Differences between revisions 3 and 5 (spanning 2 versions)

Name

sliceview-sess - the results are viewed on 2D slices of the brain

Synopsis

sliceview-sess -slice <slicenumber> -analysis <analysis name> -contrast <contrast name> -map <map name> -sf <sessidfile> -sf <sesssirfile>

Arguments

Positional Arguments

Required Flagged Arguments

-slice	slicenumber	number of the slice to view
-analysis	analysisname	name of analysis (from mkanalysis-sess)
-contrast	contrastname	name of contrast (from mkcontrast-sess)
-map	mapname	name of map produced by stxgrinder-sess (sig, t, minsig, iminsig)
-sf	sessidfile	see above
-df	sessdirfile	see above

Optional Flagged Arguments

-flag3 arg3	brief description	detailed description (eg, help file information)
-flag4 arg4	brief description	detailed description (eg, help file information)

Outputs

No output files are created. When you run sliceview, the functional results are displayed on 2D slices of the brain. You can scroll through different timepoints by using the -/+ keys. To view the hemodynamic response for a particular voxel, click on that voxel and type g.

Description

In Slice-based visualization, the results are viewed on 2D slices of the brain (either individual slices or mosaics of slices). No information about the volume is available. The slices are defined as those in the native functional space. Typically, a significance map from a particular contrast is thresholded and laid over a structural slice. Additionally, for event-related studies the hemodynamic response for each condition can be viewed by clicking on a particular voxel in the slice. To see the individual results for all subjects for a single slice, run sliceview-sess from the Study Directory with the following options.

The results for each subject will be displayed sequentially (ie, you must close the window for one subject before you can see the next). The T1 EPI image as the underlay. If the T1 does not exist, it will use mean functional image as the underlay. For event-related studies, the hemodynamic responses will be automatically loaded. See Appendix A for more details on how to operate the viewer.

Examples

Example 1

command foo -i f -o out

description

Example 2

command foo -i f -o out -f fvalue

description

Bugs

None

Links

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

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

Author/s

JaneSmith

-  ⇤ ← Revision 3 as of 2004-09-30 17:17:25 → 
  Size: 2405
  Editor: DayaGulabani
  Comment:
+   ← Revision 5 as of 2004-09-30 17:27:42 → ⇥
  Size: 3095
  Editor: DayaGulabani
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 19:
--slice      slicenumber     number of the slice to view
-analysis analysisname   name of analysis (from mkanalysis-sess)
-contrast contrastname   name of contrast  (from mkcontrast-sess)
-map       mapname        name of map produced by stxgrinder-sess (sig, t, minsig, iminsig)
-sf 	sessidfile	   see above
-df	sessdirfile	   see above
-Line 29:
+Line 21:
-|| argA || brief description || detailed description (eg, help file information)  ||
|| argB || brief description || detailed description (eg, help file information)  ||
-Line 33:
+Line 23:
-|| -slice    || || slicenumber  || || number of the slice to view || 
|| -analysis || || analysisname || || name of analysis (from mkanalysis-sess)|| 
|| -contrast || || contrastname || || name of contrast  (from mkcontrast-sess)|| 
|| -map      || || mapname      || || name of map produced by stxgrinder-sess (sig, t, minsig, iminsig)|| 
|| -sf       || || sessidfile   || || see above || 
|| -df       || || sessdirfile  || || see above ||
+|| -slice    || slicenumber  || number of the slice to view ||
|| -analysis || analysisname || name of analysis (from mkanalysis-sess)||
|| -contrast || contrastname || name of contrast  (from mkcontrast-sess)||
|| -map      || mapname      || name of map produced by stxgrinder-sess (sig, t, minsig, iminsig)||
|| -sf       || sessidfile   || see above ||
|| -df       || sessdirfile  || see above ||
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+Line 33:
-Line 46:
+Line 35:
-|| volume1 || description ||
|| volume2 || description ||
+No output files are created.  When you run sliceview, the functional results are displayed on 2D slices of the brain.  You can scroll through different timepoints by using the -/+ keys.  To view the hemodynamic response for a particular voxel, click on that voxel and type g.
-Line 50:
+Line 39:
-description
+In Slice-based visualization, the results are viewed on 2D slices of the brain (either individual slices or mosaics of slices).  No information about the volume is available.  The slices are defined as those in the native functional space.  Typically, a significance map from a particular contrast is thresholded and laid over a structural slice.  Additionally, for event-related studies the hemodynamic response for each condition can be viewed by clicking on a particular voxel in the slice.  To see the individual results for all subjects for a single slice, run sliceview-sess from the Study Directory with the following options.

The results for each subject will be displayed sequentially (ie, you must close the window for one subject before you can see the next). The T1 EPI image as the underlay.  If the T1 does not exist, it will use mean functional image as the underlay.  For event-related studies, the hemodynamic responses will  be automatically loaded.  See Appendix A for more details on how to operate the viewer.