* What is the difference between the Project Directory and a Session?
In FSFAST the Project directory is were you run all of the FSFAST commands from. A session is the folder where all the data from a given visit of a given subject are stored. All the sessions will be located in the Project directory.
* What gets stored in a Run directory?
When you first set up the data for FSFAST processing, the raw data (eg, f.nii.gz) get stored in the Run directory as well as the paradigm files (ie, stimulus timing). The output of pre-processing will also be stored in the Run directory. The Run directory is always a 3-digit, zero-padded number (eg, 003). The directory structure is set up as: Project/Session/FSD/Run, eg, WorkingMem/scz01/bold/003.
* True or False: the subjectname file goes in the FSD?
False. The subjectname file goes in the Session folder. The FSD is the Functional SubDirectory and is where the functional data runs are found.
* What does the first column of the paradigm file tell you?
The first column tells you the onset of the stimulus. The paradigm file indicates the stimulus schedule (ie, which stimulus was presented when).
* How is the functional FreeSurfer analysis linked to the antomical FreeSurfer analysis?
The link between the functional and anatomical data is supplied through the subjectname file that is stored in the functional Session. This is a text file with the name of the 'subject' of the matchin FreeSurfer anatomical analysis (ie, when you ran 'recon-all -all -i input.dicom -subject subjectid').
* Why is a directory structure useful?
Directory structures allow for automated data analysis because each stage in a processing stream knows where to get its input data and where to put its output data so that the next stage can be run.