| Deletions are marked like this. | Additions are marked like this. |
| Line 10: | Line 10: |
| [[TableOfContents]] | <<TableOfContents>> |
| Line 17: | Line 17: |
| prepoc-sess -sf <sessidfile> -df <srchdirfile> [options] [[BR]] | prepoc-sess -sf <sessidfile> -df <srchdirfile> [options] <<BR>> |
| Line 51: | Line 51: |
| ["preproc-sess"] runs the following preprocessing steps: motion correction (["mc-sess"]), smoothing (["spatialsmooth-sess"]), and brain-mask creation (["mkbrainmask-sess"]). | [[preproc-sess]] runs the following preprocessing steps: motion correction ([[mc-sess]]), smoothing ([[spatialsmooth-sess]]), and brain-mask creation ([[mkbrainmask-sess]]). |
| Line 58: | Line 58: |
| 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"] | 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]] |
| Line 67: | Line 67: |
| ["mc-sess"], ["spatialsmooth-sess"], ["inorm-sess"],["mkbrainmask-sess"], ["mkanalysis-sess.new"] | [[mc-sess]], [[spatialsmooth-sess]], [[inorm-sess]],[[mkbrainmask-sess]], [[mkanalysis-sess.new]] |
| Line 78: | Line 78: |
| ["References/Lastname###"] | [[References/Lastname###]] |
Index
Contents
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]
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
??
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>