Fastmap directories

A “fastmap” directory contains a file named “fastmap” that provides all the necessary arguments to start the program. For instance, the fastmap file may contain one line like this:

     fastmap -t timeModel.dat -a $macaque/template.nii -A $macaque/atlas.nii -o $macaque/overlay-list.dat 

Generally, such a directory will also contain a time series analysis control file named “timeModel.dat” and a series of output files showing a voxel-wise analysis. For such a directory, one can simply navigate to the directory and invoke fastmap with no arguments (e.g., “fm &”) to bring up the full analysis. To read the argument from the “fastmap” file and add additional arguments, use the “-f” option (e.g., “fm -f --map -q”). Under the “time models” menu in fastmap, one can find a list of recent directories, separated by time model types, that can be selected to review recent analyses without exiting the program.

Once a time model has been defined, the two main ways to modify an analysis are two

  • open the analysis with fastmap, make changes in the GUI, run the analysis, and save to a new fastmap directory, or
  • clone the directory from the operating system, modify the files (e.g., timeModel.dat) with a text editor, and re-run the analysis on the new directory.
Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard