Index TableOfContents

Name

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["isxavg-fe-sess"] - computes fixed effects for group average

Synopsis

["isxavg-fe-sess"] -analysis <analysisname> -group <groupname> -space <spacename> -sf <subjectfilename> -d <subjects_dir>

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["isxavg-fe-sess"] - computes fixed effects for group average

Synopsis

["isxavg-fe-sess"] -analysis <analysisname> -group <groupname> -space <spacename> -sf <subjectfilename> -d <subjects_dir>

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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

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["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"] 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

/!\ Edit conflict! Your version:

["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

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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.

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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.

/!\ Edit conflict! Your version:

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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Examples

Example 1

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["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)

/!\ Edit conflict! Your version:

["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)

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Bugs

None

See Also

["stxgrinder-sess"]

Links

FreeSurfer, FsFast

Methods Description

References

["References/Lastname###"]

Reporting Bugs

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

Author/s

DougGreve, PhD