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Walkthrough: How to use FsFast and fcseed-sess for functional connectivity analysis including example commands.

For general tips on using FsFast, download this FS-FAST powerpoint

This walkthrough is based on

*STEP 1: Unpack Data into the FSFAST Hierarchy using unpacksdcmdir

Ex: unpacksdcmdir -src dicomdir/subject/ALLDICOMS -targ fcMRI_dir/subject -cfg subject_config.txt -fsfast -unpackerr

In this example command...

• Have all fMRI dicoms linked into "ALLDICOMS" directory
• Arguement for "-targ" specifies output directory
• subject_config.txt is a configuration text file you create (format below)
• Use "-fsfast" to generate fsfast hierarchy

subject_config.txt format:

28 bold nii f.nii 29 bold nii f.nii

Col.1: scan acquisition number Col.2: output dir name will be created within "fcMRI_dir/subject" Col.3: output file format - this example is nifti format Col.4: output filename. In this example, 2 files will be created:

• fcMRI_dir/subject/028/f.nii fcMRI_dir/subject/029/f.nii

1.QA Check after unpacking:

• A - Check unpacked data (time points, # of slices ..etc)
• B - Check FSFAST hierarchy in session folder

*STEP 2: Reconstruction Anatomical data using recon-all

Ex:

setenv SUBJECTS_DIR /path/to/recon_dir/ recon-all -s subject_dirname -all -i pathtoT1dicom_scan1.dcm -i pathtoT1dicom_scan2.dcm

In this example command...

• set your SUBJECTS_DIR variable to your FreeSurfer subject recon directory

• set the subject's directory name with "-s" ... the arguement you provide will become the directory name within $SUBJECTS_DIR
• use "-i" to supply the dicoms to reconstruct. Use one "-i" per T1 acquisition.

2.QA Check:

• A - Check talairach transformation

• B - Check skull strip, white matter & pial surface

• C - Re-run "recon-all" if edits are made
• D - Check hierarchy of reconstructed anatomical data

1.Make FSFAST basic hierarchy (only if data are not unpacked in FSFAST hierarchy)

2.Link to FreeSurfer anatomical analysis

A - Make subjectname’ file in the session directory to link a subject's functional & structural data

3.Create a sessid file (text file with list of your sessions)in your Study DIR.

4.Create a Stimulus Schedule (Paradigm file) in bold folder (A "paradigm" file is a record of which stimulus was presented when & for how long.

Each paradigm file has four columns:

• A - Stimulus onset time (sec)
• B - Condition ID code (0, 1, 2, ...)
• C - Stimulus Duration (sec)
• D - Stimulus Weight (usually 1)

*STEP 3: Pre-process your bold data using preproc-sess preproc-sess

# Preprocessing of fMRI Data

preproc-sess -s <subjid> -fwhm <#>

1.By default this will do motion correction, smoothing & brain masking

2.Quality Check (plot-twf-sess) 3.Examine additions to FSFAST hierarchy (in each run of bold dir):

• f.nii (Raw fMRI data)
• fmc.nii (Motion corrected-MC)

  fmcsm5.nii (MC & smoothed)

• fmc.mcdat (Text file with the MC parameters (AFNI))
• brain.mgz (Binary mask of the brain)

# Function-Structure Registration View unregistered:

• tkregister-sess -s <subjid> -regheader)

Run automatic registration:

• spmregister-sess -s <subjid>

Check automatic registration:

• tkregister-sess -s <subjid>

A - Make edits if needed using scale as the last resort Check talairach registration:

• tkregister2 --s <subjid> --fstal --surf

*STEP 4: Use fcseed-sess to generate time-course information for your chosen seed region (as well as nuisance variable signal).

*STEP 5: Use mkanalysis-sess to setup an analysis for your FC data

*STEP 6: Use selxavg3-sess to run the subject-level analysis

*STEP 7: Use mri_glmfit or selxavg3-sess to run a group-level analysis