[wiki:FreeSurferWiki top] | [wiki:Tutorials previous]

This tutorial steps you through the analysis of an fMRI data set with the FreeSurfer Functional Analysis Stream (FSFAST), from organizing the data to group analysis.

TableOfContents

Tutorial Data Description

The data being analyzed is part of the fBIRN Phase I data set. There are 5 subjects, each scanned twice at each of 10 sites. The data in the tutorial is the data collected at MGH. The task is a simple sensory motor blocked design experiment. During each task block the subject was shown a flashing checkerboard and presented with an auditory tone. During this time, the subject was asked to press bottons with both hands. The task blocks alternated with fixation blocks during which the subject stared at a fixation cross but performed no other task. Each block type was 15 sec long. Each run started with a fixation block followed by 8 pairs of task and fixation blocks (and so ends with a fixation block) for a total run duration of 255 sec. The TR was 3 sec, so there were 85 time points. This task was performed 4 times in each visit.Anatomicals were also collected and analyzed in FreeSurfer for each of these subjects.

Getting and Organizing the Tutorial

The tutorial requires about 10G of space. Find a location for this data, download or copy the tarfile from XXX. Untar it with:

tar xvfz fsfast-tutorial.tar.gz

This will create a directory called fsfast-tutorial. You can now delete the tar file. cd fsfast-tutorial. It will be assumed that you are in this directory (or subdirectory there of) throughout the tutorial. This directory will have five folders:

• fb1-raw - raw fMRI data
• fb1-raw-study - raw data origanized as an FSFAST study but unanalyzed
• fb1-preproc-study - The same data preprocessed.
• fb1-analysis-study - The same data analyzed

• subjects - FreeSurfer reconstruction of anatomical data (plus the fsaverage subject).

If you look (ls) in fb1-raw, you will see that there are 20 NIFTI data sets with names like f.mgh-10X.1-rYYY.nii. These are the 20 fMRI runs mentioned above. X indicates the subjects number (1, 3, 4, 5, 6), and YYY indicates the run number. The sensory-motor task happend to be runs 3, 5, 7, and 10.

Quick Visualization Tutorial (tkmedit/tksurfer)

The purpose of this tutorial is to familarize you with how to use FreeSurfer volume viewer (tkmedit) and surface viewer (tksurfer) in the context of viewing functional data.See the pages below for a more detailed handling of tkmedit and tksurfer.

tkmedit

• [wiki:TkMeditGuide_2fTkMeditGeneralUsage_2fTkMeditInterface Interface] BR

• [wiki:FsTutorial/TkmeditGeneralUsage General usage] BR

• [wiki:FsTutorial/TkmeditWorkingWithData Working with data] BR

• [wiki:FsTutorial/TkmeditReference Quick reference] BR

tksufer

• [wiki:TkSurferGuide_2fTkSurferGeneralUsage_2fTkSurferInterface Interface] BR

• [wiki:FsTutorial/TksurferGeneralUsage General usage] BR

• [wiki:FsTutorial/TksurferWorkingWithData Working with data] BR

• [wiki:FsTutorial/TksurferReference Quick reference] BR

Volume viewing functional overlay data

cd into the study with all the analyzed data:

cd fb1-analysis-study

Run tkmedit-sess (this is an FSFAST wrapper for tkmedit):

tkmedit-sess -s mgh-101.v1 -a sm-gamma-fwhm5 -c 1v0 -aparc+aseg

Don't worry about what all the arguments mean, this part is only about visualization.This command will bring up two windows, one with a brain image the other a control panel.

Assembling the Data in the FSFAST Hiearchy

The Project (or Study) Directory

Create a Session

Create a Stimulus Schedule (Paradigm File)

Link to the FreeSurfer Anatomical Recontruction

Create a SessionID File

Preprocessing of fMRI Data (preproc-sess)

What preprocessing stages do you want to run?

Run preprocessing

Examine additions to hiearchy

View motion correction plots

First-Level Analysis

Configure Analysis and Contrasts (mkanalysis-sess)

Analyze First Level (selxavg3-sess)

Visualize

Volume-based visualization (tkmedit-sess)

Surface-based visualization (tksurfer-sess)

Examine additions to the hierarchy

Function-Structure Registration

View unregistered (tkregister-sess)

Run automatic registration (fslregister-sess)

Check automatic registration (tkregister-sess)

Check talairach registration

Higher-Level (Group) Analysis

Assemble the Data (isxconcat-sess)

Volume-based (talairach/MNI305)

Quality Assurance

Group Analysis

Random and Fixed Effects

Cluster Analysis

Surface-based

FsFast Tutorial SlideShow

Navigation(slideshow)

• ["/000 Frontmatter"]
• ["/300 Download data"]
• ["/400 Get familiar with sessions format"]
• ["/500 Make a directory for your study"]
• ["/600 Make paradigm files for your experiment"]
• ["/700 Motion correct the data"]
• ["/800 Normalize signal intensity"]
• ["/900 Set up session-level analysis"]
• ["/905 Average session-level data by condition"]
• ["/910 Define an omnibus contrast"]
• ["/920 Compute statistical maps of the omnibus contrast"]
• ["/930 Run functional and structural registration"]
• ["/940 Visualization"]