著者別アーカイブ： kiyotaka

Below is an excerpt from SPM-ML

(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;72ea5d13.1109)

There is an option for the newest SPM8 releases (>=4010), which enables non-stationarity
correction on the cluster level. Please set in spm_defaults.m:
defaults.stats.rft.nonstat = 1;

However, this option will result in a much longer calculation if you print the results table.
This is maybe also the reason that this option is not set as default.

SPM-MLに勉強になる話題が流れていたので、共有します。

出典はこちら。
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;a65dd354.1307

コントロールAと疾患B、疾患Cという3群がある時、Design Matrixに全部を入れてしまった方がいいのか、
もしくは、コントロールと疾患A、コントロールと疾患Bというように、別々にDesign Matrixを作った方がいいのかという質問です。

これに対し、Cyril Pernetが非常にわかりやすいたとえを使って説明をしています。
ただ、少しだけtypoがあったのでそこを補足して説明します。

続きを読む →

2013年9月に、包括脳MRIチュートリアルで、「VBMの観点からのSPMの理解」なる話をさせていただきました。
VBMに限らず、SPMで用いられる一般線形モデル（GLM）の基本をまとめてみました。
SPMユーザには多少はお役に立てる内容かと思いますので、講義の配布資料を公開させていただきます。

VBMの観点からのSPMの理解の配布資料をダウンロード

I used to write an article, “Run SPM2, SPM5, and SPM8 concurrently.” Though this is a smart way to run different version of SPM, we need to prepare scripts separately. So I came up with another script, called “SPM switcher”. This script brings up a dialog and you can select the version of SPM you want to run.

• Make a directory where you want to save scripts. (e.g. C:\Users\foo\Documents\MATLAB\)
• Add the directory to the path in Matlab. (File -> Set Path -> Add path)
• put spm_rmpath.m in SPM2 and SPM99 directory.

You find this file in SPM5 or SPM8 directory. You can just copy it from SPM5/8 to SPM2/99 directory.

• save switchspm.m in the directory you prepared.
• edit switchspm.m and change “spm_path=’C:\spm\'” according to your circumstance.

Typing switchspm in Matlab command window will bring up a dialog below and you can run different version of SPM easily.

Download switchspm.m (Right click –> Save as)

%switchspm: Run different version of SPM
%This tiny script prompts the dialog which SPM version you want to run.
%Prerequisites
%1. Each version of SPM is supporsed to be located under spm_path.
%2. Please copy spm_rmpath.m from SPM5 or later and put it into SPM99 and
%   SPM2 direcotry. Otherwise, Path removal won't work correctly.
%3. Please change the SPM path according to your environment

%%%Please change the path below according to your environment%%%
spm_path='C:\spm\';
%%%

%The path for each version of SPM
spm99_path=fullfile(spm_path,'spm99');
spm2_path=fullfile(spm_path,'spm2');
spm5_path=fullfile(spm_path,'spm5');
spm8_path=fullfile(spm_path,'spm8');
spm12_path=fullfile(spm_path,'spm12');

str = ['spm99 '; 'spm2  '; 'spm5  '; 'spm8  '; 'spm12'];
spmver = listdlg('PromptString','SPM ver you want to run...',...
                'SelectionMode','single',...
                'ListString',str);

switch spmver
    case 1, %spm99
    % remove spm path
    while true
      try
        spm_rmpath
        catch break;
      end;
    end;
    % add spm99 path
    addpath(spm99_path);
    % run spm99
    spm;
        
    case 2, %spm2
    % remove spm path
    while true
      try
        spm_rmpath
        catch break;
      end;
    end;
    % add spm2 path
    addpath(spm2_path);
    % run spm2
    spm;

    case 3, %spm5
    % remove spm path
    while true
      try
        spm_rmpath
        catch break;
      end;
    end;
    % add spm5 path
    addpath(spm5_path);
    % run spm5
    spm;
        
    case 4 %spm8
    % remove spm path
    while true
      try
        spm_rmpath;
        catch break;
      end;
    end;
    % add spm8 path
    addpath(spm8_path);
    % run spm8
    spm;

    case 5 %spm12
    % remove spm path
    while true
      try
        spm_rmpath;
        catch break;
      end;
    end;
    % add spm12 path
    addpath(spm12_path);
    % run spm12
    spm;
end