• FsFastTutorialV4.5
• 500_Make_a_directory_for_your_study

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Before proceeding to analyze the subject data for any particular study, you must create a working directory for the study analyses. This is called the Study Directory and can be thought of as a scratch space where various files are written when the processing commands are run. Your Study Directory can contain any number of the Session Directories, and all the programs are run from here, regardless of which Session is being processed. For this reason, and to avoid confusion, the Study Directory should be separate from the SESSION PARENT directory and from the Anatomical Database where you unpacked the reconstructed data set. To make a Study Directory, cd to another location--an appropriate directory that is separate from the SESSION PARENT directory--and type:

• mkdir MYSTUDY (this will be referred to as your 'Study Directory') cd MYSTUDY/

Next, you would specify which subjects you want to process in your study. In this tutorial, you will only process Bert, but the standard stream processes all the subjects in your study. You have to specify the list of each of your study subjects Session Directories in order for them to be processed.

Each subject's Session directory should be thought of as consisting of two parts:

• a) the session parent and

  b) the session identifier.

The session parent is the path to the subjects' Session directories (which should end with the name of your SESSION PARENT), and the session identifier corresponds to the subject name that you used to name a particular subject's Session, e.g.:

In Bert's Session Directory: /space/someday/users/brainmapper/bert

the session parent is: /space/someday/users/brainmapper/

and the session identifier is: bert

Bert's session parent must be entered into a textfile (sesspar). Bert's session identifier must be entered into another text file (sessid).

Doing an 'ls' to see what's in your Study Directory, then, should show this:

sessid sesspar

Your sesspar text file would contain this text:

/space/someday/users/brainmapper

Your sessid text file would contain this text:

bert

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