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| [[TableOfContents]] | <<TableOfContents>> |
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| ["intergroupavg-sess"] - computes random effects analysis between 2 groups or subject populations (i.e. controls vs. patients) | [[intergroupavg-sess]] - computes random effects analysis between 2 groups or subject populations (i.e. controls vs. patients) |
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| ["intergroupavg-sess"] -analysis <analysisname> -contrast <contrastname> -group1 <group1name> -group2 <group2name> -intergroup <intergroupname>-space <spacename> | [[intergroupavg-sess]] -analysis <analysisname> -contrast <contrastname> -group1 <group1name> -group2 <group2name> -intergroup <intergroupname>-space <spacename> |
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|| -analysis analysisname || session-level functional analysis name || analysis created by ["mkanalysis-sess.new"] and used with ["selxavg-sess"] on each individual session || || -contrast contrastname || contrast used in the random effects avg || contrast created by ["mkanalysis-sess.new"] and used when running ["isxavg-re-sess"] If the contrast is multivariate, then sig and minsig maps will be produced || || -group1 groupname || name of group1 (positive) || group name given when calling ["isxavg-re-sess"]. This refers to the group that will be "positive'' || || -group2 groupname || name of group2 (negative) || group name given when calling ["isxavg-re-sess"]. This refers to the group that will be "negative'' || |
|| -analysis analysisname || session-level functional analysis name || analysis created by [[mkanalysis-sess.new]] and used with [[selxavg-sess]] on each individual session || || -contrast contrastname || contrast used in the random effects avg || contrast created by [[mkanalysis-sess.new]] and used when running [[isxavg-re-sess]] If the contrast is multivariate, then sig and minsig maps will be produced || || -group1 groupname || name of group1 (positive) || group name given when calling [[isxavg-re-sess]]. This refers to the group that will be "positive'' || || -group2 groupname || name of group2 (negative) || group name given when calling [[isxavg-re-sess]]. This refers to the group that will be "negative'' || |
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| || -space spacename || space in which to average (tal, sph) || Space in which {\em isxavg-re-sess} was run. This is the space that each individual was transformed to so that all individuals across all groups are registered. Options are: tal (for talairach), sph (for spherical surface-based), or the name of a region-of-interest (created with ["func2roi-sess"] || | || -space spacename || space in which to average (tal, sph) || Space in which {\em isxavg-re-sess} was run. This is the space that each individual was transformed to so that all individuals across all groups are registered. Options are: tal (for talairach), sph (for spherical surface-based), or the name of a region-of-interest (created with [[func2roi-sess]] || |
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| ["intergroupavg-sess"] is a program for intergroup averaging. The | [[intergroupavg-sess]] is a program for intergroup averaging. The |
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| effects model (see ["isxavg-re-sess"]). Inter-group statistics are | effects model (see [[isxavg-re-sess]]). Inter-group statistics are |
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Run ["selxavg-sess"] on all subjects: ["selxavg-sess"] -sf a.sid -sf b.sid -df sess.dir -analysis main |
Run [[selxavg-sess]] on all subjects: [[selxavg-sess]] -sf a.sid -sf b.sid -df sess.dir -analysis main |
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| ["func2tal-sess"] -res 4 -sf a.sid -sf b.sid -df sess.dir -analysis main | [[func2tal-sess]] -res 4 -sf a.sid -sf b.sid -df sess.dir -analysis main |
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["isxavg-re-sess"] -group GroupA -sf a.sid -df sess.dir -analysis main-contrast up-vs-down -space tal ["isxavg-re-sess"] -group GroupB -sf b.sid -df sess.dir -analysis main-contrast up-vs-down -space tal |
[[isxavg-re-sess]] -group GroupA -sf a.sid -df sess.dir -analysis main-contrast up-vs-down -space tal [[isxavg-re-sess]] -group GroupB -sf b.sid -df sess.dir -analysis main-contrast up-vs-down -space tal |
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| ["intergroupavg-sess"] -analysis main -contrast up-vs-down -group1 GroupA -group2 GroupB -intergroup AMinusB -space tal | [[intergroupavg-sess]] -analysis main -contrast up-vs-down -group1 GroupA -group2 GroupB -intergroup AMinusB -space tal |
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| ["tkmedit-sess"] -analysis main -s AMinusB -isxavg random -contrast up-vs-down -space tal -d . | [[tkmedit-sess]] -analysis main -s AMinusB -isxavg random -contrast up-vs-down -space tal -d . |
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| ["intergroupavg-sess"] -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space sph -spacedir <outdir from ["sphsmooth-sess"] | [[intergroupavg-sess]] -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space sph -spacedir <outdir from [[sphsmooth-sess]] |
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| ["intergroupavg-sess"] -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space tal -polarity 1 | [[intergroupavg-sess]] -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space tal -polarity 1 |
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| ["isxavg-re-sess"] | [[isxavg-re-sess]] |
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| ["References/Lastname###"] | [[References/Lastname###]] |
Index
Contents
Name
intergroupavg-sess - computes random effects analysis between 2 groups or subject populations (i.e. controls vs. patients)
Synopsis
intergroupavg-sess -analysis <analysisname> -contrast <contrastname> -group1 <group1name> -group2 <group2name> -intergroup <intergroupname>-space <spacename>
Arguments
Positional Arguments
none |
Required Flagged Arguments
-analysis analysisname |
session-level functional analysis name |
analysis created by mkanalysis-sess.new and used with selxavg-sess on each individual session |
-contrast contrastname |
contrast used in the random effects avg |
contrast created by mkanalysis-sess.new and used when running isxavg-re-sess If the contrast is multivariate, then sig and minsig maps will be produced |
-group1 groupname |
name of group1 (positive) |
group name given when calling isxavg-re-sess. This refers to the group that will be "positive |
-group2 groupname |
name of group2 (negative) |
group name given when calling isxavg-re-sess. This refers to the group that will be "negative |
-intergroup intergroupname |
name of intergroup average |
name given to the intergroup average. This name is used in subsequent commands just as one would use the session id or the group name |
-space spacename |
space in which to average (tal, sph) |
Space in which {\em isxavg-re-sess} was run. This is the space that each individual was transformed to so that all individuals across all groups are registered. Options are: tal (for talairach), sph (for spherical surface-based), or the name of a region-of-interest (created with func2roi-sess |
Optional Flagged Arguments
-polarity +1 or -1 |
only consider voxels with avg > 0 (or < 0) |
-spacedir dir |
default is spacename |
-hemi hemisphere |
with sph space <lh rh> |
-umask umask |
set unix file permission mask |
-scriptonly |
don't run, just generate a script |
-version |
print version and exit |
Outputs
Description
intergroupavg-sess is a program for intergroup averaging. The individual groups are assumed to have been averaged using a random effects model (see isxavg-re-sess). Inter-group statistics are computed based on a t-statistic. The average and variance for each group are computed according to a random effects model. To run the random effects averaging, the user chooses a contrast which is used to collapse the hemodynamic responses across time and condition to yield a single number for each subject. The group average will be the average of this number over all the subjects. The group variance will be the variance of this number across all the subjects in the group.
Examples
Example 1: Whole Processing Stream
Say you have 10 subjects in 2 groups (A and 
with sessids: subject1a, ..., subject5a, subject1b, ..., subject5b.
Create sessid files called a.sid and b.sid and sessdir file sess.dir. Let the analysis name be "main. The contrast you are interested in is "up-vs-down.
Run selxavg-sess on all subjects:
selxavg-sess -sf a.sid -sf b.sid -df sess.dir -analysis main
Resample them into talairach space:
func2tal-sess -res 4 -sf a.sid -sf b.sid -df sess.dir -analysis main
Run random effects group averaging for each group:
isxavg-re-sess -group GroupA -sf a.sid -df sess.dir -analysis main-contrast up-vs-down -space tal isxavg-re-sess -group GroupB -sf b.sid -df sess.dir -analysis main-contrast up-vs-down -space tal
Run intergroup averaging
intergroupavg-sess -analysis main -contrast up-vs-down -group1 GroupA -group2 GroupB -intergroup AMinusB -space tal
View the results on the talairach volume:
tkmedit-sess -analysis main -s AMinusB -isxavg random -contrast up-vs-down -space tal -d .
Example 2: Spherical
intergroupavg-sess -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space sph -spacedir <outdir from sphsmooth-sess
Example 3: Volume/Talairach
intergroupavg-sess -analysis <analysisname> -contrast <contrastname> -group1 controls -group2 patients -intergroup controlsVpatients-space tal -polarity 1
performs a between-group average but only considers voxels that are <1 for the given contrast for each of the two groups (i.e. only considers voxels that were "red" in the given contrast for controls and for patients, and only uses these voxels in the between-group contrast
Bugs
None
See Also
Links
Methods Description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
Author/s
DougGreve PhD