dir-structure-description.txt

README
  describes how to customize your project. start by reading this

PROTOCOL
  initially empty. describe your data collection procedure here

scaffold
  a command that sets up the 'scaffolding' for analyzing a new subject's data

scripts
  holds scripts that support your across-subject analyses

group
  holds group-level analysis and results

group/analysis
  holds intermediary files made by your across-subject analyses, such as those
  produced by FSL

group/results
  holds the results of your across-subject analyses, such as plots and tables
  of statistical test results

design
 holds the intermediary files that are necessary for higher-level Feat analyses, 
 such as nuisance or stimulus regressors, or ROI coordinate information

fsf
 holds design files and templates needed to run Feat across subjects

subjects
  holds a directory for each of the subjects run in your experiment. see the
  description of the prototype directory for more details

prototype
  holds the 'scaffolding' information on which each subject's directory is based

prototype/copy
  holds files and directories that must exist in all subjects' directories, but
  that may differ between subjects. see subdirectory descriptions below for more
  details
    all files and directories under this one will will be copied into the new
  subject's directory. any text files in this directory that contain the text
  <<SUBJ_ID>> will have that replaced by the subject's ID before they are copied
  into the subject's directory

prototype/copy/data
  initially empty. provides a place for data to go when the subject is set up

prototype/copy/results
  initially empty. provides a place for plots and statistical results to go when
  the subject is set up
  
prototype/copy/design
 initially empty. provides a place for intermediary files, such as nuisance
 regressors or stimulus timecourse regressors
 
prototype/copy/fsf
 initially empty. provides a place for design files and templates needed to run
 Feat

prototype/copy/scripts
  initially empty. provides a home for scripts that may need to be tweaked for
  each subject. see the README

prototype/link
  holds files and directories that must exist in all subjects' directories, and
  that must be the same for all subjects, such as scripts that define your
  analysis at a high-level. all files under this directory will be linked in to
  the new subject's directory, which means that if they are changed in any
  subject's directory, the changes will simultaneously occur to those files in
  all other subject's directories

prototype/link/README
  describes how to customize the subject's directory. read this after setting
  up a new subject