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# Unpack Data into the FSFAST Hierarchy (unpackscmdir)

  1. QA Check after unpacking
    • A - Check unpacked data (time points, # of slices ..etc)

    • B - Check FSFAST hierarchy in session folder

# Reconstruction – Anatomical (recon-all –all)

  1. Set SUBJECTS_DIR
  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

# Assembling the Data into the FSFAST Hierarchy

  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)

# 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 (the raw data)

    • - fmc.nii (motion corrected-MC)

    • - fmcsm5.nii (MC & smoothed)

    • - fmc.mcdat - text file with the MC parameters (AFNI)

    • - mcextreg.bhdr - binary mask of the brain

# Function-Structure Registration

  1. View unregistered (tkregister-sess -s <subjid> -regheader)

tkregister-sess -s <subjid> -regheader
  1. Run automatic registration (spmregister-sess -s <subjid>)

spmregister-sess -s <subjid>
  1. Check automatic registration (tkregister-sess -s <subjid>)

tkregister-sess -s <subjid>


/!\ Edit conflict! Other version:


tkregister-sess -s <subjid> -regheader
spmregister-sess -s <subjid>
tkregister-sess -s <subjid>


/!\ Edit conflict! Your version:



/!\ End of edit conflict


  1. Check talairach registration (tkregister2 --s <subjid> --fstal --surf)

# First-Level (Group) Analysis (mkanalysis-sess –gui)

  1. Setting up models of the task-related components
  2. Setting up models of the nuisance components
  3. Defining contrasts
  4. Fitting the model
  5. Making inferences
  6. Input files: (*.par & fmcsm#)

# Analyze First Level (selxavg3-sess -s <subjid> -analysis <name>)

  1. Examine additions to the FSFAST hierarchy (~bold/analysis):
    • - beta.nii - regression coefficients

    • - rvar.nii - residual error variance

    • - mask.nii - mask (copy of bold/masks/brain.nii)

    • - meanfunc.nii - mean functional image

    • - fsnr.nii - functional SNR map

    • - X.mat - design matrix (in matlab format)

    • - dof - text file with degrees of freedom

    • - fwhm.dat - smoothness estimate (Full-Width/Half-Max)

    • - ~contrast folder/s:

      • - ces.nii - contrast effect size (contrast matrix * regression coef)

      • - cesvar.nii - variance of CES

      • - sig.nii - significance map (-log10(p))

  2. Visualization
    • A - Volume-based visualization (tkmedit-sess)

    • B - Surface-based visualization (tksurfer-sess)

# Higher-Level (Group) Analysis--Volume-based (MNI305/fsaverage)

  1. Assemble the contrast Data (isxconcat-sess)
    • A - (~ output dir):

      • - tal.meanfunc.nii (stack where each "time point" is the mean f image of each subject sampled in the MNI305 space)

      • - tal.masks.nii (binary masks for all the subjects)

      • - tal.fsnr.nii (functional SNR maps from each subject)

      • - tal.mask.nii (single binary mask made from the intersection of the individuals)

      • - ffxdof.dat (fixed-effects DOF across all subjects)

      • - sessid.txt (list of sessions, the corresponding freesurfer subject name, & the DOF contributed by each subject))

      • - ~contrast folder:

        • - tal.ces.nii (contrast maps for each of the subjects)

        • - tal.cesvar.nii (variance of the contrast for each subject (i.e., the square of the standard error). This variance is needed for fixed-effects & weighted random-effects analysis.)

        • - "osgm" directory (one-sample-group-mean corresponds to a group design matrix that is simply a column of 1s. This will be used later in group analysis (i.e. in mri_gmfit))

  2. Quality Assurance
    • A - Check registration (tkregister2 --s fsaverage --surf ..)

    • B - Check the individual masks (tkmedit fsaverage orig.mgz ..)

    • C - Look at the functional SNR maps(tkmedit fsaverage ...)

  3. Group GLM Analysis (mri_glmfit)
    • A - Random Effects

      • - Input: tal.ces.nii,tal.mask.nii

      • - Output: tal.rfx.osgm, beta.nii, sig.nii & osgm folder

    • B - Weighted Random Effects

      • - Similar to Random effects except that the first-level noise variances (tal.cesvar.nii) are passed

    • C - Fixed Effects

      • - Also included --yffxvar, & -- ffxdofdat

  4. Output & visualization

    • A - First concatenate sig.nii files to a single file (mri_concat)

    • B - Visualize (tkmedit fsaverage orig.mgz -aux brain.mgz ..)

  5. Correction for Multiple Comparisons/Cluster Analysis (mri_volcluster)
    • A - Examine additions to the FSFAST hierarchy:

    • - tal.rfx.osgm/osgm/cluster.sum (table shows the size of each cluster in voxels and mm^3, the talairach coordinate, the maximum significance in the cluster, & the clusterwise p-value (CWP))

    • - cwsig.cluster.nii (map of the clusters with the voxel value equal to the -log10(pvalue))

    • - sig.cluster.nii (original sig map with non-cluster voxels removed)

    • - ocn.cluster.nii (map where the value at each voxel is replaced by the number of the cluster that the voxel is associated with)

# Higher-Level (Group) Analysis--Surface-based (MNI305/fsaverage)

  1. Assemble the Data (isxconcat-sess)
    • A - Examine additions to the FSFAST hierarchy (~ output dir):

    • - ?h.meanfunc.nii

    • - ?h.mask.nii

    • - ?h.fsnr.nii

    • - ?h.ces.nii

    • - ?h.cesvar.nii

  2. Group GLM Analysis(mri_glmfit)"--surf fsaverage lh" added to volume based.)
    • A - Random Effects

    • B - Weighted Random Effects

    • C - Fixed Effects

  3. Output and visualization (mri_concat and tksurfer)
    • A - Random Effects

    • B - Weighted Random Effects

    • C - Fixed Effects

  4. Correction for Multiple Comparisons/Cluster Analysis (mri_volcluster)

An active [wiki:FreeSurferSupport e-mail list] is available to answer specific questions about processing procedures.