Quick start

  1. Create a separate directory to hold the contents of the REM analysis. This isn't a requirement, but you will find that REM analyses can create a lot of files. Also, you may want to have several separate REM analyses, with each grouped in its own directory.

  1. This REM analysis requires one top level "control file" that specifies various options and also lists the runs (data files) to be analyzed by REM. Refer to the sidebar for an example.

  1. The degrees of freedom, and the sliding scale between a random-effects analysis and a mixed-effects analysis with degrees of freedom biased toward the fixed-effects case (but a properly determined mean effect size and variance) is determined by amount of smoothing performed on the ratio of random to fixed-effects variances. The “smoothing” keyword specifies 1) the effective resolution at the first level, including voxel size and smoothing operations, and 2) the factor by which to smooth the ratio of random to fixed effects variances to boost the degrees of freedom.  The program will output the effective degrees of freedom. If the smoothing factor is 0, the result is a random-effects analysis. If the smoothing factor is very large, the result will mimic a fixed-effects analysis.

  1. Run the mixed-effects analysis, generally using a single argument to convert absolute signal changes to % changes:

rem rem.dat

     where “rem.dat" is the name of the control file in this case.

  1. Display the time series and all maps using jip-display (a.k.a, xd):

"xd -t rem.dat &"  or  "xd &”   (see below)

  1. When “ rem" was executed in step 4, it created a hidden file named ".display" with default contents "xd -t glm.dat". If no arguments are given to "xd", and if this file exists on the current directory, then the arguments within the file will be used. This is why one can type simply "xd" in step 5. Consider modifying file ".display" using an editor to include whatever arguments are useful. Then, when you revisit this directory many months later, you can simply type "xd" to bring up the analysis. Example:

xd -t glm.dat -e /space/1/me/template/anatomy.nii -o /space/1/me/template/overlay-list.dat

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard