Index TableOfContents
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 |
Outputs
This 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.
Description
isxavg-fe 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"] 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.
To run each contrast in the analysis, you must use a separate command: ["stxgrinder-sess"]. See examples below
Examples
Example 1
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
isxavg-fe-sess -analysis <analysisname> -group <groupname> -space sph sf <subjectfilename> -d <subjects_dir> stxgrinder-sess -analysis <analysisname> -s <groupname> -space sph -sf <subjectfilename> -d <subjects_dir> -contrast <contrastname> (repeat for all contrasts you want)
Bugs
None
See Also
["stxgrinder-sess"]
Links
Methods Description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
Author/s
DougGreve, PhD