Index
Contents
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
- preproc-sess -sf sessidlist -df sessdirlist -vol-fwhm 5
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
- preproc-sess -sf sessidlist -df sessdirlist -vol-fwhm 7.1 -stc
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
Methods Description
??
References
Reporting Bugs
Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >