Introduction: This manual page is for SAMsrc Version 3, only. The changes made to SAM are intended to simplify the work-flow for batch processing — minimizing the user interactions by 1) eliminating copying of required files derived from the MRI and 2) writing image results to a common named directory. Version 3 analysis programs no longer compute statistical tests for single and multiple comparisons. They compute functions of moment, power, and entropy, mutual information, and excess kurtosis. All statistical tests have been relegated to AFNI. This provides uniformity and traceability of statistical testing. New in version 3 is output of 3d and 3d+time NIFTI image files instead of .svl files. NIFTI files are compatible with AFNI tools.
Conventions: All MRIs and their derivative files should be organized under a single MRI directory with subdirectories for each subject. The subdirectories are named by a character string corresponding to the leading characters in the MEG dataset name. The default is an 8-character string for NIMH users, where the subject or patient is identified by an 8-letter hash-code. However, the length of the string can be designated by the PrefixLength keyword. For a given study, the datasets should also be placed in a master directory. This way only one copy of the parameter file is required for all datasets undergoing a given analysis. In addition, the output image files for a given analysis should be directed to a common directory (designated by the ImageDirectory keyword). Maintaining this convention is essential for group studies in which SAM images are computed in the common Talairach space.
The AFNI programs http://afni.nimh.nih.gov are recommended for all statistical analyses, and are required for performing the Talairach transform in SAMwts.
Manual Pages:
This source code, as delivered, is configured to make executables that are compatible with VSM/CTF datasets. Read this link: 4D/BTi to compile and use this software for 4D/BTi datasets.