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| Describe FsFastFunctionalConnectivityWalkthrough here. | === work in progress... === == About == Walkthrough: How to use FsFast and [[http://surfer.nmr.mgh.harvard.edu/fswiki/fcseed-sess|fcseed-sess]] for functional connectivity analysis including example commands. For general tips on using FsFast, download this powerpoint: . [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.fsfast.ppt|Using 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: Reconstruction Anatomical data using "recon-al -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) {{attachment:fsfast-hierarchy.jpg}} 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 (Raw fMRI data) . fmc.nii (Motion corrected-MC) fmcsm5.nii (MC & smoothed) . fmc.mcdat (Text file with the MC parameters (AFNI)) . brain.mgz (Binary mask of the brain) # Function-Structure Registration View unregistered: . [[http://surfer.nmr.mgh.harvard.edu/fswiki/tkregister-sess|tkregister-sess]] -s <subjid> -regheader) Run automatic registration: . [[http://surfer.nmr.mgh.harvard.edu/fswiki/spmregister-sess|spmregister-sess]] -s <subjid> Check automatic registration: . [[http://surfer.nmr.mgh.harvard.edu/fswiki/tkregister-sess|tkregister-sess]] -s <subjid> A - Make edits if needed using scale as the last resort Check talairach registration: . [[http://surfer.nmr.mgh.harvard.edu/fswiki/tkregister2|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 [[http://surfer.nmr.mgh.harvard.edu/fswiki/mkanalysis-sess|mkanalysis-sess]] to setup an analysis for your FC data *STEP 6: Use [[http://surfer.nmr.mgh.harvard.edu/fswiki/selxavg3-sess|selxavg3-sess]] to run the subject-level analysis *STEP 7: Use [[http://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit|mri_glmfit]] or [[http://surfer.nmr.mgh.harvard.edu/fswiki/selxavg3-sess|selxavg3-sess]] to run a group-level analysis |
work in progress...
About
Walkthrough: How to use FsFast and fcseed-sess for functional connectivity analysis including example commands.
For general tips on using FsFast, download this powerpoint:
*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: Reconstruction Anatomical data using "recon-al -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 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 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 (Raw fMRI data)
- fmc.nii (Motion corrected-MC)
fmcsm5.nii (MC & smoothed)
- fmc.mcdat (Text file with the MC parameters (AFNI))
- brain.mgz (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