Index TableOfContents

Name

prepoc-sess - pre-process fMRI data (motion correction, smoothing, intensity normalization (optional), and brain-mask creation)

Synopsis

prepoc-sess -sf <sessidfile> -df <srchdirfile> [options] BR prepoc-sess -s <sessid> -d <srchdir> [options]

Arguments

Positional Arguments

none

Required Flagged Arguments

-sf

sessidfile

-df

srchdirfile

-s

sessid

-d

srchdir

Optional Flagged Arguments

-mcin mcinstem

<f> stem to used as input to MC

-mcout mcoutstem

<instemmc> stem to use as output of MC

-smin sminstem

<mcoutstem>

-smout smoutstem

<sminstemsm>

-inorm inormstem

<smoutstem | mcoutstem | mcinstem>

-mask maskstem

<brain>

-fwhm fwhm

fwhm in mm

-fsd fsd

<bold>

-rlf rlf

run list file (default all runs)

-sliceorder so

turn on slice timing correction with the given slice order

-inorm

perform intensity normalization (off by default)

-update

only run a stage if input is newer than output (default)

-force

force reprocessing of all stages (turns off -update)

Outputs

<fmcsm>

output volume

Description

["preproc-sess"] runs the following preprocessing steps: motion correction (["mc-sess"]), smoothing (["spatialsmooth-sess"]), and brain-mask creation (["mkbrainmask-sess"]).

Examples

Example 1

preproc-sess -sf sessidlist -df sessdirlist -fwhm 5

The final output will be a volume called fmcsm which will be motion corrected and spatially smoothed at 5 mm FWHM. Use this name (i,e fmcsm) as the -funcstem argument in ["mkanalysis-sess.new"]

Example 2

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Bugs

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See Also

["mc-sess"], ["spatialsmooth-sess"], ["inorm-sess"],["mkbrainmask-sess"], ["mkanalysis-sess.new"]

Links

FreeSurfer, FsFast

Methods Description

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References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

DougGreve