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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 | philippboehmsturm/antx-master | gencode.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/gencode.m | 8,368 | utf_8 | bdf69ad199b1ccbc06171e39793faa4e | function [str, tag, cind] = gencode(item, tag, tagctx)
% GENCODE Generate code to recreate any MATLAB struct/cell variable.
% For any MATLAB variable, this function generates a .m file that
% can be run to recreate it. Classes can implement their class specific
% equivalent of gencode with the same calling syntax. By... |
github | philippboehmsturm/antx-master | cfg_message.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/cfg_message.m | 9,875 | utf_8 | 8d66022211a225ece4067413b1b99ed7 | function varargout = cfg_message(varargin)
% function cfg_message(msgid, msgfmt, varargin)
% Display a message. The message identifier msgid will be looked up in a
% message database to decide how to treat this message. This database is
% a struct array with fields:
% .identifier - message id
% .level - message... |
github | philippboehmsturm/antx-master | initialise.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_branch/initialise.m | 1,880 | utf_8 | ae5ccc5390fd36b56d02f477649f8a28 | function item = initialise(item, val, dflag)
% function item = initialise(item, val, dflag)
% Initialise a configuration tree with values. If val is a job
% struct/cell, only the parts of the configuration that are present in
% this job will be initialised.
% If val has the special value '<DEFAULTS>', the entire confi... |
github | philippboehmsturm/antx-master | cfg_run_subsrefvar.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/cfg_basicio/cfg_run_subsrefvar.m | 6,684 | utf_8 | e989b483543339da73d1dfadd792a91e | function varargout = cfg_run_subsrefvar(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = cfg_run_subsrefvar(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_run_subsrefvar('run', job)
% Run a job, and return its output argumen... |
github | philippboehmsturm/antx-master | cfg_run_call_matlab.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/cfg_basicio/cfg_run_call_matlab.m | 5,993 | utf_8 | 6c951c26ab12e11978df562f45ad4152 | function varargout = cfg_run_call_matlab(cmd, varargin)
% A generic interface to call any MATLAB function through the batch system
% and make its output arguments available as dependencies.
% varargout = cfg_run_call_matlab(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_run_call_matlab('run', job)
% ... |
github | philippboehmsturm/antx-master | cfg_load_vars.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/cfg_basicio/cfg_load_vars.m | 5,290 | utf_8 | d9fea1c27279512bee3dd9f1724a21a0 | function varargout = cfg_load_vars(cmd, varargin)
% Load a .mat file, and return its contents via output dependencies.
% varargout = cfg_load_vars(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_load_vars('run', job)
% Run a job, and return its output argument
% 'vout' - dep = cfg_load_va... |
github | philippboehmsturm/antx-master | initialise.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_choice/initialise.m | 3,001 | utf_8 | 0224d7c84c0e3a40bfb09279d56bc0e7 | function item = initialise(item, val, dflag)
% function item = initialise(item, val, dflag)
% Initialise a configuration tree with values. If val is a job
% struct/cell, only the parts of the configuration that are present in
% this job will be initialised. If dflag is true, then matching items
% from item.values will... |
github | philippboehmsturm/antx-master | subsasgn.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_dep/subsasgn.m | 4,222 | utf_8 | a6857a9c1bd09dc62c519bbf634712b6 | function dep = subsasgn(dep, subs, varargin)
% function dep = subsasgn(dep, subs, varargin)
% subscript references we have to deal with are:
% one level
% dep.(field) - i.e. struct('type',{'.'} ,'subs',{field})
% dep(idx) - i.e. struct('type',{'()'},'subs',{idx})
% two levels
% dep(idx).(field)
%
% to be dealt ... |
github | philippboehmsturm/antx-master | cfg_example_cumsum1.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/examples/cfg_example_cumsum1.m | 2,889 | utf_8 | f5dc70e6d60661de3c6bf62d8ea9487b | function cumsum = cfg_example_cumsum1
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as vector, the output is a vector containing the
% cumulative sums. This function differs from cfg_example_sum (except from
% names) only in the specification of the output subscript.
%
% Thi... |
github | philippboehmsturm/antx-master | cfg_example_div.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/examples/cfg_example_div.m | 3,310 | utf_8 | 902c541dac987ad9bb5ebf031e4f5180 | function div = cfg_example_div
% Example script that creates an cfg_exbranch to compute mod and rem of two
% natural numbers. The inputs are entered as two single numbers, the output
% is a struct with two fields 'mod' and 'rem'.
%
% This code is part of a batch job configuration system for MATLAB. See
% help mat... |
github | philippboehmsturm/antx-master | cfg_example_add2.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/examples/cfg_example_add2.m | 2,620 | utf_8 | 46feab1277369d412b219fc3988a1392 | function add2 = cfg_example_add2
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as 2-vector, the output is just a single
% number.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%___________________... |
github | philippboehmsturm/antx-master | cfg_example_add1.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/examples/cfg_example_add1.m | 3,289 | utf_8 | e1eb2aaadbb170eb366a96d03a8661e8 | function add1 = cfg_example_add1
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as two single numbers, the output is just a single
% number.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%_________... |
github | philippboehmsturm/antx-master | cfg_example_cumsum2.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/examples/cfg_example_cumsum2.m | 3,390 | utf_8 | 2db3649cdb98840abf80534956cbdeed | function cumsum = cfg_example_cumsum2
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as vector, the output is a vector containing the
% cumulative sums. This function differs from cfg_example_sum (except from
% names) only in the specification of the output subscript.
%
% Thi... |
github | philippboehmsturm/antx-master | cfg_example_sum.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/examples/cfg_example_sum.m | 2,704 | utf_8 | ded78850aa3b7a740bb1d79cbcdccbc4 | function sum = cfg_example_sum
% Example script that creates an cfg_exbranch to sum two numbers. The
% inputs are entered as vector, the output is just a single
% number. This function differs from cfg_example_add2 (except from names)
% only in the specification of input1.num.
%
% This code is part of a batch job confi... |
github | philippboehmsturm/antx-master | num2str.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/private/num2str.m | 6,229 | utf_8 | 35ba81d9ba6b78d182aa2136612ac3b2 | function s = num2str(x, f)
%NUM2STR Convert numbers to a string.
% T = NUM2STR(X) converts the matrix X into a string representation T
% with about 4 digits and an exponent if required. This is useful for
% labeling plots with the TITLE, XLABEL, YLABEL, and TEXT commands.
%
% T = NUM2STR(X,N) converts the matr... |
github | philippboehmsturm/antx-master | inputdlg.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/private/inputdlg.m | 12,680 | utf_8 | 3b9117e7e6d82e331df98e955c8f1203 | function Answer=inputdlg(Prompt, Title, NumLines, DefAns, Resize)
%INPUTDLG Input dialog box.
% ANSWER = INPUTDLG(PROMPT) creates a modal dialog box that returns user
% input for multiple prompts in the cell array ANSWER. PROMPT is a cell
% array containing the PROMPT strings.
%
% INPUTDLG uses UIWAIT to suspend ex... |
github | philippboehmsturm/antx-master | cfg_justify.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/private/cfg_justify.m | 4,780 | utf_8 | e63deba1ef91c37883c9de58f6f99344 | function out = cfg_justify(varargin)
% CFG_JUSTIFY Justifies a text string
% OUT = CFG_JUSTIFY(N,TXT) justifies text string TXT to
% the length specified by N.
%
% OUT = CFG_JUSTIFY(OBJ,TXT), where OBJ is a handle to a 'listbox' style
% uicontrol, justifies text string TXT to the width of the OBJ in
% ch... |
github | philippboehmsturm/antx-master | listdlg.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/private/listdlg.m | 8,510 | utf_8 | 1f4fe8c262a7bb4801e0b8abe2014870 | function [selection,value] = listdlg(varargin)
%LISTDLG List selection dialog box.
% [SELECTION,OK] = LISTDLG('ListString',S) creates a modal dialog box
% which allows you to select a string or multiple strings from a list.
% SELECTION is a vector of indices of the selected strings (length 1 in
% the single se... |
github | philippboehmsturm/antx-master | initialise.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_mchoice/initialise.m | 3,150 | utf_8 | 0f2df3f6db6f05985b97b4c89357cb92 | function item = initialise(item, val, dflag)
% function item = initialise(item, val, dflag)
% Initialise a configuration tree with values. If val is a job
% struct/cell, only the parts of the configuration that are present in
% this job will be initialised. If dflag is true, then matching items
% from item.values will... |
github | philippboehmsturm/antx-master | cfg_confgui.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/cfg_confgui/cfg_confgui.m | 31,063 | utf_8 | c3ac1e274d0982450821448a622318a6 | function menu_cfg = cfg_confgui
% This function describes the user defined fields for each kind of
% cfg_item and their layout in terms of cfg_items. Thus, the
% configuration system can be used to generate code for new configuration
% files itself.
%
% This code is part of a batch job configuration system for MATLAB.... |
github | philippboehmsturm/antx-master | cfg_run_template.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/cfg_confgui/cfg_run_template.m | 4,820 | utf_8 | 6b3abdb5d1a9cfd4401faaf597385d30 | function varargout = cfg_run_template(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = cfg_run_template(cmd, varargin)
% where cmd is one of
% 'run' - out = cfg_run_template('run', job)
% Run a job, and return its output argument
% 'v... |
github | philippboehmsturm/antx-master | subsasgn_check.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_entry/subsasgn_check.m | 8,352 | utf_8 | c0c07054289df61d4ca469b59de16097 | function [sts, val] = subsasgn_check(item,subs,val)
% function [sts, val] = subsasgn_check(item,subs,val)
% Perform validity checks for cfg_entry inputs. Does not yet support
% evaluation of inputs.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overv... |
github | philippboehmsturm/antx-master | showdoc.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_entry/showdoc.m | 1,961 | utf_8 | 4470b2abb40c7db525283b910ac13664 | function str = showdoc(item, indent)
% function str = showdoc(item, indent)
% Display help text for a cfg_entry item.
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%_______________________________________________________________________
% C... |
github | philippboehmsturm/antx-master | resolve_deps.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_item/resolve_deps.m | 3,620 | utf_8 | 3ed76ebe16ad02f135f4a83f428654f3 | function [val, sts] = resolve_deps(item, cj)
% function [val, sts] = resolve_deps(item, cj)
% Resolve dependencies for an cfg item. This is a generic function that
% returns the contents of item.val{1} if it is an array of cfg_deps. If
% there is more than one dependency, they will be resolved in order of
% appearance... |
github | philippboehmsturm/antx-master | initialise.m | .m | antx-master/freiburgLight/matlab/spm8/matlabbatch/@cfg_repeat/initialise.m | 4,833 | utf_8 | 318adce123a9102e6369cf2d4f428e3f | function item = initialise(item, val, dflag)
% function item = initialise(item, val, dflag)
% Initialise a configuration tree with values. If val is a job
% struct/cell, only the parts of the configuration that are present in
% this job will be initialised. If dflag is true, then matching items
% from item.values will... |
github | philippboehmsturm/antx-master | spm_hrf_timeshift_demo.m | .m | antx-master/freiburgLight/matlab/spm8/demo/spm_hrf_timeshift_demo.m | 7,324 | utf_8 | f198b9d5ad85ad5f98540f291c660b4f | function spm_hrf_timeshift_demo
%% Modelling time shifts in hemodynamic responses
% In some situations, the time course of the canonical hrf might not fit
% the observed time course. In particular, the observed time-to-peak might
% vary between different areas of the brain (or different event types in
% the same brain ... |
github | philippboehmsturm/antx-master | spm_conv_demo.m | .m | antx-master/freiburgLight/matlab/spm8/demo/spm_conv_demo.m | 804 | utf_8 | dc62d248d1d683bf767fa551bf708054 | function spm_conv_demo
global defaults;
defaults.stats.fmri.t=16;
RT=.1;
[hrf phrf]=spm_hrf(RT);
hrf=hrf/max(hrf);
t=0:1/defaults.stats.fmri.t:500;
scans=zeros(size(t));
scans(1:defaults.stats.fmri.t:end)=1;
f=figure(2);
clf;
axscans=axes('position',[.3 .1 .6 .2]);
axons=axes('position',[.3 .4 .6 .2]);
axconv=axes(... |
github | philippboehmsturm/antx-master | spm_ovhelper_3Dreg.m | .m | antx-master/freiburgLight/matlab/spm8/spm_orthviews/spm_ovhelper_3Dreg.m | 3,534 | utf_8 | 1820adca26f6de47595faa8162381cda | function spm_ovhelper_3Dreg(cmd, varargin)
% Helper function to register spm_orthviews plugins via spm_XYZreg
% FORMAT spm_ovhelper_3Dreg('register', h, V)
% Register a (3D) graphics with the main spm_orthviews display. This will
% draw 3D crosshairs at the current spm_orthviews position and update
% them whenever the ... |
github | philippboehmsturm/antx-master | spm_ov_title.m | .m | antx-master/freiburgLight/matlab/spm8/spm_orthviews/spm_ov_title.m | 2,474 | utf_8 | dbb8c641fb8dfe619909aac75fa7deb5 | function spm_ov_title(varargin)
global st;
if isempty(st)
error(sprintf('spm:%s', mfilename), '%s: This routine can only be called as a plugin for spm_orthviews!', mfilename);
end;
if nargin < 2
error(sprintf('spm:%s', mfilename), '%: Wrong number of arguments. Usage: spm_orthviews(''title'', cmd, volhandle, ... |
github | philippboehmsturm/antx-master | spm_ov_roi.m | .m | antx-master/freiburgLight/matlab/spm8/spm_orthviews/spm_ov_roi.m | 36,776 | utf_8 | aeb54afe2f51c5c9e637c2e3b31f8e18 | function ret = spm_ov_roi(varargin)
% ROI tool - plugin for spm_orthviews
%
% With ROI tool it is possible to create new or modify existing mask images
% interactively. ROI tool can be launched via the spm_orthviews image
% context menu.
% While ROI tool is active, mouse buttons have the following functions:
% left ... |
github | philippboehmsturm/antx-master | spm_cfg_sendmail.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/spm_cfg_sendmail.m | 5,377 | utf_8 | 202a73a362717243076b2289fd67484c | function sendmail = spm_cfg_sendmail
% SPM Configuration file for sendmail
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% $Id: spm_cfg_sendmail.m 2923 2009-03-23 18:34:51Z guillaume $
% --------------------------------------------... |
github | philippboehmsturm/antx-master | Neural_demo.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Neural_Models/Neural_demo.m | 4,316 | utf_8 | 1266d6ca90e707c689e0ad1c471d8909 | function varargout = Neural_demo(varargin)
% NEURAL_DEMO M-file for Neural_demo.fig
% NEURAL_DEMO, by itself, creates a new NEURAL_DEMO or raises the existing
% singleton*.
%
% H = NEURAL_DEMO returns the handle to a new NEURAL_DEMO or the handle to
% the existing singleton*.
%
% NEURAL_DEMO('C... |
github | philippboehmsturm/antx-master | spm_freqs.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Neural_Models/spm_freqs.m | 3,737 | utf_8 | 62139edd7cd9d8687d5af3ac86f25027 | function [h,ww] = freqs(b,a,w)
%FREQS Laplace-transform (s-domain) frequency response.
% H = FREQS(B,A,W) returns the complex frequency response vector H
% of the filter B/A:
% nb-1 nb-2
% B(s) b(1)s + b(2)s + ... + b(nb)
% H(s) = ---- = -----------------... |
github | philippboehmsturm/antx-master | spm_shoot_update.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Shoot/spm_shoot_update.m | 4,384 | utf_8 | effbd61be58eeeacba046cd940be6612 | function [u0,ll1, ll2,grad_norm] = spm_shoot_update(g,f,u0,phi,dt,prm,int_args, bs_args,scale)
% Shooting Of Diffeomorphisms (Spawn Of Dartel).
% FORMAT u0 = spm_shoot_update(g,f,u0,phi,dt,prm,int_args, bs_args)
% g - template
% f - individual
% u0 - initial velocity
% phi - deformation
% dt ... |
github | philippboehmsturm/antx-master | spm_shoot3di.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Shoot/spm_shoot3di.m | 6,901 | utf_8 | 4db8d50018ee6679cfb375dc8e01c81c | function varargout = spm_shoot3di(v0,prm,args)
% Geodesic shooting
% FORMAT [theta,Jtheta,v1,phi,Jphi] = spm_shoot3di(v0,prm,args)
% v0 - Initial velocity field n1*n2*n3*3 (single prec. float)
% prm - 7 Differential operator parameter settings
% - [1] Regularisation type (ie the form of the differential... |
github | philippboehmsturm/antx-master | spm_shoot_template.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Shoot/spm_shoot_template.m | 11,515 | utf_8 | a1f2b9608195d776adafa0fdb535d298 | function out = spm_shoot_template(job)
% Iteratively compute a template with mean shape and intensities
% format spm_shoot_template(job)
% Fields of job:
% job.images{1} first set of images (eg rc1*.nii)
% job.images{2} second set of images (eg rc2*.nii)
% etc
%
% Other settings are defined in spm_shoot_def... |
github | philippboehmsturm/antx-master | spm_shoot_blur.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Shoot/spm_shoot_blur.m | 6,581 | utf_8 | 44fc0c3ca2a43f6ffcd3af5a35660c45 | function [sig,a] = spm_shoot_blur(t,prm,its,sig)
% A function for blurring ("smoothing") tissue probability maps
% FORMAT [sig,a_new] = spm_shoot_blur(t,prm,its,sig)
% t - sufficient statistics
% prm - regularisation parameters (2, 1,1,1, 1,0.01,0.01)
% its - max no. iterations (12)
% sig - optional s... |
github | philippboehmsturm/antx-master | spm_shoot3d.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Shoot/spm_shoot3d.m | 6,488 | utf_8 | 7f1ca5842f35b820190834c523353944 | function varargout = spm_shoot3d(v0,prm,args)
% Geodesic shooting
% FORMAT [phi,Jphi,v1,theta,Jtheta] = spm_shoot3d(v0,prm,args)
% v0 - Initial velocity field n1*n2*n3*3 (single prec. float)
% prm - Differential operator parameters
% prm - 7 parameters (settings)
% - [1] Regularisation type (ie the form of t... |
github | philippboehmsturm/antx-master | tbx_cfg_shoot.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Shoot/tbx_cfg_shoot.m | 38,664 | utf_8 | 0fd083d5d34a604dfcaeb7f4cd3568d1 | function shoot = tbx_cfg_shoot
% MATLABBATCH Configuration file for toolbox 'Shoot Tools'
% $Id: tbx_cfg_shoot.m 4136 2010-12-09 22:22:28Z guillaume $
addpath(fullfile(spm('dir'),'toolbox','DARTEL'));
addpath(fullfile(spm('dir'),'toolbox','Shoot'));
% ------------------------------------------------------------------... |
github | philippboehmsturm/antx-master | ArtRepair.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/ArtRepair.m | 4,284 | utf_8 | 30332ef73082be065bb6166cb5330bd2 | function varargout = spm_artifactrepair(varargin)
% SPM_ARTIFACTREPAIR M-file for spm_artifactrepair.fig
% SPM_ARTIFACTREPAIR, by itself, creates a new SPM_ARTIFACTREPAIR or raises the existing
% singleton*.
%
% H = SPM_ARTIFACTREPAIR returns the handle to a new SPM_ARTIFACTREPAIR or the handle to
... |
github | philippboehmsturm/antx-master | art_summary.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_summary.m | 13,264 | utf_8 | f92ca4faeb9ae93562b3fd58332e3ccd | function [GQout,GQmean,Resout] = art_summary(ImageFullName,MaskFullName,OutputFolder,Figname,Fignum,AutoParams);
% FUNCTION art_summary (v3) FEB 2009
% For manual GUI:
% >>art_summary will use GUI to ask for images
%
% SUMMARY
% Summarizes the overall quality of estimates produced during GLM
% estimat... |
github | philippboehmsturm/antx-master | art_groupcheck.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_groupcheck.m | 30,844 | utf_8 | 9668b36f736e66de0d687cde18c8b60c | function art_groupcheck(Action)
% FUNCTION art_groupcheck - v4
%
% FUNCTIONS:
% Allows a user to perform visual quality checks on contrast images
% associated with a user-supplied group level SPM.mat file. These checks
% can compare con and ResMS values for all subjects on a voxel, or
% view contrast... |
github | philippboehmsturm/antx-master | art_groupsummary.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_groupsummary.m | 13,707 | utf_8 | 7f3f9b92ccadf33ed0ed88767af8aab2 | function [GQout,GQmean, Resout] = art_groupsummary(ImageFullName,MaskFullName,OutputFolder,Figname,Fignum,AutoParams);
% FUNCTION art_groupsummary (v1)
% For manual GUI:
% >>art_groupsummary will use GUI to ask for images
%
% SUMMARY
% Summarizes the overall quality of estimates produced during group level
% ... |
github | philippboehmsturm/antx-master | art_addmargin.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_addmargin.m | 7,400 | utf_8 | 677f4d80c4296d3358e74d0486c2d1a8 | function art_addmargin
% Function art_addmargin
%
% Helper function for art_global. For a set of indices to be repaired,
% returns a list of indices to be deweighted. The list is
% returned as outdw_idx. The list will be written to file when the
% art_global REPAIR button is pushed.
% The logic is:
% ... |
github | philippboehmsturm/antx-master | art_motionregress.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_motionregress.m | 18,338 | utf_8 | 239207e5377f255eec3cc544d5b3f778 | function art_motionregress(ReslicedDir,ReslicedImages,RealignDir,RealignImages)
% function art_motionregress
% >> art_motionregress for use by GUI
% See below for batch.
%
% FUNCTIONS
% Remove residual interpolation errors after the realign and reslice
% operations (see Grootoonk 2000 for theory).
% It is an ... |
github | philippboehmsturm/antx-master | art_motionadjust.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_motionadjust.m | 2,638 | utf_8 | a618fe5bcfdfdec770bc4ef563572143 | function art_motionadjust(Images, Mgammas, Regressors)
% FORMAT art_motionadjust
% Support function for art_motionregress
% SUMMARY
% Reads a set of images to motion adjust
% Reads six mgamma images to use for regressors.
% Reads a set of images to get their realignment .mat files.
% Writes a set of motion a... |
github | philippboehmsturm/antx-master | art_automask.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_automask.m | 8,663 | utf_8 | 00761162b94e9340128d2fb96852aab6 | function Y = art_automask(Image,Threshold,WriteVol);
% Y = art_automask( Image, Threshold, WriteVol ) (v2.2)
% art_automask;
%
% Calculates a pretty good mask image from an input full-head Image
% in order to detect artifacts in the data. The threshold
% is higher than us... |
github | philippboehmsturm/antx-master | art_groupoutlier.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_groupoutlier.m | 18,950 | utf_8 | 2d22a294e3de9362486a0b535eb4b591 | function art_groupoutlier(ConImageNames, GroupMaskName,Groupscale, OutputDir)
% FUNCTION art_groupoutlier
% >> art_groupoutlier to run by GUI
%
% Program runs the global quality metrics for a contrast image from all
% subjects. Creates a summary over all subjects of GQ scores per
% per subject, visually disp... |
github | philippboehmsturm/antx-master | art_despike.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_despike.m | 11,589 | utf_8 | 5e3e7b11e4139268b7cdbae79a22893f | function zout = art_despike(Images,FiltType,Despike)
% FUNCTION art_despike(Images,FiltType,Despike)
% >> art_despike to run by GUI
%
% Removes spikes and slow variations using clipping and a high pass filter.
% Generally, these functions remove large noise at the expense of slightly
% reducing the contrast between ... |
github | philippboehmsturm/antx-master | art_slice.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ArtRepair/art_slice.m | 14,002 | utf_8 | f6d5e310ed66a7afb86a5318abe94963 | function art_slice
% FORMAT art_slice (v2.3)
%
% SUMMARY
% Reads a set of images and writes a new set of images
% after filtering the data for noise. User is asked to choose the
% repair method or methods. This program is best applied
% to the raw images, so the cleaned output images can be fed into
% sli... |
github | philippboehmsturm/antx-master | tbx_cfg_render.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/SRender/tbx_cfg_render.m | 19,186 | utf_8 | 52ec82ded599415d96ecaba3b38013d5 | function render = tbx_cfg_render
% Configuration file for toolbox 'Rendering'
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: tbx_cfg_render.m 3802 2010-03-29 13:07:15Z john $
% -------------------------------... |
github | philippboehmsturm/antx-master | spm_sextract.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/SRender/spm_sextract.m | 2,032 | utf_8 | 4a45ee93e484bacd762c3aa2c4cc0003 | function out = spm_sextract(job)
% Surface extraction
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: spm_sextract.m 2210 2008-09-26 20:14:13Z john $
images = job.images;
Vi = spm_vol(strvcat(images));
n ... |
github | philippboehmsturm/antx-master | spm_eeg_ft_beamformer_cva.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Beamforming/spm_eeg_ft_beamformer_cva.m | 40,809 | utf_8 | 83ce46ca11b2e5c61aa5660790a64ae5 | function [stats,talpositions,gridpositions,grid,fftnewdata,alllf,allepochdata]=spm_eeg_ft_beamformer_cva(S)
% Computes power-based beamformer image
% FORMAT [outfilenames,ctf_inside,ctf_weights]=spm_eeg_ft_beamformer_cva (S)
%
% S MEEG object where coregistration has been performed.
%
%
% Outputs (1) normalised... |
github | philippboehmsturm/antx-master | tbx_cfg_tbx_Icc.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/icc/tbx_cfg_tbx_Icc.m | 3,628 | utf_8 | 164fe7ffc0377b56b9330df0aae45f34 | function tbx_Icc = tbx_cfg_tbx_Icc
% Russ Poldrack and Volkmar Glauche
% $Id: tbx_cfg_tbx_Icc.m,v 1.1 2008-04-14 08:53:10 vglauche Exp $
%_______________________________________________________________________
rev='$Revision: 1.1 $';
addpath(fullfile(spm('dir'),'toolbox','icc'));
% see how we are called - if no o... |
github | philippboehmsturm/antx-master | tbx_config_icc.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/icc/tbx_config_icc.m | 2,243 | utf_8 | e395073628088e0bc7895a43bb0073d9 | function opts = spm_config_Icc
%_______________________________________________________________________
% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
% Russ Poldrack and Volkmar Glauche
% $Id: tbx_config_icc.m,v 1.2 2007-03-30 07:58:52 glauche Exp $
%______________________________________________... |
github | philippboehmsturm/antx-master | timediff.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/tsdiffana/timediff.m | 3,340 | utf_8 | 1cc63d946f7f8d629436d4357c2a419d | function [imdiff, g, slicediff] = timediff(imgs, flags)
% Analyses slice by slice variance across time series
% FORMAT [imdiff, g, slicediff] = timediff(imgs, flags)
%
% imgs - string or cell or spm_vol list of images
% flags - specify options; if contains:
% m - create mean var image (vmean*), max slice v... |
github | philippboehmsturm/antx-master | run_tsdiffana.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/tsdiffana/run_tsdiffana.m | 2,148 | utf_8 | f201c026bb24af7be0e0ffc49ac908b8 | function varargout = run_tsdiffana(cmd, varargin)
% Wrapper function for tsdiffana routines
switch cmd,
case 'run'
subfun = varargin{1};
job = varargin{2};
switch subfun
case 'timediff'
for k = 1:numel(job.imgs)
[p f e] = spm_fileparts(job.... |
github | philippboehmsturm/antx-master | moh_unified_segmentation.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ALI/moh_unified_segmentation.m | 10,685 | utf_8 | 3bd937b04b9b19314f52a21a31907abc | function moh_unified_segmentation(V, c4prior)
% based on spm segmentation routines
% V: volume structure to be segmented
% c4prior: image that defines the spatial priors for the extra class
%
% Mohamed Seghier 05.08.2008
% =======================================
%
if ~isstruct(V), V = spm_vol(V) ; end
[pth,na... |
github | philippboehmsturm/antx-master | moh_config_ALI.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ALI/moh_config_ALI.m | 18,900 | utf_8 | b23f41a3961164c0d0deb0b12c729b63 | function job = moh_config_ALI
% Configuration file for the Automatic Lesion Identification (ALI)
%_______________________________________________________________________
% Copyright (C) 2009 Wellcome Trust Centre for Neuroimaging
%
% Mohamed Seghier, 28.05.2009
% =========================
entry = inline(['struct(''ty... |
github | philippboehmsturm/antx-master | tbx_fbi_bruker2nifti.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FBIBruker/tbx_fbi_bruker2nifti.m | 6,253 | utf_8 | 448d1d0132da5c52633a2902758bfc18 | function varargout = tbx_fbi_bruker2nifti(cmd, varargin)
% Convert bruker 2dseq files to NIfTI. The calling
% syntax is
% varargout = tbx_fbi_bruker2nifti(cmd, varargin)
% where cmd is one of
% 'run' - out = tbx_fbi_bruker2nifti('run', job)
% Convert data.
% 'vout' - dep = tbx_fbi_bruker2nifti('vo... |
github | philippboehmsturm/antx-master | vgtbx_config_Volumes.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/vgtbx_config_Volumes.m | 45,782 | utf_8 | 2f279a3167e39ed2d3d812e69e9093c5 | function opt = vgtbx_config_Volumes
% Volumes toolbox
%_______________________________________________________________________
%
% This toolbox contains various helper functions to make image
% manipulation within SPM5 more convenient. Help on each individual item
% can be obtained by selecting the corresponding entr... |
github | philippboehmsturm/antx-master | tbx_cfg_vgtbx_Volumes.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/tbx_cfg_vgtbx_Volumes.m | 103,487 | utf_8 | 0e4f45d959bdbdd19f162cff91b351de | function vgtbx_Volumes = tbx_cfg_vgtbx_Volumes
% Volumes toolbox
%_______________________________________________________________________
%
% This toolbox contains various helper functions to make image
% manipulation within SPM5 more convenient. Help on each individual item
% can be obtained by selecting the corresp... |
github | philippboehmsturm/antx-master | tbxvol_normalise.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Multiple_Volumes/tbxvol_normalise.m | 16,914 | utf_8 | b6240c42997c1004290a795f609a7858 | function tbxvol_normalise(varargin)
job = varargin{1};
eflags = job.eoptions.iteration;
for i=1:numel(job.subj.source),
[pth,nam,ext,ind] = spm_fileparts(char(job.subj.source{i}));
matname{i} = fullfile(pth,[nam '_gr_sn.mat']);
end;
if isfield(job.eoptions.starting,'stempl')
VG = char(job.eoptions.starting.st... |
github | philippboehmsturm/antx-master | tbxvol_spike_mask.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Multiple_Volumes/tbxvol_spike_mask.m | 6,666 | utf_8 | 6653019fed50774babb90f080393b12e | function varargout = tbxvol_spike_mask(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = tbxvol_spike_mask(cmd, varargin)
% where cmd is one of
% 'run' - out = tbxvol_spike_mask('run', job)
% Run a job, and return its output argument
%... |
github | philippboehmsturm/antx-master | tbxvol_spike.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Multiple_Volumes/tbxvol_spike.m | 3,212 | utf_8 | 2008e72d56a97eef2685b07a7f2f3083 | function tbxvol_spike(bch)
% Detect slices with abnormal intensities or standard deviations
% FORMAT tbxvol_spike(bch)
% ======
% For each volume, normalised mean signal and standard deviation are computed per
% slice. These values are then compared to their mean over all volumes,
% and slices that deviate from these... |
github | philippboehmsturm/antx-master | spm_ov_extract.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/spm_orthviews/spm_ov_extract.m | 15,182 | utf_8 | 375359110bf9079b2bb1552b44279cf7 | function ret = spm_ov_extract(varargin)
% Wrapper for tbxvol_extract
% This function provides an interface to tbxvol_extract from
% an spm_orthviews display. The main features include:
% ROI selection alternatives
% - cross hair selection for start and end point of a profile line
% (after selection, the line will be ad... |
github | philippboehmsturm/antx-master | tbxvol_laterality.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Stats_Tools/tbxvol_laterality.m | 1,709 | utf_8 | 21c27d2d5e1d04f27ceebbe0b9334c1f | function varargout = tbxvol_laterality(bch)
% Compute laterality index of images with range [0,1]
% FORMAT tbxvol_laterality(bch)
% ======
% Input arguments:
% bch.srcimg - file name of input image
%
% This routine computes the laterality index for images with positive
% data range as (normal-flipped)./(normal+flipped)... |
github | philippboehmsturm/antx-master | tbxvol_orth_conditions.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Stats_Tools/tbxvol_orth_conditions.m | 5,935 | utf_8 | 2aaafa037ff5edeefe25805fee8b3a71 | function varargout = tbxvol_orth_conditions(cmd, varargin)
% Orthogonalise conditions in an SPM design matrix.
% By default, SPM does not orthogonalise timeseries of different
% conditions. Under some conditions two conditions may be highly correlated
% (usually due to an imperfect experimental design). If only one of ... |
github | philippboehmsturm/antx-master | tbxvol_hist_summary.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Stats_Tools/tbxvol_hist_summary.m | 4,425 | utf_8 | bda66ed96d74109d394c178884a9f31e | function varargout = tbxvol_hist_summary(cmd, varargin)
% Compute histogramm summary
% FORMAT tbxvol_hist_summary(bch)
% ======
%
% This function is part of the volumes toolbox for SPM5. For general help
% about this toolbox, bug reports, licensing etc. type
% spm_help vgtbx_config_Volumes
% in the matlab comman... |
github | philippboehmsturm/antx-master | tbxvol_changeSPM.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Stats_Tools/tbxvol_changeSPM.m | 6,862 | utf_8 | ecf4e78064941de74e69f7a0bfd78cf5 | function varargout = tbxvol_changeSPM(bch)
% Change path names or byte order of image files in SPM structure
% FORMAT tbxvol_changeSPM(bch)
% ======
% Input arguments:
% bch.srcspm - file name of SPM.mat files to change
% bch.chpaths - which paths to change: one of
% - .dpaths - data files
% ... |
github | philippboehmsturm/antx-master | tbxvol_extract.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Single_Volumes/tbxvol_extract.m | 8,179 | utf_8 | 27680807150f62c0c527f5fe5638f7a9 | function varargout=tbxvol_extract(bch)
% read an intensity profile along a given trajectory
% FORMAT extr=tbxvol_extract(bch)
% ======
% Read intensity values from a set of images within one or more given
% regions of interest. The images to be sampled can be specified by an
% SPM.mat or a list of images.
% Multiple RO... |
github | philippboehmsturm/antx-master | tbxvol_extract2image.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Volumes/Single_Volumes/tbxvol_extract2image.m | 6,869 | utf_8 | 7503acd7ed22a4ca14ae4dfb97f9ae1e | function varargout = tbxvol_extract2image(cmd, varargin)
% Place output from tbxvol_extract back into an image
% varargout = tbxvol_extract2image(cmd, varargin)
% where cmd is one of
% 'run' - out = tbxvol_extract2image('run', job)
% Run a job, and return its output argument
% job has the... |
github | philippboehmsturm/antx-master | amr_test_fit.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Perfusion/amr_test_fit.m | 3,362 | utf_8 | 02b23187c24963f7c81571e691674dc2 | function [fitfunc] = amr_test_fit(base, tail, rcbv,at,alpha,beta,method);
%
% function [fitfunc] = amr_test_fit(base, tail, rcbv,at,alpha,beta,method);
%
% method: 'ge' or 'se'; default is 'ge'
%
% Examples:
% for ge:
% [fitfunc_ge] = amr_test_fit(base_ge, tail_ge, rcbv_ge,at_ge,alpha_ge,beta_ge,'ge');
% for se:
%... |
github | philippboehmsturm/antx-master | tbxrend_nifti_to_df3.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Render3D/tbxrend_nifti_to_df3.m | 1,912 | utf_8 | b2c969d334a35385f40a16d7579aa38a | function tbxrend_nifti_to_df3(bch)
% export NIfTI image to POVray df3 format
% produces the df3 file itself and a coordinate transform from unit cube
% to NIfTI world space
% bch.srcimg
% bch.outimg.fname
% bch.outimg.swd
% bch.outres - 'uint8','uint16','uint32'
% data will be scaled to fit range, non-finite values s... |
github | philippboehmsturm/antx-master | tbxrend_export_surf.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Render3D/tbxrend_export_surf.m | 1,692 | utf_8 | 2ddd5ddf94e98d9dd38aa20da08a4f47 | function tbxvol_export_surf(srf)
% export surfaces to blender format
% can handle either patch structures or patch graphics objects
% in the latter case, colouring will be approximately translated
% (blender does not seem to allow for vertex colouring, so colours need
% to be interpolated per face)
for cs=1:numel(srf)... |
github | philippboehmsturm/antx-master | tbxrend_multi_cmip.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Render3D/tbxrend_multi_cmip.m | 9,147 | utf_8 | b2e36164911fe0ffc5edd6c198f2c8f6 | function varargout = tbxrend_multi_cmip(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = tbxrend_multi_cmip(cmd, varargin)
% where cmd is one of
% 'run' - out = tbxrend_multi_cmip('run', job)
% Run a job, return an object handle for e... |
github | philippboehmsturm/antx-master | tbxrend_fancy_render.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/Render3D/tbxrend_fancy_render.m | 37,531 | utf_8 | ffbbc76d528fbc3c3bcfd24be5437ee9 | function varargout = tbxrend_fancy_render(varargin)
% Fancy rendering of intensities of one brain superimposed on surface
% FORMAT fr = tbxrend_fancy_render(cmd, ...)
% ======
% Commands are
% 'init' - Initialise rendering
% 'load' - Load rendering from fr*.mat file
% 'save' - Save information about used da... |
github | philippboehmsturm/antx-master | pm_segment.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FieldMap/pm_segment.m | 25,512 | utf_8 | 37ff3bd4d9d649e61cc402f3b114c256 | function [VO,M] = pm_segment(VF,PG,flags)
% Segment an MR image into Gray, White & CSF.
%
% FORMAT VO = pm_segment(PF,PG,flags)
% PF - name(s) of image(s) to segment (must have same dimensions).
% PG - name(s) of template image(s) for realignment.
% - or a 4x4 transformation matrix which maps from the image... |
github | philippboehmsturm/antx-master | FieldMap_applyvdm.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FieldMap/FieldMap_applyvdm.m | 8,720 | utf_8 | 9761a5b5d2184cd48650ef88da884109 | function out = FieldMap_applyvdm(job)
% Apply VDM and reslice images
% FORMAT FieldMap_applyvdm(job)
% job.data(sessnum).scans - images for session/run sessnum
% job.data(sessnum).vdmfile - VDM file for session/run sessnum
% job.roptions.rinterp - interpolation method
% job.roptions.wrap - perform warp arou... |
github | philippboehmsturm/antx-master | pm_brain_mask.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FieldMap/pm_brain_mask.m | 4,163 | utf_8 | 1c73d1378400faa40089ab34da5760d1 | function bmask = pm_brain_mask(P,flags)
% Calculate a brain mask
% FORMAT bmask = pm_brain_mask(P,flags)
%
% P - is a single pointer to a single image
%
% flags - structure containing various options
% template - which template for segmentation
% fwhm - fwhm of smoothing kernel for generating mask
%... |
github | philippboehmsturm/antx-master | FieldMap.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FieldMap/FieldMap.m | 83,497 | utf_8 | 26a90d75ac07852199822d233d5c731a | function varargout=FieldMap(varargin)
%
% FieldMap is an SPM8 Toolbox for creating field maps and unwarping EPI.
% A full description of the toolbox and a usage manual can be found in
% FieldMap.man. This can launched by the toolbox help button or using
% spm_help FieldMap.man.The theoretical and practical principles... |
github | philippboehmsturm/antx-master | tbx_cfg_fieldmap.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FieldMap/tbx_cfg_fieldmap.m | 42,259 | utf_8 | 8319c4da246db18dcc1d188a72a84d01 | function fieldmap = tbx_cfg_fieldmap
% MATLABBATCH Configuration file for toolbox 'FieldMap'
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% $Id: tbx_cfg_fieldmap.m 4571 2011-11-23 17:34:12Z chloe $
addpath(fullfile(spm('dir'),'too... |
github | philippboehmsturm/antx-master | spmmouse.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/spmmouse/spmmouse.m | 14,273 | utf_8 | d9d85092bf19b02c78ec7c433004ca7b | function spmmouse(varargin)
%SPMMouse - toolbox for SPM for animal brains
%Stephen Sawiak - http://www.wbic.cam.ac.uk/~sjs80/spmmouse.html
global spmmouseset
fg = spm_figure('FindWin','Menu');
if isempty(fg)
spm('PET');
end
% what should we do
if nargin == 0
showinfo;
... |
github | philippboehmsturm/antx-master | tbx_cfg_spmmouse.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/spmmouse/tbx_cfg_spmmouse.m | 4,675 | utf_8 | b22be77a04d0c4a276ccaf167b8ddb45 | function cfg = tbx_cfg_spmmouse
% Adapted GUI for SPM Segment, New Segment and VBM8 including modified
% choices for bias regularisation and affine registration options. Although
% computation is done by standard SPM functions and the defaults are
% changed in the global defaults variable, the cfg_menu GUIs can not
% ... |
github | philippboehmsturm/antx-master | spm_klaff.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/DARTEL/spm_klaff.m | 8,314 | utf_8 | 0f0299ab4f49e2fbfa31b23c2f939ae1 | function M = spm_klaff(Nf, Ng)
% Affine registration by minimising Kullback-Leibler Divergence
% FORMAT M = spm_klaff(Nf,Ng)
% Nf - NIfTI handle for one image
% Ng - Nifti handle for the other. If not passed, then
% spm*/toolbox/Seg/TPM.nii is used.
% M - The voxel-for-voxel affine transform
%
% The images that ... |
github | philippboehmsturm/antx-master | spm_dartel_norm_fun.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/DARTEL/spm_dartel_norm_fun.m | 10,295 | utf_8 | 63e79a297027d2f2790b757b50bede30 | function out = spm_dartel_norm_fun(job)
% Spatially normalise and smooth fMRI/PET data to MNI space, using DARTEL flow fields
% FORMAT out = spm_dartel_norm_fun(job)
% job - a structure generated by the configuration file
% job.template - DARTEL template for aligning to MNI space
% job.subj(n) - Subject n
% ... |
github | philippboehmsturm/antx-master | tbx_cfg_dartel.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/DARTEL/tbx_cfg_dartel.m | 65,076 | utf_8 | da29ad1825a2e216ba03f7c83d417021 | function dartel = tbx_cfg_dartel
% Configuration file for toolbox 'DARTEL Tools'
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: tbx_cfg_dartel.m 4650 2012-02-09 08:14:54Z volkmar $
if ~isdeployed, addpath(ful... |
github | philippboehmsturm/antx-master | spm_dartel_smooth.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/DARTEL/spm_dartel_smooth.m | 1,773 | utf_8 | b7c32a058585a98c2722f80112a61f05 | function [sig,a] = spm_dartel_smooth(t,lam,its,vx,a)
% A function for smoothing tissue probability maps
% FORMAT [sig,a_new] = spm_dartel_smooth(t,lam,its,vx,a_old)
%________________________________________________________
% (c) Wellcome Centre for NeuroImaging (2007)
% John Ashburner
% $Id: spm_dartel_smooth.m 3102 2... |
github | philippboehmsturm/antx-master | spm_dartel_import.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/DARTEL/spm_dartel_import.m | 11,025 | utf_8 | b77410a96c6ed6cad8a8077f59075ab7 | function out = spm_dartel_import(job)
% Import subjects' data for use with DARTEL
% FORMAT spm_dartel_import(job)
% job.matnames - Names of *_seg_sn.mat files to use
% job.odir - Output directory
% job.bb - Bounding box
% job.vox - Voxel sizes
% job.GM/WM/CSF - Options fo different tissue classes
% j... |
github | philippboehmsturm/antx-master | stat_thresh.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/ns/stat_thresh.m | 16,232 | utf_8 | d2613cd524b47b58778eae21cddbf866 | function [peak_threshold, extent_threshold, peak_threshold_1, extent_threshold_1] = ...
stat_thres(search_volume, num_voxels, fwhm, df, p_val_peak, ...
cluster_threshold, p_val_extent, nconj, nvar, EC_file, expr)
%
% stat_thresh.m
% Modified version of STAT_THRESHOLD function by Keith Worsley. The original
% STAT... |
github | philippboehmsturm/antx-master | tbx_cfg_hdw.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/HDW/tbx_cfg_hdw.m | 9,492 | utf_8 | f45f5115b3ab70be34ef72399f52ff5d | function hdw = tbx_cfg_hdw
% Configuration file for toolbox 'High-Dimensional Warping'
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: tbx_cfg_hdw.m 3960 2010-06-30 17:41:24Z ged $
% --------------------------... |
github | philippboehmsturm/antx-master | spm_hdw.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/HDW/spm_hdw.m | 10,972 | utf_8 | 40c05cd670bad0c86a761d18e32f7811 | function spm_hdw(job)
% Warp a pair of same subject images together
%
% Very little support can be provided for the warping routine, as it
% involves optimising a very nonlinear objective function.
% Also, don't ask what the best value for the regularisation is.
%________________________________________________________... |
github | philippboehmsturm/antx-master | run_correction.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/physiotools/run_correction.m | 6,131 | utf_8 | f3e5799b94a4622ea9d01182fc9c113d | function varargout = run_correction(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = run_correction(cmd, varargin)
% where cmd is one of
% 'run' - out = run_correction('run', job)
% Run a job, and return its output argument
% 'vout' ... |
github | philippboehmsturm/antx-master | run_phases_and_cycles.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/physiotools/run_phases_and_cycles.m | 9,577 | utf_8 | 1e141800f7c7283857f0e5c97d9643cd | function varargout = run_phases_and_cycles(cmd, varargin)
% Run the physiotool functions from SPM8 batch system
% varargout = run_phases_and_cycles(cmd, varargin)
% where cmd is one of
% 'run' - out = run_phases_and_cycles('run', job)
% Run a job, and return its output argument
% 'vout' - dep = ru... |
github | philippboehmsturm/antx-master | run_est_apply.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/physiotools/run_est_apply.m | 5,573 | utf_8 | 12e58502fd85bc798bfe0f7195391a9a | function varargout = run_est_apply(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = run_est_apply(cmd, varargin)
% where cmd is one of
% 'run' - out = run_est_apply('run', job)
% Run a job, and return its output argument
% 'vout' ... |
github | philippboehmsturm/antx-master | tbx_run_fbi_dicom.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FBIDicom/tbx_run_fbi_dicom.m | 4,924 | utf_8 | 07da3d668a76b3d2908774b7c8e5f7ae | function out = tbx_run_fbi_dicom(job)
% SPM job execution function
% takes a harvested job data structure and call SPM functions to perform
% computations on the data.
% Input:
% job - harvested job data structure (see matlabbatch help)
% Output:
% out - computation results, usually a struct variable.
% tbx_run_... |
github | philippboehmsturm/antx-master | spm_dicom_query.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FBIDicom/spm_dicom_query.m | 19,806 | utf_8 | 73257342ab7e797a1d6d9fdb52a49fb1 | function spm_dicom_query
f=findobj(0,'tag',mfilename);
if ishandle(f)
clf(f,'reset');
set(f,'units','normalized','tag',mfilename, 'position',[.1 .25 .8 .5]);
else
f=figure('units','normalized','tag',mfilename, 'position',[.1 .25 ...
.8 .7], 'name',[spm('ver') ': DICOM query'], ...
'numberti... |
github | philippboehmsturm/antx-master | tbx_run_fbi_ima.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FBIDicom/tbx_run_fbi_ima.m | 8,880 | UNKNOWN | 6885a91a97bcd2487e1df40d70e9e9dc | function out = tbx_run_fbi_ima(cmd, job)
%
% (c) Sebastian Thees 17.2.2001, email: s_thees@yahoo.com
%
% Dept. of Neurologie, Charite, Berlin, Germany
%
switch lower(cmd)
case 'run'
params.file = detImaParams(job.imaFileList{1});
order = genSliceOrder( params.file.nSlices, job.i... |
github | philippboehmsturm/antx-master | tbx_cfg_fbi_dicom_dti.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FBIDicom/tbx_cfg_fbi_dicom_dti.m | 4,637 | utf_8 | 175dcc76897ab728ac7945dc7dff3290 | function dicom = tbx_cfg_fbi_dicom_dti
% SPM Configuration file
% automatically generated by the MATLABBATCH utility function GENCODE
% Modified version for FBIDicom conversion for DTI data - needs to be
% kept in sync with tbx_cfg_fbi_dicom.m
%_______________________________________________________________________
% C... |
github | philippboehmsturm/antx-master | tbx_cfg_fbi_dicom.m | .m | antx-master/freiburgLight/matlab/spm8/toolbox/FBIDicom/tbx_cfg_fbi_dicom.m | 10,299 | utf_8 | 3cd48e1bd7669f5b1d12bfa4e8a3ff53 | function dicom = tbx_cfg_fbi_dicom
% SPM Configuration file
% automatically generated by the MATLABBATCH utility function GENCODE
% Modified version for FBIDicom conversion - needs to be kept in sync
% with spm_cfg_dicom.m
%_______________________________________________________________________
% Copyright (C) 2008 Fre... |
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