Index

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

Warning: Size vector should be a row vector with integer elements. > In space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fmri_par2scm.m at line 43 In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_selxavg.m at line 271 Warning: Integer operands are required for colon operator when used as index. > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fmri_par2scm.m at line 126 > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_selxavg.m at line 271 Warning: Subscript indices must be integer values. > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_selxavg.m at line 277 ??? Error using ==> horzcat All matrices on a row in the bracketed expression must have the same number of rows. Error in ==> /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 ERROR: fast_selxavg() failed ERROR (/space/thor/1/users/chen/mvrr/subjects/020612BW): selxavg failed

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

paradigm is ill-conditioned (2.01206e+36) Check your paradigm file for file for periodicities >> >> quiting matlab

ERROR: fast_selxavg() failed ERROR (/space/orsay/3/users/SEMPRSCZ/controls/010114MO): selxavg failed

Solution

: This error means one of two things is wrong with your .par file (located in each run of each subject’s bold directory): 1) there are not two or more occurrences of one of your conditions; or 2) there is a pattern to your conditions (for example condition 3 always follows condition 4). You can avoid this error message for the sake of analysis by 1) replacing other conditions with occurrences of your missing condition, so that each condition is represented at least twice; or 2) by changing your conditions so that they break the pattern at least twice. Even though the effect of this change is quite small, you should distribute the added conditions evenly across the other conditions. Ideally, however, you would alter your stimuli so that you do not get this error in the first place.

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