Index
Contents
Name
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 subjects 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
Links
Methods Description
??
References
none
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>