Differences between revisions 1 and 8 (spanning 7 versions)

Index

Contents

Name
Synopsis
Arguments
Outputs
Description
Examples
1. Example 1
2. Example 2
Bugs
See Also
Links
Methods Description
References
Reporting Bugs
Author/s

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"

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

Links

FreeSurfer, FsFast

Methods Description

??

References

References/Lastname###

Reporting Bugs

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

Author/s

DougGreve

-  ⇤ ← Revision 1 as of 2004-09-13 15:35:14 → 
  Size: 2132
  Editor: DavidTuch
  Comment:
+   ← Revision 8 as of 2012-03-21 17:00:45 → ⇥
  Size: 3657
  Editor: DanielWakeman
  Comment: added -surface
-Deletions are marked like this.
+Additions are marked like this.
 Line 8:
-'''Index'''
[[TableOfContents]]
+'''Index''' <<TableOfContents>>
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+Line 11:
-prepoc-sess - pre-process fMRI data
+preproc-sess - pre-process fMRI data (motion correction, smoothing, intensity normalization (optional), and brain-mask creation)
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+Line 14:
-prepoc-sess -sf <sessidfile> -df <srchdirfile> [options] [[BR]]
prepoc-sess -s <sessid> -d <srchdir> [options]
+preproc-sess -sf <sessidfile> -df <srchdirfile> [options] <<BR>> preproc-sess -s <sessid> -d <srchdir> [options]
-Line 25:
+Line 21:
-||   -sf || sessidfile  ||
||   -df || srchdirfile ||
||   -s  || sessid      ||
||   -d  || srchdir     ||
+||-sf ||sessidfile ||
||-df ||srchdirfile ||
||-s ||sessid ||
||-d ||srchdir ||
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+Line 28:
-||  -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)||
+||-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 ||||<style="text-align:center">'''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 ||
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+Line 50:
-= Outputs =
|| <fmcsm> || output volume ||
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+Line 52:
-["preproc-sess"] runs the following preprocessing steps: motion correction (["mc-sess"]), smoothing ["spatialsmooth-sess"], intensity normalization (["inorm-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]]). 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.
-Line 53:
+Line 56:
-preproc-sess -sf sessidlist -df sessdirlist -fwhm 5
+To perform MC, smoothing by fwhm of 5mm, and brain mask, run
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+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"]
+ . 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]]
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+Line 63:
-??
+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
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+Line 73:
-["mc-sess"], ["spatialsmooth-sess"], ["inorm-sess"],["mkbrainmask-sess"], ["mkanalysis-sess.new"]
+[[mc-sess]], [[spatialsmooth-sess]], [[inorm-sess]],[[mkbrainmask-sess]], [[mkanalysis-sess.new]]
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+Line 82:
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+Line 83:
-["References/Lastname###"]
+[[References/Lastname|References/Lastname###]]
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+Line 86:
-Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
+Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >