[[FreeSurferWiki|top]] '''# 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 -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 -regheader) }}} Run automatic registration {{{ spmregister-sess -s }}} Check automatic registration {{{ tkregister-sess -s }}} * '''A''' - Make edits if needed using scale as the last resort Check talairach registration {{{ tkregister2 --s --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 -analysis }}} 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 -analysis -c -o }}} * '''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 using "tkregister2" * '''B''' - Check the individual masks using "tkmedit" * '''C''' - Look at the functional SNR mapsusing "tkmedit" 3. 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 4. Output & visualization * '''A''' - First concatenate sig.nii files to a single file using "mri_concat" * '''B''' - Visualize using "tkmedit" 5. 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 -analysis -c -o -hemi }}} * '''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 [[FreeSurferSupport|e-mail list]] is available to answer specific questions about processing procedures.