iTT
iTT toolbox for SPM
iTT toolbox for SPM implements the itertive Two-Threshold (iTT) approach to determine height thresholds in SPM.
Reference: Auer T, Schweizer R, Frahm J. An iterative two-threshold analysis for single-subject functional MRI of the human brain. DOI: 10.1007/s00330-011-2184-5
This file contains information about Install Configuration Usage of the toolbox.
Copyright (C) 2011 Biomedizinische NMR Forschungs GmbH
Tibor Auer
System requirements
MATLAB (The MathWorks)
- MATLAB 7.6 or later is required.
- Curve Fitting Toolbox - required for Gaussian fitting.
- Optimization Toolbox - required for iterative optimization.
SPM
Note: You need write permission - during installation and running - in the 'spm' directory (SPMDIR) and in its subdirectories where other spm_getSPM.m files might be stored (e.g. SPMDIR\toolbox\vbm5).
Testing environment
Red Hat Enterprise Linux 6.8 64-bit, Ubuntu 11.04. 64-bit, Windows 7 64-bit MATLAB 7.10 (R2010a), MATLAB 8.6 (R2015b) SPM8 v4290, SPM12 v6906
Install
Simply copy the iTT folder into the SPMDIR\toolbox dircetory. spm_config_iTT.m will arrange everything during startup of SPM.
Note: Previous spm_getSPM.m files (e.g. in SPMDIR) will be renamed to spm_getSPM.m.org. restore_getSPM.m file will be created in the iTT folder to roll back these changes, using cmd_restore.m.
Configure
By default, the lower threshold is set to p=0.05, itertive optimization is employed (iTT) to determined the lower and upper cuts as well as the upper threshold, and results of the fitting will be displayed. Without the itertive optimization (TT) the central portion of the histogram determined by the 20% and 80% maximum height will be fitted and the upper threshold of p=0.0001 will be used. Launch iTT toolbox in the SPM's toolboxes to modify these settings. This Configuration Toolbox can be also used to disable automatic check for spm_get_SPM.m files during startup (not recommended), or to roll back changes during Install (see above). After accepting changes, they will have an immediate effect and changes will be also written into the configuration file (config.ini) to store them for the next session.
Use
After sucessfull install, iTT and TT can be used as easily as other approaches (FWE or FDR). During displaying Result, simlpy select iTT or TT when asked for "p-value adjustment". For TT, give probaility threshold for the lower threshold (default: 0.05).
Note: For calculation and application of the thresholds are performed in one step, iTT and TT may need more time than other approaches.
Uninstall
Note: Run cmd_restore.m file in to roll back renaming previous spm_getSPM.m files (e.g. in SPMDIR).
Simply remove the TT folder from the SPMDIR\toolbox directory.
Versions
- 1.2 - compatible with SPM12
- 1.1 - cell_index.m has been added
- 1.0 - Initial Release