linear model), data specification, a... |
github | philippboehmsturm/antx-master | spm_minmax.m | .m | antx-master/xspm8/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 | philippboehmsturm/antx-master | spm_create_vol.m | .m | antx-master/xspm8/spm_create_vol.m | 4,967 | utf_8 | 7a051f745805c44e02ffd7b190e4a2c8 | function V = spm_create_vol(V,varargin)
% Create a volume
% FORMAT V = spm_create_vol(V)
% V - image volume information (see spm_vol.m)
%____________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: spm_create_vol.m 1169... |
github | philippboehmsturm/antx-master | spm_check_results.m | .m | antx-master/xspm8/spm_check_results.m | 2,501 | utf_8 | a9b2a3fb54c8c128a16928e69bb03bb4 | 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.
%____... |
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