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| Describe FsFastFunctionalConnectivityWalkthrough here. |
===work in progress...=== ==About== Walkthrough: How to use FsFast and fcseed-sess for functional connectivity analysis [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.fsfast.ppt|Functional Analysis with FS-FAST]] *STEP 1: Unpack Data into the FSFAST Hierarchy using "unpackscmdir" [[https://surfer.nmr.mgh.harvard.edu/fswiki/unpacksdcmdir| unpacksdcmdir]] 1.QA Check after unpacking A - Check unpacked data (time points, # of slices ..etc) B - Check FSFAST hierarchy in session folder *STEP 2: reconstruct anatomical data using # 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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all recon-all]] 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 [[http://surfer.nmr.mgh.harvard.edu/fswiki/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 (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 *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 |
===work in progress...===
==About== Walkthrough: How to use FsFast and fcseed-sess for functional connectivity analysis
*STEP 1: 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
*STEP 2: reconstruct anatomical data using # 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 https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all recon-all
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 http://surfer.nmr.mgh.harvard.edu/fswiki/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 (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
*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