Index

Name

selxavg3-sess

Synopsis

selxavg3-sess –sf <subjectfilename> –df <srchdirfile> –analysis <sem_assoc> [options]

Arguments

Required Arguments:

-analysis <analysisname>

name of functional analysis that you created under the analysis flag in mkanalysis-sess.gui

-sf <sessidfile>

text file list of subjects

-df <srchdirfile>

text file list of directories where subjects can be found

-s <sessid>

use instead of sf if specifying only one subject

-d <srchdir>

use instead of –df if specifying only one dir

Optional Arguments

-overwrite

delete analysis if session of already analyzed

-contrasts-only

only compute contrasts (estimation already done)

-c c1 <-c c2 ...>

compute contrasts c1, c2, .. (default is to compute all)

-no-con-ok

run even if no contrasts in analysis

-fwhm

compute FWHM of residual

-no-preproc

do not run preprocessing

-svres

saves residuals (usually not needed)

-svres-unwhitened

save unwhitened residuals (usually not needed)

-run-wise

analyze each run separately

-nolog

do not create a log file

-log logfile

specify log file explicitly

-max-threads

use all CPUs (default is to use one)

-outparent dir

save output to this dir instead of in session

-version

print version and exit

Outputs

This will create a subdirectory with the same name as your “analysisname” under the bold directory in subjects directory. This folder has all of the results for this analysis, including:

Description

General Description

selxavg3-sess computes the average signal intensity maps for each condition for each individual subject. This program separately analyzes the data in each session indicated in the sessid file, then computes the average signal intensity maps for each condition. This average data can be further processed on an individual basis and/or can be used for group analyses. This also compute contrasts for testing hypotheses based on a GeneralLinearModel (GLM), including t and F statistics, significances of those statistics, and contrast effects sizes (ces).This is the new version of stxgrinder, implicit intensity normalization, better whitening

This program performs the first-level fMRI analysis. Specify the analysis configuration with -analysis. This is the configuration created with mkanalysis-sess. The analysis should already have contrasts created (by mkcontrast-sess), though you can add contrasts afterwards.

By default, selxavg3-sess will check the preprocessing to make sure that it has been run properly (turn off with -no-preproc).

By default, it will only run the analysis on data sets that actually need to be re-run based on the time stamps of the input data. To force a re-analysis run with -force or -overwrite.

This program will construct the design matrix for each run, fit the GLM, save regression coefficients, compute contrasts and significances of contrasts. The runs are combined together so the output is the average across runs (some would call this a "second-level" analysis).

This program requires matlab or octave.

Bugs

none

See Also

mkanalysis-sess.new

Links

FsFast

Methods Description

??

References

none

Reporting Bugs

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

Author/s

DougGreve

selxavg3-sess (last edited 2018-01-04 16:49:48 by MorganFogarty)