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== 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. |
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== About == Walkthrough: How to use FsFast and fcseed-sess for functional connectivity analysis |
For general tips on using FsFast, download this powerpoint: |
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| [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.fsfast.ppt|Functional Analysis with FS-FAST]] | [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.fsfast.ppt|Using FS-FAST]] |
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| *STEP 1: Unpack Data into the FSFAST Hierarchy using "unpackscmdir" | *STEP 1: Unpack Data into the FSFAST Hierarchy using "unpackscmdir" |
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| [[https://surfer.nmr.mgh.harvard.edu/fswiki/unpacksdcmdir| unpacksdcmdir]] | [[https://surfer.nmr.mgh.harvard.edu/fswiki/unpacksdcmdir|unpacksdcmdir]] |
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1.QA Check after unpacking A - Check unpacked data (time points, # of slices ..etc) B - Check FSFAST hierarchy in session folder |
1.QA Check after unpacking: |
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*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]] |
* A - Check unpacked data (time points, # of slices ..etc) * B - Check FSFAST hierarchy in session folder |
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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 2: Reconstruction Anatomical data using "recon-al -all" |
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| 1.Set SUBJECTS_DIR | |
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*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 |
2.QA Check: |
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* 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 |
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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 (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