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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)

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 including example commands.

For general tips on using FsFast, download this powerpoint:

*STEP 1: Unpack Data into the FSFAST Hierarchy using "unpackscmdir"

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 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 (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

FsFastFunctionalConnectivityWalkthrough (last edited 2024-01-16 14:11:01 by DougGreve)