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["selxavg-sess"] - computes the average signal intensity maps for each condition for each individual subject. ["selxavg-sess"]
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||Error || there are $ncondact non-null conditions in the paradigm file. However, $ncond non-null conditions were specified when mkanalysis was run. These must be made consistent in order to run selxavg-sess.||
||Solution||Your par files may not have the same number of conditions as you specified in mkanalysis.||

||Error || /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_selxavg.m On line 323 ==> Xi = [Xpar Xdrift extregrun]; >> ??? Undefined function or variable 'r'. >> quiting matlab ||

||Solution||Notice that the Warnings at the beginning of this error say something about integer elements. You are getting this error because your TR is not an integer. You must go to all of your subjects’ bold directory and emacs the seq.info file. Change the TR in seq.info to an integer (such as 2 or 2.0000). You must re-run mkanalysis-sess with this new TR, then try selxavg-sess again.||



||Error ||
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["mkanalysis"] must me run ["mkanalysis"] must be run
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?? none
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{{{
description
description
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??
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["References/Lastname###"] none
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DougGreve DougGreve and DaphneRobakis

Index TableOfContents

Name

["selxavg-sess"]

Synopsis

["selxavg-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.new"]

-sf <sessidfile>

text file list of subjects

-df <srchdirfile>

text file list of directories where subjects can be found

-d <srchdir>

use instead of –df if specifying only one dir

Optional Arguments

-sveres

save residual error to analysis/eres/eRRR

-svsignal

save signal estimate to analysis/signal/sRRR

-svsnr

save estimate of SNR to analysis/estsnr

-umask umask

set unix file permission mask [not necessary, but can use 002]

-version

print version and exit

Outputs

h

contains the estimated hemodynamic response at each voxel, along with the standard deviation of the residual error

h-offset

contains a map of the mean value at each voxel

This will create a subdirectory with the same name as your “analysisname” under the bold directory in subjects directory. There will be two volumes in this directory, one with stem “h” and one with stem “h-offset”. These are where the hemodynamic averages are stored, i.e.:

There is also a text file called h.dat with information about the parameters used during the analysis. Future processing of this analysis will create other subdirectories under “analysisname”.

Description

General Description

["selxavg-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.

Resolving Common Errors

Error

Run 6/6, 6.50608 Excluding 0 Points:??? Error using ==> +Matrix dimensions must agree.Error in =>/space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_selxavg.m On line 512 ==>SumESSMtx = SumESSMtx + ESSMtx;>> ??? Undefined function or variable 'r'.>> quiting matlab ERROR: fast_selxavg()failed ERROR(/autofs/space/thor_009/users/kk/filter_fMRI/0112_071004): selxavg failed

Solution

All runs do not contain the same number of timepoints. This may be due to a scanner error. The affected run should be excluded from averaging

Error

there are $ncondact non-null conditions in the paradigm file. However, $ncond non-null conditions were specified when mkanalysis was run. These must be made consistent in order to run selxavg-sess.

Solution

Your par files may not have the same number of conditions as you specified in mkanalysis.

Error

/space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_selxavg.m On line 323 ==> Xi = [Xpar Xdrift extregrun]; >> ??? Undefined function or variable 'r'. >> quiting matlab

Solution

Notice that the Warnings at the beginning of this error say something about integer elements. You are getting this error because your TR is not an integer. You must go to all of your subjects’ bold directory and emacs the seq.info file. Change the TR in seq.info to an integer (such as 2 or 2.0000). You must re-run mkanalysis-sess with this new TR, then try selxavg-sess again.

||Error ||

Examples

Example 1: For spherical analysis

selxavg-sess -analysis tau_sm6 -sf subjects-id -df dir

Example 2: For talairach analysis

selxavg-sess -analysis tau_sm8 -sf subjects-id -df dir

["mkanalysis"] must be run

Paradigm files placed in each bold directory

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 and DaphneRobakis

selxavg-sess (last edited 2008-04-29 11:45:33 by localhost)