• FsFastAnlysisBySteps

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# Unpack Data into the FSFAST Hierarchy using "unpackscmdir"

1. QA Check after unpacking

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

   • B - Check FSFAST hierarchy in session folder

# Reconstruction – Anatomical using "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

• 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

# 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 <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 using "tkmedit-sess"

   • B - Surface-based visualization using "tksurfer-sess"

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

1. Assemble the contrast Data using "isxconcat-sess"

isxconcat-sess -s <sessid> -analysis <analysis name> -c <contrast name> -o <outdir>

• 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))

1. Quality Assurance

   • A - Check registration using "tkregister2"

   • B - Check the individual masks using "tkmedit"

   • C - Look at the functional SNR mapsusing "tkmedit"

2. Group GLM Analysis using "mri_glmfit"

   • A - Random Effects

mri_glmfit --y tal.ces.nii --osgm --mask ../tal.mask.nii --glmdir tal.rfx.osgm --nii 

• - Input: tal.ces.nii,tal.mask.nii

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

• B - Weighted Random Effects

mri_glmfit --y tal.ces.nii --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii \
    --wls tal.cesvar.nii

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

• C - Fixed Effects

mri_glmfit --y tal.ces.nii --osgm --glmdir tal.ffx.osgm --nii --mask ../tal.mask.nii \
   --yffxvar tal.cesvar.nii --ffxdofdat ../ffxdof.dat

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

1. Output & visualization

   • A - First concatenate sig.nii files to a single file using "mri_concat"

   • B - Visualize using "tkmedit"

2. Correction for Multiple Comparisons/Cluster Analysis using "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)

isxconcat-sess -s <sessid> -analysis <analysis name> -c <contrast name> -o <outdir> -hemi <?h>

• A - Examine additions to the FSFAST hierarchy (~ output dir):

• - ?h.meanfunc.nii

• - ?h.mask.nii

• - ?h.fsnr.nii

• - ?h.ces.nii

• - ?h.cesvar.nii

1. Group GLM Analysis(mri_glmfit)"--surf fsaverage lh" added to volume based.)

   • A - Random Effects

   • B - Weighted Random Effects

   • C - Fixed Effects

2. Output and visualization (mri_concat and tksurfer)

   • A - Random Effects

   • B - Weighted Random Effects

   • C - Fixed Effects

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

An active e-mail list is available to answer specific questions about processing procedures.