Deletions are marked like this. | Additions are marked like this. |
Line 14: | Line 14: |
["selxavg-sess"] - computes the average signal intensity maps for each condition for each individual subject. | ["selxavg-sess"] |
Line 55: | Line 55: |
Line 58: | Line 57: |
||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 || |
|
Line 59: | Line 68: |
Line 67: | Line 75: |
["mkanalysis"] must me run | ["mkanalysis"] must be run |
Line 72: | Line 80: |
?? | none |
Line 81: | Line 89: |
{{{ description description }}} |
?? |
Line 87: | Line 92: |
["References/Lastname###"] | none |
Line 93: | Line 98: |
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
Methods Description
??
References
none
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>