plateform stringclasses 1
value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | gopmc/SRD-master | text2bin.m | .m | SRD-master/BookFiles/text2bin.m | 232 | utf_8 | c58f4e161ca738c8f824631fc1a843e7 | % n=text2bin(textstring)
% transform text string into a vector of binary 0-1
function n=text2bin(textstring)
bintext=dec2bin(double(textstring),7); % text into binary
[rp,cp]=size(bintext);
n=str2num(reshape(bintext',1,rp*cp)')';
|
github | gopmc/SRD-master | firpm_octave.m | .m | SRD-master/BookFiles/firpm_octave.m | 187 | utf_8 | a8d949de4a4cc1a60659c8c27ba59c6f | % firpm.m: Wrapper for remez function. Filename be renamed
% to simply "firpm.m" for older version of Matlab, as well
% as Octave.
function [b]=firpm(varargin)
[b]=remez(varargin{:})';
|
github | gopmc/SRD-master | pam2letters.m | .m | SRD-master/BookFiles/pam2letters.m | 332 | utf_8 | abd544e2196c5685cf5bd42a5f49b0e8 | % f = pam2letters(seq)
% reconstruct string of +/-1 +/-3 into letters
function f = pam2letters(seq)
S = length(seq);
off = mod(S,4);
if off ~= 0
sprintf('dropping last %i PAM symbols',off)
seq = seq(1:S-off);
end
N = length(seq)/4;
f=[];
for k = 0:N-1
f(k+1) = base2dec(char((seq(4*k+1:4*k+4)+99)/2),4);
end
f ... |
github | gopmc/SRD-master | BigTransmitter.m | .m | SRD-master/BookFiles/BigTransmitter.m | 3,988 | utf_8 | 970da2ff9a70d6e9c4a03f61cfb4c457 | function [r, s]=BigTransmitter(m, frameParams, rfParams, chanParams)
% re-organize m
linesOfText=floor(size(m,2)/frameParams.userDataLength);
numUsers=size(m,1);
m2=zeros(linesOfText,frameParams.userDataLength,numUsers);
for i=1:numUsers
m2(:,:,i)=reshape(m(i,1:frameParams.userDataLength*linesOfText),frameParams.u... |
github | gopmc/SRD-master | letters2pam.m | .m | SRD-master/BookFiles/letters2pam.m | 388 | utf_8 | 30c1dab025409bfab5d0dfb98bb25fd3 | % f = letters2pam(str)
% encode a string of ASCII text into +/-1, +/-3
function f = letters2pam(str); % call as Matlab function
N=length(str); % length of string
f=zeros(1,4*N); % store 4-PAM coding here
for k=0:N-1 % change to "... |
github | gopmc/SRD-master | pam.m | .m | SRD-master/BookFiles/pam.m | 179 | utf_8 | 1776de0314394c79d9948bb8868d3846 | % seq=pam(len,M,Var);
% Create an M-PAM source sequence with
% length 'len' and variance 'Var'
function seq=pam(len,M,Var);
seq=(2*floor(M*rand(1,len))-M+1)*sqrt(3*Var/(M^2-1));
|
github | gopmc/SRD-master | bin2text.m | .m | SRD-master/BookFiles/bin2text.m | 198 | utf_8 | 36b19a1a8c46cd76e7228becc748a8b6 | % ztext=bin2text(z)
% transform a vector of 7-bit binary 0-1 into a text string
function ztext=bin2text(z)
rp=floor(length(z)/7);
rez=num2str(z(1:7*rp)')';
ztext=char(bin2dec(reshape(rez,7,rp)'))';
|
github | gopmc/SRD-master | plotspec.m | .m | SRD-master/BookFiles/plotspec.m | 702 | utf_8 | dec5ed48a1a58f377a9a9fdaf8078706 | % plotspec(x,Ts) plots the spectrum of the signal x
% Ts = time (in seconds) between adjacent samples in x
function plotspec(x,Ts)
N=length(x); % length of the signal x
t=Ts*(1:N); % define a time vector
ssf=(ceil(-N/2):ceil(N/2)-1)/(Ts*N); % frequency ... |
github | gopmc/SRD-master | pow.m | .m | SRD-master/BookFiles/pow.m | 99 | utf_8 | 3599eb6a95e5a9a74e7d35129b1201be | % y=pow(x) calculates the power in the input sequence x
function y=pow(x)
y=x(:)'*x(:)/length(x);
|
github | gopmc/SRD-master | chancode.m | .m | SRD-master/BookFiles/Q3AM/chancode.m | 616 | utf_8 | 5dccb77bbf2bde2810ce37e558a76bda | % Channel Coding for 4QAM
% January 15, 2002
% Sean Leventhal, Katie Orlicki
% chancode.m
%******************************************************************
% input:
% data - data to be coded in binary form
% G - matrix to code the data (lookup)
% output: coded - coded data
%*****************************************... |
github | gopmc/SRD-master | qamTx.m | .m | SRD-master/BookFiles/Q3AM/qamTx.m | 7,674 | utf_8 | 7fa0a4ad919bd65afe81ec2dd7d4d452 | %=============================================
% Modem Transmitter and Channel Simulator
%---------------------------------------------
% John Walsh
%---------------------------------------------
% This software and manual is based upon
% work done by John MacLaren Walsh, Katie
% Orlicki, Adam Pierce, Johnson Smith, ... |
github | gopmc/SRD-master | chandecode.m | .m | SRD-master/BookFiles/Q3AM/chandecode.m | 1,055 | utf_8 | d5532dc1e50abcfcef406976fe222a58 | % Channel Decoding for 4QAM
% January 15, 2002
% Sean Leventhal, Katie Orlicki
% chandecode.m
%******************************************************************
% input:
% data - data to be decoded
% H - matrix to decode the data (lookup)
% syn - syndrome table to look up errors (lookup)
% ginv - pseudo inverse of G... |
github | gopmc/SRD-master | qpskRx.m | .m | SRD-master/BookFiles/Q3AM/qpskRx.m | 10,257 | utf_8 | 1b9738a37a4da2adfefb5dc25daa4b6c | %=============================================
% Modem Receiver Simulator/ SER Determination
%---------------------------------------------
% John Walsh
%---------------------------------------------
% This software and manual is based upon
% work done by John MacLaren Walsh, Katie
% Orlicki, Adam Pierce, Johnson Smi... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_installOpenFmriAnalysisToolbox.m | .m | OpenFmriAnalysis-master/tvm_installOpenFmriAnalysisToolbox.m | 2,979 | utf_8 | 9b18065c8ad0376fa7cbb8d04f37dc2c | function tvm_installOpenFmriAnalysisToolbox(configuration)
% TVM_INSTALLOPENFMRIANALYSISTOOLBOX
% TVM_INSTALLOPENFMRIANALYSISTOOLBOX(configuration)
%
%
% Copyright (C) Tim van Mourik, 2015, DCCN
%
%%
rootDirectory = mfilename('fullpath');
rootDirectory = fileparts(rootDirectory);
%% Parse configuration
if nar... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_realignFunctionals.m | .m | OpenFmriAnalysis-master/Interface/Preprocessing/tvm_realignFunctionals.m | 3,465 | utf_8 | 1681df6e5f908df77c310d3012112a01 | function tvm_realignFunctionals(configuration, realignmentConfiguration)
% TVM_REALIGNFUNCTIONALS Moves niftis to destination folder
% TVM_REALIGNFUNCTIONALS(configuration, realignmentConfiguration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_SourceDirectory
% i_Characteristic
% Outpu... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_filterFunctionals.m | .m | OpenFmriAnalysis-master/Interface/Preprocessing/tvm_filterFunctionals.m | 3,270 | utf_8 | 31ffe05d3aabc0771db2be15041d3767 | function tvm_filterFunctionals(configuration)
% TVM_FILTERFUNCTIONALS
% TVM_FILTERFUNCTIONALS(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_SourceDirectory
% i_LowPass
% i_HighPass
% i_TR
% i_Qsub
% Output:
% o_OutputDirectory
%
% Copyright (C) Tim van M... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_retroicorBackProject.m | .m | OpenFmriAnalysis-master/Interface/Utilities/tvm_retroicorBackProject.m | 4,062 | utf_8 | f91f4dd534f82f3247d4f84e3357a9f8 | function tvm_retroicorBackProject(configuration)
% TVM_RETROICORBACKPROJECT
% TVM_RETROICORBACKPROJECT(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_DesignMatrix
% i_Betas
% i_TemplateVolume
% i_Resolution
% i_Order
% i_PhysioType
% Output:
% o_BackProjection
%
% Copy... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_computeDivergence.m | .m | OpenFmriAnalysis-master/Interface/LaminarAnalysis/tvm_computeDivergence.m | 4,583 | utf_8 | cd10ae08fef327158f8353e515443692 | function tvm_computeDivergence(configuration)
% TVM_COMPUTEGRADIENT
% TVM_COMPUTEGRADIENT(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_VectorField
% i_Order
% Output:
% o_Divergence
%
% Copyright (C) Tim van Mourik, 2015-2016, DCCN
%
% This file is part of the fmri analysis ... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_designMatrixToTimeCourse.m | .m | OpenFmriAnalysis-master/Interface/LaminarAnalysis/tvm_designMatrixToTimeCourse.m | 7,251 | utf_8 | 58990a57d9f994f416272416c994b3e6 | function tvm_designMatrixToTimeCourse(configuration)
% TVM_DESIGNMATRIXTOTIMECOURSE
% TVM_DESIGNMATRIXTOTIMECOURSE(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_DesignMatrix
% i_FunctionalFolder
% i_FunctionalFiles
% i_RegressionApproach
% Output:
% o_TimeCourse
%
% Copyr... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_gradient.m | .m | OpenFmriAnalysis-master/Interface/LaminarAnalysis/tvm_gradient.m | 4,845 | utf_8 | cbd1ce35b59c85c7b1667946974d4fda | function tvm_gradient(configuration)
% TVM_GRADIENT
% TVM_GRADIENT(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_Potential
% i_Normalise
% Output:
% o_Gradient
% Copyright (C) Tim van Mourik, 2015-2016, DCCN
%
% This file is part of the fmri analysis toolbox, see
% https://g... |
github | TimVanMourik/OpenFmriAnalysis-master | gradnan.m | .m | OpenFmriAnalysis-master/Interface/LaminarAnalysis/private/gradnan.m | 5,282 | utf_8 | dae41a0401beec3360b6e1cf7d856666 | function varargout = gradnan(f,varargin)
% GRADNAN Approximate gradient.
%
% [FX,FY] = GRADNAN(F) returns the numerical gradient of the
% matrix F. FX corresponds to dF/dx, the differences in the
% x (column) direction. FY corresponds to dF/dy, the differences
% in the y (row) direction. The spacing between ... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_convertRegisterDat.m | .m | OpenFmriAnalysis-master/Interface/Registration/tvm_convertRegisterDat.m | 7,602 | utf_8 | 0d6c12a8993d6b79867c1e95a491a5fa | function tvm_convertRegisterDat(configuration)
% TVM_CONVERTREGISTERDAT
% TVM_CONVERTREGISTERDAT(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_RegistrationVolume
% i_FreeSurferFolder
% i_RegisterDat
% Output:
% o_Boundaries
% o_CoregistrationMatrix
%
% Copyright (C) Tim v... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_useBbregister.m | .m | OpenFmriAnalysis-master/Interface/Registration/tvm_useBbregister.m | 9,864 | utf_8 | 6bad04382fc24e32042e9d0dde238a27 | function tvm_useBbregister(configuration)
% TVM_USEBBREGISTER(configuration)
% TVM_USEBBREGISTER(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_RegistrationVolume
% i_FreeSurferFolder
% i_SpmInitialisation
% i_FslInitialisation
% i_Contrast
% i_DegreesOfFreedom
... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_registerVolumes.m | .m | OpenFmriAnalysis-master/Interface/Registration/tvm_registerVolumes.m | 5,312 | utf_8 | 5fef6674948eb16f5777eea701a1c27e | function tvm_registerVolumes(configuration, registrationConfiguration)
% TVM_REGISTERVOLUMES
% TVM_REGISTERVOLUMES(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_ReferenceVolume
% i_FreeSurferFolder
% i_CoregistrationMatrix
% Output:
% o_CoregistrationMatrix
% o_B... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_freesurferBoundariesToVolume.m | .m | OpenFmriAnalysis-master/Interface/Registration/tvm_freesurferBoundariesToVolume.m | 6,617 | utf_8 | eaea90e699a6d3cf60b8614016d7a78b | function tvm_freesurferBoundariesToVolume(configuration)
% TVM_FREESURFERBOUNDARIESTOVOLUME
% TVM_FREESURFERBOUNDARIESTOVOLUME(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_RegistrationVolume
% i_FreeSurferFolder
% Output:
% o_Boundaries
%
% Copyright (C) Tim van Mourik, 2014... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_recursiveBoundaryRegistration.m | .m | OpenFmriAnalysis-master/Interface/Registration/tvm_recursiveBoundaryRegistration.m | 26,498 | utf_8 | 649cc94da10f8c9c18585dc0a5ee5377 | function tvm_recursiveBoundaryRegistration(configuration, registrationConfiguration)
% TVM_RECURSIVEBOUNDARYREGISTRATION
% TVM_RECURSIVEBOUNDARYREGISTRATION(configuration)
% @todo Add description
%
% Input:
% i_SubjectDirectory
% i_ReferenceVolume
% i_Boundaries
% i_Mask
% i_MinimumVoxels
% i... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_labelToTimecourse4D.m | .m | OpenFmriAnalysis-master/Old/tvm_labelToTimecourse4D.m | 2,706 | utf_8 | 40427a1a22e5f5aec76759d85d8159d6 | function output = tvm_labelToTimecourse4D(configuration)
memtic
subjectDirectory = configuration.SubjectDirectory;
functionalScan = spm_vol([subjectDirectory configuration.MeanFunctional]);
allVolumes = spm_vol([subjectDirectory configuration.FunctionalFiles]);
if ~exist([subjectDirectory configuratio... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_makeWallpaper2.m | .m | OpenFmriAnalysis-master/Old/tvm_makeWallpaper2.m | 4,619 | utf_8 | 20b3b49c53bfa08f84f2af25ed436f97 | function output = tvm_makeWallpaper(configuration)
memtic
concatProfiles = cell(configuration.NumberOfRegions, 1);
for subject = 1:length(configuration.Subjects)
subjectDirectory = sprintf(configuration.SubjectDirectory, subject);
% load([subjectDirectory configuration.Profiles], 'profiles');
loa... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_offDiagonalShift.m | .m | OpenFmriAnalysis-master/Old/tvm_offDiagonalShift.m | 2,828 | utf_8 | 76a0d5caf15320bfe3c01c5aeedd62e0 | function output = tvm_offDiagonalShift(configuration)
memtic
concatProfiles = cell(configuration.NumberOfRegions, 1);
for subject = 1:length(configuration.Subjects)
subjectDirectory = sprintf(configuration.SubjectDirectory, subject);
% load([subjectDirectory configuration.Profiles], 'profiles');
... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_findVerticesOfInterest.m | .m | OpenFmriAnalysis-master/Old/tvm_findVerticesOfInterest.m | 3,360 | utf_8 | be608e847f746f9f081becd20a4db0fa | function output = tvm_findVerticesOfInterest(configuration)
memtic
subjectDirectory = configuration.SubjectDirectory;
meanFunctional = spm_vol([subjectDirectory configuration.Functional]);
load([subjectDirectory configuration.CorrelationFolder configuration.PeakFile], 'peaks')
meanFunctional.volume = ze... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_threshold.m | .m | OpenFmriAnalysis-master/Old/tvm_threshold.m | 1,130 | utf_8 | a525b2129bc288c0e24b8dde55fd0c2e | function output = tvm_threshold(configuration)
memtic
subjectDirectory = configuration.SubjectDirectory;
folderContent = dir([subjectDirectory configuration.CorrelationFolder '*.nii']);
folderContent = {folderContent.name};
for volume = 1:length(folderContent)
correlationVolume = spm_vol([subjectDirect... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_makeWallpaperWithTimecourse.m | .m | OpenFmriAnalysis-master/Old/tvm_makeWallpaperWithTimecourse.m | 4,151 | utf_8 | 01753a0146def7578804bed69f7151d8 | function output = tvm_makeWallpaperWithTimecourse(configuration)
memtic
concatTimecourses = cell(configuration.NumberOfTimeCourses, 1);
concatProfiles = cell(configuration.NumberOfRegions, 1);
for subject = 1:length(configuration.Subjects)
subjectDirectory = sprintf(configuration.SubjectDirectory, configu... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_makeWallpaper.m | .m | OpenFmriAnalysis-master/Old/tvm_makeWallpaper.m | 4,963 | utf_8 | abb27285df3cf74cacbf4a2ac08b0970 | function output = tvm_makeWallpaper(configuration)
memtic
s = sprintf(configuration.SubjectDirectory, configuration.Subjects(1));
load([s configuration.Profiles], 'collapsedProfile');
numberOfRegions = size(collapsedProfile, 1); %#ok<NODEF>
concatProfiles = cell(numberOfRegions, 1);
for subject = 1:length(con... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_makeWallpaperStd.m | .m | OpenFmriAnalysis-master/Old/tvm_makeWallpaperStd.m | 4,599 | utf_8 | 723a1e69ea6164d85844e64e8164c144 | function output = tvm_makeWallpaperStd(configuration)
memtic
concatProfiles = cell(configuration.NumberOfRegions, 1);
for subject = 1:length(configuration.Subjects)
subjectDirectory = sprintf(configuration.SubjectDirectory, subject);
% load([subjectDirectory configuration.Profiles], 'profiles');
... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_hrf.m | .m | OpenFmriAnalysis-master/Core/tvm_hrf.m | 3,452 | utf_8 | ae96b0a48604233ab70becadc9ab929a | function stimulusRegressors = tvm_hrf(configuration)
%
% For duration = 0 an impuls response is taken and a regular HRF is used.
%
% Note that the area under the HRF curve is computed for a given time step.
% This will be small for small duration. Only when duration = 0, an impuls
% response is used. This may result in... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_constructFirModel.m | .m | OpenFmriAnalysis-master/Core/tvm_constructFirModel.m | 1,591 | utf_8 | 6e3e6e9170fef93f675635f15b0a3ca1 | function regressorMatrix = tvm_constructFirModel(configuration)
%
% Make sure the segment spacing, time points and stimulus have the same
% time units.
%
% Copyright (C) Tim van Mourik, 2014, DCCN
%
%% Parse configuration
segmentSpacing = tvm_getOption(configuration, 'SegmentSpacing', 1);
%no defa... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_showObjectContourOnSlice.m | .m | OpenFmriAnalysis-master/Core/tvm_showObjectContourOnSlice.m | 5,468 | utf_8 | e19d760a125e3ff11e6bdfbe738d328a | function tvm_showObjectContourOnSlice(configuration)
%
%
% Copyright (C) Tim van Mourik, 2015, DCCN
%
%% Parse configuration
volume = tvm_getOption(configuration, 'i_Volume');
%no default
roi = tvm_getOption(configuration, 'i_ROI', '');
%no default
slice = tvm_... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_resample.m | .m | OpenFmriAnalysis-master/Core/tvm_resample.m | 6,599 | utf_8 | f9ddd7611727c473d826ee0f0a20b235 | function outputMatrix = tvm_resample(inputMatrix, outputSize, isReal)
%
% updownsample - up-sample or down-sample an input series using fourier domain
% input series needs to be continuous of a high degree
%
% format: out_m = updownsample( in_m,out_x_sz,out_y_sz,is_fourier_flag,is_real_flag )
%
% input... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_dicomToMdhTime.m | .m | OpenFmriAnalysis-master/Core/tvm_dicomToMdhTime.m | 537 | utf_8 | 88f7b2556aefe0257ca6fe910c0a28ab | % convert the volume acquisition time stamps of dicom files to MDH time
% stamps (msec after midnight)
function msTimestamp = tvm_dicomToMdhTime(time)
time = str2double(time);
hours = fix(time / 10000);
time = time - hours * 10000;
minutes = fix(time / 100);
time = tim... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_loadFreeSurferAsciiFile.m | .m | OpenFmriAnalysis-master/Core/tvm_loadFreeSurferAsciiFile.m | 4,373 | utf_8 | b503949dbf43d4cf539441045d0c3ac3 | function outputData = tvm_loadFreeSurferAsciiFile(fileNames)
%LOADFREESURFERASCIIFILE(DATAFILENAMES)
%Loads FreeSurfer output
%
%Example:
% fileNames = []
% fileNames.SurfaceWhite = '?h.white.asc';
% fileNames.SurfacePial = '?h.pial.asc';
% fileNames.CurvatureWhite = '?h.curv.asc';
% file... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_computeCurvatureFromSdf.m | .m | OpenFmriAnalysis-master/Core/tvm_computeCurvatureFromSdf.m | 4,024 | utf_8 | fcc11341f5638808c1b173bea42bfd7a | function tvm_computeCurvatureFromGradient(configuration)
%% Parse configuration
subjectDirectory = tvm_getOption(configuration, 'i_SubjectDirectory');
%no default
sdfFile = fullfile(subjectDirectory, tvm_getOption(configuration, 'i_SDF'));
%no default
curv1File = fullfile(subjectDir... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_partialVolumeArea.m | .m | OpenFmriAnalysis-master/Core/tvm_partialVolumeArea.m | 6,432 | utf_8 | 6b6be762727a9d15a5945cc70ea6485f | function distance = tvm_partialVolumeArea(distance, method, normals)
% The mode needs to be added as soon a different method is implementedy
% function distance = partialVolumeArea(distance, mode)
%
% The integral of a partial volume kernel from negative infinity to [input]
% Starting at zero, going to 1
%
% NB. distan... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_bbregister.m | .m | OpenFmriAnalysis-master/Core/tvm_bbregister.m | 9,912 | utf_8 | b85810aaf555f5011e338b9a25ed8f06 | function [transformationMatrix, registrationParameters] = tvm_bbregister(arrayW, arrayP, voxelGrid, configuration)
%BOUNDARYBASEDREGISTRATION A method of using the boundaries that enclose
%the grey matter for registration of brain volume data. It is a five-stage
%process proposed by Greve & Fischl (2009).
%
% T = BO... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_mdhToDicomTime.m | .m | OpenFmriAnalysis-master/Core/tvm_mdhToDicomTime.m | 594 | utf_8 | 08ddf937e657b5bde89597feee9afdf5 | % convert the volume acquisition time stamps of dicom files to MDH time
% stamps (msec after midnight)
function trueTime = tvm_mdhToDicomTime(msTimestamp)
microSeconds = mod(msTimestamp, 1000);
trueTime = (msTimestamp - microSeconds) / 1000;
seconds = mod(trueTime, 60);
trueTime = (trueTime -... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_sampleHrf.m | .m | OpenFmriAnalysis-master/Core/private/tvm_sampleHrf.m | 4,222 | utf_8 | 381094aa7b06c4fa08e2e1cdbd4d58a7 | function regressor = tvm_sampleHrf(timePoints, stimulusOnsets, stimulusDurations, hrfParameters, type)
%
% For duration = 0 an impuls response is taken and a regular HRF is used.
%
% Note that the area under the HRF curve is computed for a given time step.
% This will be small for small duration. Only when duration = 0... |
github | TimVanMourik/OpenFmriAnalysis-master | findContrast.m | .m | OpenFmriAnalysis-master/Core/private/findContrast.m | 9,253 | utf_8 | 1ac2be57e086baa3551147795fe3db54 | function contrast = findContrast(arrayW, arrayP, voxelgrid, configuration)
%FINDCONTRAST Finds the contrast near a boundary of a given mesh.
% FINDCONTRAST(INNERBOUNDARY, OUTERBOUNDARY, VOXELGRID)
% Finds the contrast in a VOXELGRID, near the INNERBOUNDARY.
%
% FINDCONTRAST(INNERBOUNDARY, OUTERBOUNDARY, VOXELGRID... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_toTranslationMatrix.m | .m | OpenFmriAnalysis-master/Core/private/tvm_toTranslationMatrix.m | 214 | utf_8 | 2beace2293fabecf62be87a39c3aba38 |
function matrix = tvm_toTranslationMatrix(translation)
matrix = [1, 0, 0, 0; ...
0, 1, 0, 0; ...
0, 0, 1, 0; ...
translation(1), translation(2), translation(3), 1];
end |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_curvature.m | .m | OpenFmriAnalysis-master/Core/Curvature/tvm_curvature.m | 2,357 | utf_8 | 7b22f05633401b50f586cd7cf4b992f2 | function tvm_curvature(configuration)
% TVM_COMPUTECURVATURE
% TVM_COMPUTECURVATURE(configuration)
%
%
% Copyright (C) Tim van Mourik, 2014, DCCN
%
% configuration.SubjectDirectory
% configuration.White
% configuration.Pial
% configuration.WhiteCurvature
% configuration.PialCurvature
%% Parse configu... |
github | TimVanMourik/OpenFmriAnalysis-master | load_nii_ext.m | .m | OpenFmriAnalysis-master/External/NifTI/load_nii_ext.m | 5,337 | utf_8 | fa0e831b0a596c3208b21bddc1c6d812 | % Load NIFTI header extension after its header is loaded using load_nii_hdr.
%
% Usage: ext = load_nii_ext(filename)
%
% filename - NIFTI file name.
%
% Returned values:
%
% ext - Structure of NIFTI header extension, which includes num_ext,
% and all the extended header sections in the header extension.
% ... |
github | TimVanMourik/OpenFmriAnalysis-master | rri_orient.m | .m | OpenFmriAnalysis-master/External/NifTI/rri_orient.m | 2,251 | utf_8 | 4253fb96b9189a8a4bad49661d9ecac3 | % Convert image of different orientations to standard Analyze orientation
%
% Usage: nii = rri_orient(nii);
% Jimmy Shen (jimmy@rotman-baycrest.on.ca), 26-APR-04
%___________________________________________________________________
function [nii, orient, pattern] = rri_orient(nii, varargin)
if nargin > 1
... |
github | TimVanMourik/OpenFmriAnalysis-master | save_untouch0_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/save_untouch0_nii_hdr.m | 8,594 | utf_8 | 7e8b1b327e1924837820f75780d52d01 | % 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 | TimVanMourik/OpenFmriAnalysis-master | rri_zoom_menu.m | .m | OpenFmriAnalysis-master/External/NifTI/rri_zoom_menu.m | 737 | utf_8 | d8151523470b0fba970eb1d98ba56030 | % Imbed a zoom menu to any figure.
%
% Usage: rri_zoom_menu(fig);
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%--------------------------------------------------------------------
function menu_hdl = rri_zoom_menu(fig)
if isnumeric(fig)
menu_hdl = uimenu('Parent',fig, ...
'Label','Zoom on', ..... |
github | TimVanMourik/OpenFmriAnalysis-master | rri_select_file.m | .m | OpenFmriAnalysis-master/External/NifTI/rri_select_file.m | 16,599 | utf_8 | e349954ca803370f62ceeabdbab5912e | function [selected_file, selected_path] = rri_select_file(varargin)
%
% USAGE: [selected_file, selected_path] = ...
% rri_select_file(dir_name, fig_title)
%
% Allow user to select a file from a list of Matlab competible
% file format
%
% Example:
%
% [selected_file, selected_path] = ...
% rri_select_... |
github | TimVanMourik/OpenFmriAnalysis-master | clip_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/clip_nii.m | 3,306 | utf_8 | a70bdbed5a0813312d4c83f94b99a710 | % CLIP_NII: Clip the NIfTI volume from any of the 6 sides
%
% Usage: nii = clip_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be cut from which side.
%
% option.cut_from_L = ( number of voxel )
% option.cut_from_R = ( number of voxel )
% option.cut_from_P ... |
github | TimVanMourik/OpenFmriAnalysis-master | affine.m | .m | OpenFmriAnalysis-master/External/NifTI/affine.m | 16,110 | utf_8 | 768d2303e551a9584685bdb01abf6f8b | % Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
% shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
% 3D volume is represented by a 3D matrix, and data type can be real
% integer or floating-point.
%
% You may notice that MATLAB has a function called 'imtransform.m' fo... |
github | TimVanMourik/OpenFmriAnalysis-master | load_untouch_nii_img.m | .m | OpenFmriAnalysis-master/External/NifTI/load_untouch_nii_img.m | 14,756 | utf_8 | 688b2a42f8071c6402a037c7ca923689 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_untouch_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('U... |
github | TimVanMourik/OpenFmriAnalysis-master | load_untouch_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/load_untouch_nii.m | 6,182 | utf_8 | 93108a725d2e357d773c8aa0acf71328 | % Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
% geometric transform or voxel intensity scaling.
%
% Although according to NIFTI website, all those header information are
% supposed to be applied to the loaded NIFTI image, there are some
% situations that people do want to leave the origi... |
github | TimVanMourik/OpenFmriAnalysis-master | collapse_nii_scan.m | .m | OpenFmriAnalysis-master/External/NifTI/collapse_nii_scan.m | 6,778 | utf_8 | 64b1cb0f7cd9e095d3c11ca66453df69 | % Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_folder is... |
github | TimVanMourik/OpenFmriAnalysis-master | rri_orient_ui.m | .m | OpenFmriAnalysis-master/External/NifTI/rri_orient_ui.m | 5,384 | utf_8 | e1196b81940d9f93fbdb43c33799e587 | % Return orientation of the current image:
% orient is orientation 1x3 matrix, in that:
% Three elements represent: [x y z]
% Element value: 1 - Left to Right; 2 - Posterior to Anterior;
% 3 - Inferior to Superior; 4 - Right to Left;
% 5 - Anterior to Posterior; 6 - Superior to Inferior;
% e.g.:
% Standard RAS Or... |
github | TimVanMourik/OpenFmriAnalysis-master | load_untouch0_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/load_untouch0_nii_hdr.m | 8,093 | utf_8 | 3de9ff6a1da47b56ae680e7660eaa041 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine)
fn = sprintf('%s.hdr',fileprefix);
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr =... |
github | TimVanMourik/OpenFmriAnalysis-master | load_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/load_nii.m | 6,808 | utf_8 | d098a5dbea3cd4ad76cea624ffbef9db | % Load NIFTI or ANALYZE dataset. Support both *.nii and *.hdr/*.img
% file extension. If file extension is not provided, *.hdr/*.img will
% be used as default.
%
% A subset of NIFTI transform is included. For non-orthogonal rotation,
% shearing etc., please use 'reslice_nii.m' to reslice the NIFTI file.
% It will... |
github | TimVanMourik/OpenFmriAnalysis-master | unxform_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/unxform_nii.m | 1,181 | utf_8 | a77d113be34b09d588b2eb326a3c65c8 | % Undo the flipping and rotations performed by xform_nii; spit back only
% the raw img data block. Initial cut will only deal with 3D volumes
% strongly assume we have called xform_nii to write down the steps used
% in xform_nii.
%
% Usage: a = load_nii('original_name');
% manipulate a.img to make array... |
github | TimVanMourik/OpenFmriAnalysis-master | load_untouch_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/load_untouch_nii_hdr.m | 8,522 | utf_8 | 2d4bc8c8ffb83b37daf1e8dd87c108e6 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine, filetype)
if filetype == 2
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
... |
github | TimVanMourik/OpenFmriAnalysis-master | save_nii_ext.m | .m | OpenFmriAnalysis-master/External/NifTI/save_nii_ext.m | 977 | utf_8 | b60a98ab7537a883dc3ffef3175f19ae | % Save NIFTI header extension.
%
% Usage: save_nii_ext(ext, fid)
%
% ext - struct with NIFTI header extension fields.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function save_nii_ext(ext, fid)
if ~exist('ext','var') | ~exist('fid','var')
... |
github | TimVanMourik/OpenFmriAnalysis-master | view_nii_menu.m | .m | OpenFmriAnalysis-master/External/NifTI/view_nii_menu.m | 14,415 | utf_8 | 32dd591fa1070721f0255f47f6e02510 | % Imbed Zoom, Interp, and Info menu to view_nii window.
%
% Usage: view_nii_menu(fig);
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%--------------------------------------------------------------------
function menu_hdl = view_nii_menu(fig, varargin)
if isnumeric(fig)
menu_hdl = init(fig);
retur... |
github | TimVanMourik/OpenFmriAnalysis-master | save_untouch_header_only.m | .m | OpenFmriAnalysis-master/External/NifTI/save_untouch_header_only.m | 2,132 | utf_8 | 5f0515ef6a35f171bc8371d0f3fd365d | % This function is only used to save Analyze or NIfTI header that is
% ended with .hdr and loaded by load_untouch_header_only.m. If you
% have NIfTI file that is ended with .nii and you want to change its
% header only, you can use load_untouch_nii / save_untouch_nii pair.
%
% Usage: save_untouch_header_only(hd... |
github | TimVanMourik/OpenFmriAnalysis-master | pad_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/pad_nii.m | 3,712 | utf_8 | 0b9de8feba6840e2d8ea1ab1752747c7 | % PAD_NII: Pad the NIfTI volume from any of the 6 sides
%
% Usage: nii = pad_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be padded from which side.
%
% option.pad_from_L = ( number of voxel )
% option.pad_from_R = ( number of voxel )
% option.pad_from_P ... |
github | TimVanMourik/OpenFmriAnalysis-master | load_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/load_nii_hdr.m | 10,031 | utf_8 | e95839e314863f7ee463cc2626dd447c | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [hdr, filetype, fileprefix, machine] = load_nii_hdr(fileprefix)
if ~exist('fileprefix','var'),
error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)');
end
machine = 'ieee-le';
new_ext = 0;
if fin... |
github | TimVanMourik/OpenFmriAnalysis-master | save_untouch_slice.m | .m | OpenFmriAnalysis-master/External/NifTI/save_untouch_slice.m | 19,683 | utf_8 | 364468e5dbd3790c1aadf9a768534f1f | % Save back to the original image with a portion of slices that was
% loaded by "load_untouch_nii". You can process those slices matrix
% in any way, as long as their dimension is not altered.
%
% Usage: save_untouch_slice(slice, filename, ...
% slice_idx, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
%
% slice ... |
github | TimVanMourik/OpenFmriAnalysis-master | load_nii_img.m | .m | OpenFmriAnalysis-master/External/NifTI/load_nii_img.m | 12,328 | utf_8 | b1b9dd2838a8f217b10fefdc8a931d5e | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: [img,hdr] = ... |
github | TimVanMourik/OpenFmriAnalysis-master | bresenham_line3d.m | .m | OpenFmriAnalysis-master/External/NifTI/bresenham_line3d.m | 4,493 | utf_8 | c19f06df423676afeb59762ac55c0c2f | % Generate X Y Z coordinates of a 3D Bresenham's line between
% two given points.
%
% A very useful application of this algorithm can be found in the
% implementation of Fischer's Bresenham interpolation method in my
% another program that can rotate three dimensional image volume
% with an affine matrix:
% http... |
github | TimVanMourik/OpenFmriAnalysis-master | make_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/make_nii.m | 6,849 | utf_8 | 3c7c8b81655c111a9ce4b82086bde4f5 | % Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI fil... |
github | TimVanMourik/OpenFmriAnalysis-master | verify_nii_ext.m | .m | OpenFmriAnalysis-master/External/NifTI/verify_nii_ext.m | 1,676 | utf_8 | db3d32ecba688905185f5ed01b409fd1 | % Verify NIFTI header extension to make sure that each extension section
% must be an integer multiple of 16 byte long that includes the first 8
% bytes of esize and ecode. If the length of extension section is not the
% above mentioned case, edata should be padded with all 0.
%
% Usage: [ext, esize_total] = verif... |
github | TimVanMourik/OpenFmriAnalysis-master | get_nii_frame.m | .m | OpenFmriAnalysis-master/External/NifTI/get_nii_frame.m | 4,333 | utf_8 | 8b0cba9d07733a6f82753b0c40b51107 | % Return time frame of a NIFTI dataset. Support both *.nii and
% *.hdr/*.img file extension. If file extension is not provided,
% *.hdr/*.img will be used as default.
%
% It is a lightweighted "load_nii_hdr", and is equivalent to
% hdr.dime.dim(5)
%
% Usage: [ total_scan ] = get_nii_frame(filename)
%
% filen... |
github | TimVanMourik/OpenFmriAnalysis-master | flip_lr.m | .m | OpenFmriAnalysis-master/External/NifTI/flip_lr.m | 3,484 | utf_8 | a0b2d0189d90339a841863efeb60681a | % 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:
%
% http... |
github | TimVanMourik/OpenFmriAnalysis-master | save_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/save_nii.m | 9,404 | utf_8 | 88aa93174482539fe993ac335fb01541 | % 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 of NIFTI... |
github | TimVanMourik/OpenFmriAnalysis-master | rri_file_menu.m | .m | OpenFmriAnalysis-master/External/NifTI/rri_file_menu.m | 3,974 | utf_8 | 1ec91620ceb4108dde9a63945380028f | % 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 | TimVanMourik/OpenFmriAnalysis-master | reslice_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/reslice_nii.m | 9,817 | utf_8 | 05783cd4f127a22486db67a9cc89ad2a | % 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 NIfTI fi... |
github | TimVanMourik/OpenFmriAnalysis-master | save_untouch_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/save_untouch_nii.m | 6,494 | utf_8 | 50fa95cbb847654356241a853328f912 | % 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)
%
% nii -... |
github | TimVanMourik/OpenFmriAnalysis-master | view_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/view_nii.m | 139,608 | utf_8 | 74f9dea7539a45a7993beb22becf2fa2 | % 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;
% option is... |
github | TimVanMourik/OpenFmriAnalysis-master | mat_into_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/mat_into_hdr.m | 2,608 | utf_8 | d53006b93ff90a4a5561d16ff2f4e9a6 | %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 Reor... |
github | TimVanMourik/OpenFmriAnalysis-master | xform_nii.m | .m | OpenFmriAnalysis-master/External/NifTI/xform_nii.m | 18,107 | utf_8 | 29a1cff91c944d6a93e5101946a5da4d | % 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 degree... |
github | TimVanMourik/OpenFmriAnalysis-master | make_ana.m | .m | OpenFmriAnalysis-master/External/NifTI/make_ana.m | 5,455 | utf_8 | 2f62999cbcad72129c892135ff492a1e | % 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 detail,... |
github | TimVanMourik/OpenFmriAnalysis-master | extra_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/extra_nii_hdr.m | 7,830 | utf_8 | 853f39f00cbf133e90d0f2cf08d79488 | % 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.datatype
ca... |
github | TimVanMourik/OpenFmriAnalysis-master | rri_xhair.m | .m | OpenFmriAnalysis-master/External/NifTI/rri_xhair.m | 2,208 | utf_8 | b3ae9df90d43e5d9538b6b135fa8af20 | % 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
% be used.... |
github | TimVanMourik/OpenFmriAnalysis-master | save_untouch_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/save_untouch_nii_hdr.m | 8,514 | utf_8 | 582f82c471a9a8826eda59354f61dd1a | % 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 | TimVanMourik/OpenFmriAnalysis-master | expand_nii_scan.m | .m | OpenFmriAnalysis-master/External/NifTI/expand_nii_scan.m | 1,333 | utf_8 | 748da05d09c1a005401c67270c4b94ab | % 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, newpath)
... |
github | TimVanMourik/OpenFmriAnalysis-master | load_untouch_header_only.m | .m | OpenFmriAnalysis-master/External/NifTI/load_untouch_header_only.m | 7,068 | utf_8 | 8996c72db42b01029c92a4ecd88f4b21 | % 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 | TimVanMourik/OpenFmriAnalysis-master | bipolar.m | .m | OpenFmriAnalysis-master/External/NifTI/bipolar.m | 2,145 | utf_8 | 295f87ece96ca4c5dff8dce4cd912a34 | %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 the color... |
github | TimVanMourik/OpenFmriAnalysis-master | save_nii_hdr.m | .m | OpenFmriAnalysis-master/External/NifTI/save_nii_hdr.m | 9,270 | utf_8 | f97c194f5bfc667eb4f96edf12be02a7 | % 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
if hdr.h... |
github | TimVanMourik/OpenFmriAnalysis-master | tvm_useFlirt.m | .m | OpenFmriAnalysis-master/Development/tvm_useFlirt.m | 6,647 | utf_8 | 9a55fb2820aef546feee84e8fdf52711 | function tvm_useFlirt(configuration)
% TVM_REGISTERVOLUMES
% TVM_REGISTERVOLUMES(configuration)
%
%
% Copyright (C) Tim van Mourik, 2014, DCCN
%
%% Parse configuration
subjectDirectory = tvm_getOption(configuration, 'i_SubjectDirectory');
%no default
referenceFile = fullfile(subjectDirectory, ... |
github | cemsaz/NGSIM-trajectories-master | getTrajectoryPairs.m | .m | NGSIM-trajectories-master/getTrajectoryPairs.m | 2,177 | utf_8 | d433d0a39422c8a863c31b7fad41b65c |
function table = getTrajectoryPairs(data, lane, minTrajectoryLenght)
% Filter the data based on the lane and make sure follower - leader
% fields are not -1
lane_data = data((data(:,3)==lane & data(:,9)~=-1 & data(:,10)~=-1),:);
unique_vehicles = unique(lane_data(:,1));
pairArr = [];
... |
github | huajh/quad_kanpsack_brucker-master | quad_kanpsack_brucker.m | .m | quad_kanpsack_brucker-master/quad_kanpsack_brucker.m | 2,856 | utf_8 | ad8928bf5a76660050b43e0e21d6c094 | function [ x ] = quad_kanpsack_brucker( d,a,b,b0,l,u )
%QUAD_KANPSACK_BRUCKER Summary of this function goes here
%
% x = quad_kanpsack_brucker(v, b) returns the vector x which is the solution
% to the following constrained minimization problem:
%
% min sum_i^n 1/2*d_i*x_i^2 - a_i x_i
% s.t. sum_i^n b_i*x_i ... |
github | syyeung/pyvision-master | showModel.m | .m | pyvision-master/experiments/showModel.m | 1,025 | utf_8 | 32ac42289acd5878575a8909f2e86946 | function showModel(ww,sc)
if nargin < 2,
%Set the scale so that the maximum weight is 255
sc = max(abs(ww(:)));
end
sc = 255/sc;
siz = 20;
im1 = HOGpicture( ww,siz)*sc;
im2 = HOGpicture(-ww,siz)*sc;
%Combine into 1 image
buff = 10;
im1 = padarray(im1,[buff buff],200,'both');
im2 = padarray(im2,[buff buff],200,... |
github | pengsun/MatConvDAG-master | mnist_small_te_all.m | .m | MatConvDAG-master/examples2/mnist_small_te_all.m | 1,819 | utf_8 | b47f7455b92dd779789625e7bc61a5ce | function [err_ep, err] = mnist_small_te_all(varargin)
% config
% TODO: add more properties here
if ( nargin==0 )
ep = 1 : 5;
batch_sz = 128;
dir_mo = fullfile(dag_path.root,'\examples2\mo_zoo\mnist_small\lenetTriCon');
fn_data = fullfile(dag_path.root,'\examples2\data\mnist_small_cv5\imdb.mat');
fn_mo_tmpl... |
github | pengsun/MatConvDAG-master | mnist_small_tr_lenetDropout.m | .m | MatConvDAG-master/examples2/mnist_small_tr_lenetDropout.m | 3,192 | utf_8 | c29bd452fc6f669ade7ab15d6688bf9d | function mnist_small_tr_lenetDropout()
%% init dag: from file or from scratch
beg_epoch = 3;
dir_mo = fullfile(dag_path.root,'examples2/mo_zoo/mnist_small/lenetDropout');
fn_mo = fullfile(dir_mo, sprintf('dag_epoch_%d.mat', beg_epoch-1) );
if ( exist(fn_mo, 'file') )
h = create_dag_from_file (fn_mo);
flag_from_scra... |
github | pengsun/MatConvDAG-master | mnist_small_tr_lenetTriCon.m | .m | MatConvDAG-master/examples2/mnist_small_tr_lenetTriCon.m | 1,781 | utf_8 | 8c8adbf8c98cfdf8aa5493e47752d39a | function mnist_small_tr_lenetTriCon()
%% init dag: from file or from scratch
beg_epoch = 8;
dir_mo = fullfile(dag_path.root,'examples2/mo_zoo/mnist_small/lenetTriCon');
fn_mo = fullfile(dir_mo, sprintf('dag_epoch_%d.mat', beg_epoch-1) );
if ( exist(fn_mo, 'file') )
h = create_dag_from_file (fn_mo);
else
beg_epoch =... |
github | pengsun/MatConvDAG-master | mnist_small_te_all.m | .m | MatConvDAG-master/examples/mnist_small_te_all.m | 1,782 | utf_8 | 5d8bf8630626022149cca99b2149a49e | function [err_ep, err] = mnist_small_te_all(varargin)
% config
% TODO: add more properties here
if ( nargin==0 )
ep = 1 : 5;
batch_sz = 128;
dir_mo = fullfile(dag_path.root,'\examples\mo_zoo\mnist_small\lenetTriCon');
fn_data = fullfile(dag_path.root,'\examples\data\mnist_small_cv5\imdb.mat');
fn_mo_tmpl =... |
github | pengsun/MatConvDAG-master | mnist_small_tr_lenetDropout.m | .m | MatConvDAG-master/examples/mnist_small_tr_lenetDropout.m | 2,662 | utf_8 | 8698b1d0846e4bd5af8859629e17ddd6 | function mnist_small_tr_lenetDropout()
%% put all the stuff in a static method if you like
%% init dag: from file or from scratch
beg_epoch = 2;
dir_mo = fullfile(dag_path.root, 'examples/mo_zoo/mnist_small/lenetDropout');
fn_mo = fullfile(dir_mo, sprintf('dag_epoch_%d.mat', beg_epoch-1) );
if ( exist(fn_mo, 'file') )
... |
github | pengsun/MatConvDAG-master | cifar_tr.m | .m | MatConvDAG-master/examples/cifar_tr.m | 2,709 | utf_8 | 1fe00e5c92f5b833913d47031dedaae8 | function cifar_tr()
%% init dag: from file or from scratch
beg_epoch = 4;
dir_mo = fullfile(dag_path.root,'examples/mo_zoo/cifar/cifar');
fn_mo = fullfile(dir_mo, sprintf('dag_epoch_%d.mat', beg_epoch-1) );
if ( exist(fn_mo, 'file') )
h = create_dag_from_file (fn_mo);
else
beg_epoch = 1;
h = create_dag_from_scra... |
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