SPM

https://www.fil.ion.ucl.ac.uk/spm/
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SPM (Statistical Parametric Mapping) is an open-source software package for analyzing neuroimaging...
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### Navigate to SPM Example Data Directory

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/dcm/dcm_ir

Change the current directory to where the example MEG data is stored. This is a prerequisite for loading the dataset.

```bash
cd cdbespm12_SPM_CTF_MEG_example_faces1_3D.mat
cdbespm12_SPM_CTF_MEG_example_faces1_3D.dat
```

--------------------------------

### Install MATLAB Runtime via Command Line

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone

Perform a non-GUI installation of the MATLAB Runtime on Linux or macOS.

```bash
chmod 755 runtime_installer/Runtime_R2024b_for_spm_standalone_24.11.install
runtime_installer/Runtime_R2024b_for_spm_standalone_24.11.install -agreeToLicense yes
```

--------------------------------

### Execute SPM via Command Line

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone

Start the SPM application by providing the path to the MATLAB Runtime installation.

```bash
./run_spmxx.sh /usr/local/MATLAB/MATLAB_Runtime/<matlab_version>/
```

--------------------------------

### Install MSYS2 development tools

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/windows

Use pacman to update the system and install the necessary MinGW-w64 toolchain.

```bash
pacman -Syu
pacman -Su  
pacman -S --needed base-devel mingw-w64-x86_64-toolchain
```

--------------------------------

### MATLAB Test Class Setup

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/testing

Example of using TestClassSetup to configure SPM defaults before all tests in a class run. This is useful for shared test initialization.

```matlab
methods (TestClassSetup)
    function setupSPM(testCase)
        spm('defaults','fmri');
        spm_jobman('initcfg');
        spm_get_defaults('cmdline',true);
    end
end

```

--------------------------------

### Install SPM12 Desktop Entry and Icon on Linux

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone

Use xdg-utils to install the created .desktop file and SPM icon for a faster launch and menu integration.

```bash
xdg-desktop-menu install --novendor spm12.desktop
xdg-icon-resource install --novendor --size 32 spm.png
```

--------------------------------

### Setup workspace directories

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/MEEG/meeg_firstlevel

Initializes the analysis and data paths for the SPM project.

```matlab
clear;
cwd      = pwd;
workpath = fullfile(cwd, 'analysis');
datapath = fullfile(cwd, 'data');
spm_mkdir(workpath);
```

--------------------------------

### Start Octave

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/windows

Launch the Octave GUI from the MSYS2 environment.

```bash
/mingw64/bin/octave --gui
```

--------------------------------

### Install Octave for MSYS2

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/windows

Install the Octave package via pacman.

```bash
pacman -S mingw64/mingw-w64-x86_64-octave
```

--------------------------------

### Install build-essential Package

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/linux

If you encounter 'cannot find -lstdc++' or 'math.h' errors, install the 'build-essential' package on Debian/Ubuntu systems.

```bash
sudo apt install build-essential
```

--------------------------------

### Load and Run Phantom Example Batch Script

Source: https://www.fil.ion.ucl.ac.uk/spm/data/fieldmap/PhantomExample_readme.txt

Execute the example batch script for the FieldMap toolbox at the Matlab command line. Ensure the 'pm_defaults_PhantomExample.m' file is correctly configured.

```matlab
PhantomExample_fieldmap_batch.m
```

--------------------------------

### Install libXp on Linux (yum)

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone

Use yum to install the libXp package on your Linux distribution to resolve 'libXp.so.6' errors.

```bash
yum install libXp.x86_64
```

--------------------------------

### Load Batch for Phantom Example

Source: https://www.fil.ion.ucl.ac.uk/spm/data/fieldmap/PhantomExample_readme.txt

Load a pre-saved batch configuration for the Phantom Example in SPM. This allows for easy execution of the FieldMap processing pipeline.

```matlab
Batch->Load Batch to load PhantomExample_fieldmap_batch.mat and select run
```

--------------------------------

### Install libstdc++5 Package

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/linux

For older systems or specific 'lstdc++' issues, try installing the 'libstdc++5' package. Replace '5' with your system's version if necessary.

```bash
sudo apt-get install libstdc++5
```

--------------------------------

### Compile libXp manually on Linux (Ubuntu/Debian)

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone

Manually compile and install libXp if the package is not found on Ubuntu or Debian. This may require installing additional development packages.

```bash
git clone [git://anongit.freedesktop.org/xorg/lib/libXp](git://anongit.freedesktop.org/xorg/lib/libXp)
cd libXp
./autogen.sh
./configure
make
sudo make install
```

--------------------------------

### Example Public Key Content

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/ssh_authentication

The expected format of the public key string to be pasted into GitHub.

```text
ssh-ed25519 AAAAC5NzaC1lZDI1NTE4AAAANI/iaJJ7eHWs+i2hxxQTX+xcalwd+QlhDSwgIkh3cvEc *your_email_here*
```

--------------------------------

### Test SPM Installation

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/beginners/installing_spm

Run this command in the MATLAB command window after restarting MATLAB to verify that SPM has been installed correctly. A successful execution will launch the SPM GUI for fMRI analysis.

```matlab
spm fmri
```

--------------------------------

### Query SPM version and release

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/versioning

Retrieve the version and release strings from the SPM installation.

```matlab
[v, r] = spm('ver')
```

```matlab
spm('version')
```

--------------------------------

### Display Condition Labels

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/dcm/dcm_ir

Example output showing the mapping of indices to condition labels.

```text
    ans = 

        'faces'    'scrambled'
```

--------------------------------

### Configure MATLAB compilation environment

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/windows

Set the MinGW location and run the MEX setup command within MATLAB.

```matlab
setenv('MW_MINGW64_LOC', 'C:\msys64\mingw64')
mex -setup
% MEX configured to use 'MinGW64 Compiler (C)' for C language compilation.
```

--------------------------------

### FieldMap Defaults Configuration

Source: https://www.fil.ion.ucl.ac.uk/spm/data/fieldmap/SubjectExample_readme.txt

Configuration file containing parameters specifically set for the Subject Example data.

```MATLAB
pm_defaults_SubjectExample.m
```

--------------------------------

### Get Help for MATLAB Command

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/courses/fmri_vbm/maths/linear_algebra

Displays the help documentation for a specified MATLAB command or function, such as 'plot'.

```matlab
help plot
```

--------------------------------

### Octave Script for SPM12 Download, Configuration, and Installation

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/octave

This Octave script automates the download, patching, compilation of MEX files, and installation of SPM12. It also adds SPM12 to the function search path and starts SPM.

```octave
%% Store current working directory
cwd = pwd;
%% Download SPM12 r7771
unzip ("https://github.com/spm/spm12/archive/r7771.zip", cwd);
%% Patch SPM12
urlwrite ("https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch", "spm12_r7771.patch");
system ("patch -p3 -d spm12-r7771 < spm12_r7771.patch");
%% Compile MEX files
cd (fullfile (cwd, "spm12-r7771", "src"));
system ("make PLATFORM=octave");
system ("make PLATFORM=octave install");
%% Add SPM12 to the function search path
addpath (fullfile (cwd, "spm12-r7771"));
cd (cwd);
%% Start SPM12
spm
```

--------------------------------

### Format Commit Messages

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/git

Example of the required commit message structure, starting with a prefix and including a detailed body.

```text
Enhancement: replace this with that in such and such

Longer description that might contain bullet points:
* item 1
* item 2
```

--------------------------------

### View SSH Key Generation Output

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/ssh_authentication

Example output showing the successful creation of the public and private key files.

```text
Generating public/private ed25519 key pair.
Enter file in which to save the key (/home/*your_user*/.ssh/id_ed25519): 
Enter passphrase (empty for no passphrase): 
Enter same passphrase again: 
Your identification has been saved in /home/*your_user*/.ssh/id_ed25519
Your public key has been saved in /home/*your_user*/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:T3kB6rMhciPlSqcHp3SDmmoFu+ZDqs7IxFVcuj4JNeY *your_email*
The key's randomart image is:
+--[ED25519 256]--+
|       .  .      |
|    . o  . .     |
|   . S  .   .    |
| .. * o.   . .   |
|  o* E. D o .    |
|..=oB.+. * .     |
| +=*.X  . .      |
|**. *.o          |
|X= u.u           |
+----[SHA256]+-----
```

--------------------------------

### Get M/EEG Object Information

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/MEEG/multimodal/eeg

Retrieve specific information about the M/EEG object 'D' using its methods. For example, D.ntrials returns the number of trials, D.conditions lists condition labels, and D.reject shows rejected trials.

```matlab
D.ntrials

```

```matlab
D.conditions

```

```matlab
D.reject

```

```matlab
D.condlist

```

```matlab
D.chanlabels

```

```matlab
D.chantype

```

```matlab
D.size

```

```matlab
D.nchannels

```

```matlab
D.nsamples

```

```matlab
D.ntrials

```

--------------------------------

### Check and Install SPM12 Updates

Source: https://www.fil.ion.ucl.ac.uk/spm/software/spm12

Use the spm_update function to check for and install new SPM12 updates. The 'update' argument initiates the download and installation process.

```matlab
>> spm_update
         A new version of SPM is available.
```

```matlab
>> spm_update update
         Download and install in progress...
         Success: xx files have been updated.
```

--------------------------------

### Initialize SPM and Load Data

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/opm/neuro1_aef

Add the SPM path, initialize the environment, and create the SPM OPM object from BIDS-formatted files.

```matlab
% Run spm (change path as appropriate)
addpath('D:\GitHub\spm')
spm eeg

% Reference the meg and peripheral files
S = [];
S.category = 'meg';
S.description = 'meg';
S.type = '.lvm';
S.derivative = 0;
S.BIDS = BIDS;
meg_dir = spm_BIDS_file(S);

S.description = 'positions';
S.type = '.tsv';
pos_dir = spm_BIDS_file(S);

S.description = 'channels';
chan_dir = spm_BIDS_file(S);

S.category = 'anat';
S.description = 'mri';
S.type = '.nii';
S.detailed = 0;
anat_dir = spm_BIDS_file(S);

% Load the raw data
S = [];
S.data = meg_dir.file;
S.sMRI = anat_dir.file;
S.channels = chan_dir.file;
S.positions = pos_dir.file;
S.lead = 0; % We will calculate leadfields later
S.fs = 375;
D = spm_opm_create(S)
```

--------------------------------

### Automate File Selection in MATLAB Script

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/MEEG/multi/preprocessing

Example of using fullfile and sprintf to dynamically define input paths for multiple runs.

```matlab
inputs{1, crun} = cellstr(fullfile(rawpth,'Sub15','MEEG',sprintf('run_%02d_sss.fif',crun)));
     inputs{2, crun} = cellstr(fullfile(rawpth,'Sub15','MEEG','Trials',sprintf('run_%02d_trldef.mat',crun)));
     inputs{3, crun} = cellstr(fullfile(rawpth,'Sub15','MEEG','bad_channels.mat'));
```

--------------------------------

### Create Statistics Directory

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/MEEG/multimodal

Initial step to prepare a workspace for statistical output files.

```bash
mkdir XYTstats
```

--------------------------------

### Perform Initial CTF Unpacking

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone

Execute the application with the 'quit' argument to unpack the CTF file, typically required when installing system-wide.

```bash
./run_spmxx.sh /usr/local/MATLAB/MATLAB_Runtime/<matlab_version>/ quit
```

--------------------------------

### Compile SPM MEX Files

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/development/compilation/linux

Run these commands in the 'src' folder of your SPM installation to compile MEX files. Ensure you have a C/C++ compiler and 'make' installed.

```bash
make distclean
make && make install
make external-distclean
make external && make external-install
```

--------------------------------

### Start SPM in MATLAB

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/beginners/vbm/displaying_images

Launch SPM from the MATLAB command line. Use 'spm' for the default interface or 'spm pet' for a PET-specific interface.

```matlab
spm
```

```matlab
spm pet
```

--------------------------------

### Run SPM Docker Container with GUI

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/containers

Use this command to start the SPM Docker container with graphical user interface support. Ensure X11 forwarding is correctly set up.

```bash
xhost +local:docker
docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp:/tmp -v /tmp/.X11-unix:/tmp/.X11-unix ghcr.io/spm/spm-docker:docker-matlab-latest fmri
```

--------------------------------

### Install SPM12 Updates on Unix Systems

Source: https://www.fil.ion.ucl.ac.uk/spm/software/spm12

Command line instructions for installing SPM12 updates on Unix-based systems (Linux, macOS) using unzip. Ensure newer files overwrite existing ones.

```bash
unzip spm12.zip
unzip -o spm12_updates_rxxxx.zip -d spm12
```

--------------------------------

### Troubleshoot SPM Startup Crash

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/installation/matlab

Example error output from a segmentation fault and the command to disable the HTML browser to fix it.

```text
BadWindow (invalid Window parameter)
serial 20133 error_code 3 request_code 20 minor_code 0
Pango-CRITICAL **: pango_font_description_from_string: assertion 'str != NULL' failed
GLib-CRITICAL **: g_once_init_leave: assertion 'result != 0' failed
GLib-GObject-CRITICAL **: g_type_register_dynamic: assertion 'parent_type > 0' failed
```

```matlab
setenv('SPM_HTML_BROWSER','0')
```

--------------------------------

### GET /events

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/reference/MEEG/eeg_preprocessing

Retrieves event information stored with trials.

```APIDOC
## GET /events

### Description
Returns a structure array of events associated with trials.

### Response
#### Success Response (200)
- **type** (string) - Event type
- **value** (number/string) - Event value
- **time** (number) - Time in seconds
- **duration** (number) - Optional duration in seconds
```

--------------------------------

### Function Usage and Plotting

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/beginners/control_flow

Example of calling a built-in function and plotting the results.

```MATLAB
x = 0:0.01:2*pi;
y = sin(x);
plot(x,y)
figure(gcf)
```

--------------------------------

### Set up DCM Analysis

Source: https://www.fil.ion.ucl.ac.uk/spm/download/data/attention/README_GLM_DCM.txt

Initiates the Dynamic Causal Modelling (DCM) analysis setup. Requires specifying the SPM.mat file, VOIs, and connections.

```matlab
Press DCM
Specify or review [specify]
Select the SPM.mat file you created in README_GLM
Name for DCM_???.mat [VisFroPar]
Select all VOIs in order VOI_V1_1, VOI_V5_1, VOI_PPC_1, VOI_PFC_1
Include Photic [Yes]
Incluse Motion [Yes]
Include Attention [Yes]
Make the following intrinsic connections 
   V1 to V5, V5 to V1, V5 to PPC, PPC to V5, PPC to PFC and PFC to PPC
   ie. a hierarchy with bidirectional connections
Just connect Photic to V2
Connect Motion to modulate the bottom-up connection from V1 to V5
Connect Attention to modulate the top-down connections from PFC to PPC and from PFC to PPC.
```

--------------------------------

### Make SPM Path Permanent (Local Installation)

Source: https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/beginners/installing_spm

This code snippet creates or appends to the MATLAB startup.m file to permanently add the SPM directory to the path. Ensure you replace 'yourusername' with your actual username and adjust the path if SPM was installed elsewhere. Note the double backslashes required in the fprintf function.

```matlab
fid = fopen('C:\Users\yourusername\Documents\MATLAB\startup.m','w');
fprintf(fid, 'addpath(''C:\Users\yourusername\Documents\MATLAB'');');
fclose(fid);
```
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