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'''# Analyze First Level (selxavg3-sess -s <subjid> -analysis <name>)''' |
'''# Analyze First Level ''' {{{ selxavg3-sess -s <subjid> -analysis <analysis name> }}} |
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{{{ isxconcat-sess -s <sessid> -analysis <analysis name> -c <contrast name> -o <outdir> }}} |
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{{{ mri_glmfit --y tal.ces.nii --osgm --mask ../tal.mask.nii --glmdir tal.rfx.osgm --nii }}} |
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{{{ mri_glmfit --y tal.ces.nii --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii \ --wls tal.cesvar.nii }}} |
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{{{ mri_glmfit --y tal.ces.nii --osgm --glmdir tal.ffx.osgm --nii --mask ../tal.mask.nii \ --yffxvar tal.cesvar.nii --ffxdofdat ../ffxdof.dat }}} |
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{{{ isxconcat-sess -s <sessid> -analysis <analysis name> -c <contrast name> -o <outdir> -hemi <?h> }}} |
[wiki:FreeSurferWiki top]
# Unpack Data into the FSFAST Hierarchy (unpackscmdir)
- 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)
- Set SUBJECTS_DIR
- 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
- Make FSFAST basic hierarchy (only if data are not unpacked in FSFAST hierarchy)
Link to FreeSurfer anatomical analysis
A - Make subjectname file in the session directory to link a subject's functional & structural data
- Create a sessid file (text file with list of your sessions)in your Study DIR.
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 <#>)
By default this will do motion correction, smoothing & brain masking
- Quality Check (plot-twf-sess)
- 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)
- Setting up models of the task-related components
- Setting up models of the nuisance components
- Defining contrasts
- Fitting the model
- Making inferences
Input files: (*.par & fmcsm#)
# Analyze First Level
selxavg3-sess -s <subjid> -analysis <analysis name>
- 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))
- Visualization
A - Volume-based visualization (tkmedit-sess)
B - Surface-based visualization (tksurfer-sess)
# Higher-Level (Group) Analysis--Volume-based (MNI305/fsaverage)
- Assemble the contrast Data (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))
- 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 ...)
- Group GLM Analysis (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
Output & visualization
A - First concatenate sig.nii files to a single file (mri_concat)
B - Visualize (tkmedit fsaverage orig.mgz -aux brain.mgz ..)
- 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)
- 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
- Group GLM Analysis(mri_glmfit)"--surf fsaverage lh" added to volume based.)
A - Random Effects
B - Weighted Random Effects
C - Fixed Effects
- Output and visualization (mri_concat and tksurfer)
A - Random Effects
B - Weighted Random Effects
C - Fixed Effects
- Correction for Multiple Comparisons/Cluster Analysis (mri_volcluster)
An active [wiki:FreeSurferSupport e-mail list] is available to answer specific questions about processing procedures.