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| isxavg-fe-sess - computes fixed effects for group average | [[isxavg-fe-sess]] - computes fixed effects for group average |
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| isxavg-fe-sess -analysis (analysisname) -group (groupname) -space (spacename) -sf (subjectfilename) -d (subjects_dir) | [[isxavg-fe-sess]] -analysis <analysisname> -group <groupname> -space <spacename> -sf <subjectfilename> -d <subjects_dir> |
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| || -spacedir || outdir specified in [[sphsmooth-sess]] step || | |
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| || volume1 || description || || volume2 || description || |
[[isxavg-fe-sess]] will create a directory called groupname in the study directory. This directory will have the same structure as an individual session and can be accessed with the s and sf flags as if it were an individual session. Inside this directory, you will see bold/analysisname/spacename-ffx in which there will be two volumes, h and h-offset, in which the intersubject averages are stored. [[stxgrinder-sess]] will create a subdirectory called "contrastname" under the bold/analysisname/spacename-ffx/ directory for each session. Within this directory, there will be 4 new volumes with stems "sig", "minsig", "iminsig" and "t". The variate-by-variate t-statistic is stored in the "t" volume and its significance in the "sig" volume. The variate is a time-point (or ideal hemodynamic curve). Multiple variates only apply to event-related design. In addition, the best variate (as measured by the minimum significance) at each voxel is also determined and stored as a map (after bonferroni correction) in the "minsig" volume. The index of the best variate is stored in the "iminsig" volume. In subsequent stages, you will be required to enter a map. This refers to one of these volumes. |
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| description | [[isxavg-fe-sess]] is a program for intersubject averaging using a fixed-effects model in which all the data from all subjects are treated as if they came from a single subject (see [[isxavg-re-sess]] for random effects model). It operates on the output of [[selxavg-sess]], and produces the same set of files. Once the subjects have been resampled into a common space (Talairach or spherical), the averages from the individual subjects can be averaged together using a Fixed-Effects model (also see [[isxavg-re-sess]] for Random Effects averaging). You may want to combine all of your subjects into a grand average, or you may want to divide your subjects into groups and compute grand averages for each group. In any event, you will need to specify which subjects will be included in the average. This collection of subjects will be referred to as a group, and you will be required to assign each group a name <groupname> which will be needed for subsequent processing. After using [[isxavg-fe-sess]], to run each contrast in the analysis, you must use a separate command: [[stxgrinder-sess]]. [[stxgrinder-sess]] is used to create statistical, significance, and parametric maps for the grand average (fixed-effects) based on a particular contrast and analysis. Note that the same program with different options is used for the individual analysis. See that section ([[stxgrinder-sess]]) and the examples below for more detail. |
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| == Example 1 == command foo -i f -o out |
== Example 1:Volume/Talairach == [[isxavg-fe-sess]] -analysis <analysisname> -group <groupname> -space tal -sf <subjectfilename> -d <subjects_dir> |
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| description | [[stxgrinder-sess]] -analysis <analysisname> -s <groupname> -space tal -sf <subjectfilename> -d <subjects_dir> -contrast <contrastname> (repeat for all contrasts you want) |
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| == Example 2 == command foo -i f -o out -f fvalue |
== Example 2: Spherical == [[isxavg-fe-sess]] -analysis <analysisname> -group <groupname> -space sph sf <subjectfilename> -d <subjects_dir> |
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| description | ['stxgrinder-sess"] -analysis <analysisname> -s <groupname> -space sph -spacedir <outdir_[[sphsmooth-sess]]>-sf <subjectfilename> -d <subjects_dir> -contrast <contrastname> (repeat for all contrasts you want) |
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| ["stxgrinder-sess"] | [[stxgrinder-sess]] |
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| ["References/Lastname###"] | [[References/Lastname###]] |
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| Doug Greve, PhD | DougGreve, PhD |
Index
Contents
Name
isxavg-fe-sess - computes fixed effects for group average
Synopsis
isxavg-fe-sess -analysis <analysisname> -group <groupname> -space <spacename> -sf <subjectfilename> -d <subjects_dir>
Arguments
Positional Arguments
none |
Required Flagged Arguments
-analysis analysisname |
session-level functional analysis name |
-group groupname |
name of group |
-space spacename |
space in which to average (native, tal, sph) |
-sf sessidfile ... |
|
-df srchdirfile ... |
|
-d srchdir ... |
Optional Flagged Arguments
-hemi hemisphere |
with sph space <lh rh> |
-trunc sign |
truncation (pos or neg; neg = set neg vals to 0) |
-logcode |
add a unique suffix to log file |
-umask umask |
set unix file permission mask |
-scriptonly |
don't run, just generate a script |
-version |
print version and exit |
-spacedir |
outdir specified in sphsmooth-sess step |
Outputs
isxavg-fe-sess will create a directory called groupname in the study directory. This directory will have the same structure as an individual session and can be accessed with the s and sf flags as if it were an individual session. Inside this directory, you will see bold/analysisname/spacename-ffx in which there will be two volumes, h and h-offset, in which the intersubject averages are stored.
stxgrinder-sess will create a subdirectory called "contrastname" under the bold/analysisname/spacename-ffx/ directory for each session. Within this directory, there will be 4 new volumes with stems "sig", "minsig", "iminsig" and "t". The variate-by-variate t-statistic is stored in the "t" volume and its significance in the "sig" volume. The variate is a time-point (or ideal hemodynamic curve). Multiple variates only apply to event-related design. In addition, the best variate (as measured by the minimum significance) at each voxel is also determined and stored as a map (after bonferroni correction) in the "minsig" volume. The index of the best variate is stored in the "iminsig" volume. In subsequent stages, you will be required to enter a map. This refers to one of these volumes.
Description
isxavg-fe-sess is a program for intersubject averaging using a fixed-effects model in which all the data from all subjects are treated as if they came from a single subject (see isxavg-re-sess for random effects model). It operates on the output of selxavg-sess, and produces the same set of files.
Once the subjects have been resampled into a common space (Talairach or spherical), the averages from the individual subjects can be averaged together using a Fixed-Effects model (also see isxavg-re-sess for Random Effects averaging). You may want to combine all of your subjects into a grand average, or you may want to divide your subjects into groups and compute grand averages for each group. In any event, you will need to specify which subjects will be included in the average. This collection of subjects will be referred to as a group, and you will be required to assign each group a name <groupname> which will be needed for subsequent processing.
After using isxavg-fe-sess, to run each contrast in the analysis, you must use a separate command: stxgrinder-sess. stxgrinder-sess is used to create statistical, significance, and parametric maps for the grand average (fixed-effects) based on a particular contrast and analysis. Note that the same program with different options is used for the individual analysis. See that section (stxgrinder-sess) and the examples below for more detail.
Examples
Example 1:Volume/Talairach
isxavg-fe-sess -analysis <analysisname> -group <groupname> -space tal -sf <subjectfilename> -d <subjects_dir>
stxgrinder-sess -analysis <analysisname> -s <groupname> -space tal -sf <subjectfilename> -d <subjects_dir> -contrast <contrastname> (repeat for all contrasts you want)
Example 2: Spherical
isxavg-fe-sess -analysis <analysisname> -group <groupname> -space sph sf <subjectfilename> -d <subjects_dir>
['stxgrinder-sess"] -analysis <analysisname> -s <groupname> -space sph -spacedir <outdir_sphsmooth-sess>-sf <subjectfilename> -d <subjects_dir> -contrast <contrastname> (repeat for all contrasts you want)
Bugs
None
See Also
Links
Methods Description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
Author/s
DougGreve, PhD