• FsFastTutorialV6.0
• StudyAnswers

These are answers to the 'Study Questions' found in the FSFAST Tutorial.

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 matching 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.

What would the preproc-sess command be to analyze session sess02?

It would be the same as for sess01 but use '-s sess02' instead of '-s sess01':

preproc-sess -s sess02 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run 

What would the preproc-sess command be to smooth by 7mm FWHM?

It would be the same as for a FWHM of 5mm but use '-fwhm 7' instead of '-fwhm 5':

preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 7 -per-run 

What would the preproc-sess command be to analyze data in a functional subdirectory (FSD) called 'rest'?

It would be the same as for a for analyzing data in the 'bold' FSD except use '-fsd rest' instead of '-fsd bold':

preproc-sess -s sess01 -fsd rest -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run 

What would the preproc-sess command be if you did not want to use slice-timing correction?

In this case you would exclude the '-stc' option to preproc-sess:

preproc-sess -s sess01 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 5 -per-run 

Configure a contrast for Probe following Emotional Distractor vs Probe following Neutral Distractor.

Condition 4 is Probe following Emotional Distractor, and condition 5 is Probe following Neutral Distractor.

mkcontrast-sess -analysis my-workmem.sm05.lh -contrast distractor.avg-v-base -a 4 -c 5

How would you configure an analysis with a paradigm file called wmfir.par?

The analysis is configured with mkanalysis-sess. It would be run in the same way as in the tutorial except that the paradigm file would be 'wmfir.par' instead of 'workmem.par':

mkanalysis-sess \
  -fsd bold -stc up  -surface fsaverage lh -fwhm 5  \
  -event-related  -paradigm wmfir.par -nconditions 5 \
  -spmhrf 0 -TR 2 -refeventdur 16 -nskip 4 -polyfit 2 \
  -analysis my-workmem.sm05.lh

How many times will you need to run mkanalysis-sess?

For a given set of parameters, you will need to run mkanalysis-sess three times, once for each space (lh, rh, and mni305). You do NOT need to run it for each session. mkanalysis-sess only collects the parameters needed to run an anlysis. It does not run the analysis itself.

How many times will you need to run selxavg3-sess?

For a given set of parameters, you will need to run selxavg3-sess three times for each session, once for each space (lh, rh, and mni305).