Index

Name

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

Synopsis

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

Arguments

Positional Arguments

none

Required Flagged Arguments

-sf

sessidfile

-df

srchdirfile

-s

sessid

-d

srchdir

Optional Flagged Arguments

-surface

self or fsaverage followed by hemi lh rh lhrh (for both, the default)

-mcin mcinstem

stem to used as input to MC

-mcout mcoutstem

stem to use as output of MC

-smin sminstem

Expected "=" to follow "mcoutstem"

-smout smoutstem

Expected "=" to follow "sminstemsm"

-inorm inormstem

Expected "=" to follow "smoutstem"

-mask maskstem

Expected "=" to follow "brain"

-fwhm fwhm

fwhm in mm (volume and surface separately)

-fsd fsd

Expected "=" to follow "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

Expected "=" to follow "fmcsm"

Expected "=" to follow "fmcsm"

output volume

Description

preproc-sess runs the following preprocessing steps: motion correction (mc-sess), smoothing (spatialsmooth-sess), and brain-mask creation (mkbrainmask-sess). This will run preprocessing steps: motion correction (MC), slice-timing correction (STC), smoothing, intensity normalization (INorm), and brain mask creation. By default, it will perform MC, smoothing, and masking, but not STC or INorm. All stages producde a new volume that can be used as input to mkanalysis-sess. Note: MC and INorm require matlab but none of the other stages does. By default, motion correction uses the first volume of the first run as the reference for all runs.

Examples

Example 1

To perform MC, smoothing by fwhm of 5mm, and brain mask, run

For MC the input will be f and the output will be fmc For Smoothiing the input will be fmc and the output will be fmcsm5 Use this name (i,e fmcsm5) as the -funcstem argument in mkanalysis-sess.new

Example 2

To perform MC, STC, smoothing by fwhm of 7.1 mm, and brain mask, run

For MC the input will be f and the output will be fmc For STC the input will be fmc and the output will be fmcstc For Smoothiing the input will be fmcstc and the output will be fmcstcsm7.1

Bugs

??

See Also

mc-sess, spatialsmooth-sess, inorm-sess,mkbrainmask-sess, mkanalysis-sess.new

Links

FreeSurfer, FsFast

Methods Description

??

References

References/Lastname###

Reporting Bugs

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

Author/s

DougGreve

preproc-sess (last edited 2012-03-21 17:00:45 by DanielWakeman)