Differences between revisions 1 and 11 (spanning 10 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

-mapanalysis	analysisname	get map/contrast from this analysis
-thmin	thresh	minimum threshold for display (2)
-thmax	thresh	maximum threshold for display (7)
-thmask		set thmin = .5 and thmax = 1 (good for masks)
-nohdr		do not load/show hemodynamic response
-nosig		do not load/show significance map
-raw	run	display raw MR from run
-rawstem	stem	display raw MR from run/stem
-motioncor		display motion corrected raw data (with -raw)
-base	volume	t2epi, t1epi, t2conv
-mask	maskid	mask using FSD/masks/maskid
-subject	subjectname	display on subject's talairached anatomical.only with -space tal; spec -base bshortBI where B = tal res, and I is 1, 2, or 4
-s	sessid
-d	srchdir
-fsd	dir	functional subdirectory (bold)
-scriptonly		don't run, just generate a script
-umask	umask	set unix file permission mask
-version		print version and exit

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.

Variation 1

Viewing raw/motion-corrected time courses. To view a raw or motion corrected time course, cd into the Study Directory and run sliceview with the following options:

-raw	runnumber
-slice	slicenumber	number of the slice to view
-sf	sessidfile	see above
-df	sessdirfile	see above

where runnumber is the number of the run whose raw data you want to view. To view motion corrected data, add the flag "-motioncor". If the functional subdirectory is not named "bold" then use the fsd flag to specify the name. The raw and fsd flags can be use at the same time with analysis, -contrast, and map flags to simultaneously view raw time courses, hemodynamic responses, and statistical maps.

Variation 2

Viewing Individual Talairach-Resampled Results. Add space tal (cannot view raw data with tal).

Examples

Example 1

sliceview-sess -slice mos -s 020710JG -df dir -analysis tau_sm6 -contrast all_fix_6-10 -map sig

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

DougGreve

-  ⇤ ← Revision 1 as of 2004-09-30 16:55:38 → 
  Size: 1686
  Editor: DayaGulabani
  Comment:
+   ← Revision 11 as of 2004-09-30 17:53:32 → ⇥
  Size: 5119
  Editor: DayaGulabani
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 14:
-command - 1/2 sentence summary
+sliceview-sess - the results are viewed on 2D slices of the brain
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-command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4]
+sliceview-sess -slice <slicenumber> -analysis <analysis name> -contrast <contrast name> -map <map name> -sf <sessidfile> -sf <sesssirfile>
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-|| argA || brief description || detailed description (eg, help file information)  ||
|| argB || brief description || detailed description (eg, help file information)  ||
-Line 25:
+Line 23:
-|| -flag1 arg1 || brief description || detailed description (eg, help file information) ||
|| -flag2 arg2 || brief description || detailed description (eg, help file information) ||
+|| -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 31:
-|| -flag3 arg3 || brief description ||detailed description (eg, help file information) ||
|| -flag4 arg4 || brief description ||detailed description (eg, help file information) ||
+||-mapanalysis|| ||analysisname|| ||get map/contrast from this analysis||
||-thmin||       ||thresh      || ||minimum threshold for display (2)||
||-thmax||       ||thresh      || ||maximum threshold for display (7)||
||-thmask||      ||            || ||set thmin = .5 and thmax = 1 (good for masks)||
||-nohdr||       ||            || ||do not load/show hemodynamic response||
||-nosig||       ||            || ||do not load/show significance map||
||-raw||         ||run         || ||display raw MR from run||
||-rawstem||     ||stem        || ||display raw MR from run/stem||
||-motioncor||   ||            || ||display motion corrected raw data (with -raw)||
||-base||        ||volume      || ||t2epi, t1epi, t2conv||
||-mask||        ||maskid      || ||mask using FSD/masks/maskid||
||-subject||     ||subjectname || ||display on subject's talairached anatomical.only with -space tal; spec -base bshortBI where B = tal res, and I is 1, 2, or 4 ||
||-s||           ||sessid||       ||     ||
||-d||           ||srchdir||      || ||
||-fsd||         ||dir||          ||functional subdirectory (bold)||
||-scriptonly||  ||     ||        ||don't run, just generate a script||
||-umask||       ||umask||        ||set unix file permission mask||
||-version||     ||     ||        ||print version and exit||
-Line 33:
+Line 51:
-|| 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 37:
+Line 55:
-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.

== Variation 1 ==

Viewing raw/motion-corrected time courses.  To view a raw or motion corrected time course, cd into the Study Directory and run sliceview with the following options:
||-raw  || ||runnumber||
||-slice|| ||slicenumber|| ||number of the slice to view||
||-sf 	|| ||sessidfile||  ||see above||
||-df	|| ||sessdirfile|| ||see above||

where runnumber is the number of the run whose raw data you want to view.  To view motion corrected data, add the flag "-motioncor".  If the functional subdirectory is not named "bold" then use the fsd flag to specify the name.  The raw and fsd flags can be use at the same time with analysis, -contrast, and map flags to simultaneously view raw time courses, hemodynamic responses, and statistical maps.

== Variation 2 ==

Viewing Individual Talairach-Resampled Results. Add space tal (cannot view raw data with tal).
-Line 41:
+Line 76:
-command foo -i f -o out

description

== Example 2 ==
command foo -i f -o out -f fvalue

description
+sliceview-sess  -slice mos -s 020710JG -df dir -analysis tau_sm6 -contrast all_fix_6-10 -map sig
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+Line 100:
-JaneSmith
+DougGreve