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help > RE: CONN v14p: Second-level analyses error
Apr 17, 2015 04:04 PM | sanja2012
RE: CONN v14p: Second-level analyses error
Hi Alfonso,
Thank you for your prompt response. The confusing thing is that I have definitely run everything with this condition name and the resultsROI_Condition004.mat file is there and I can look at the Z matrix - which looks fine and has the expected dimension ( ( # of sources) x (# of targets) x (# of subjects)) . I can do all the follow-up 2nd level analyses using this matrix manually in Matlab, just not in the toolbox :( Of course, I am relying on the assumption that this Z matrix has been computed correctly.
The project itself was created from an old project (where everything was working), I just changed the name of the condition (duration is still the same) and loaded different functional data and first level covariates.
I am guessing that this would have worked fine had I just started from scratch rather than trying to reuse parts of the old project?
Thanks again.
Best,
Sanja
Originally posted by Alfonso Nieto-Castanon:
Thank you for your prompt response. The confusing thing is that I have definitely run everything with this condition name and the resultsROI_Condition004.mat file is there and I can look at the Z matrix - which looks fine and has the expected dimension ( ( # of sources) x (# of targets) x (# of subjects)) . I can do all the follow-up 2nd level analyses using this matrix manually in Matlab, just not in the toolbox :( Of course, I am relying on the assumption that this Z matrix has been computed correctly.
The project itself was created from an old project (where everything was working), I just changed the name of the condition (duration is still the same) and loaded different functional data and first level covariates.
I am guessing that this would have worked fine had I just started from scratch rather than trying to reuse parts of the old project?
Thanks again.
Best,
Sanja
Originally posted by Alfonso Nieto-Castanon:
Hi
Sanja,
Could you please check in the folder .../phase1_resting_project_001_01/results/firstlevel/ANALYSIS_01 for files named resultsROI_Condition*.mat? If you do not find there a file named resultsROI_Condition004.mat (but you potentially find files named resultsROI_Condition001.mat through resultsROI_Condition003.mat) then the most likely reason for this issue would be if you have changed the name of your condition in Setup.Conditions but you have not yet re-run the denoising or first-level analysis step for this newly defined condition. If that is the case then, either re-naming the condition to its old name (the name that was used when running the denoising and first-level analysis steps), or re-running the denoising and first-level analysis steps under this new condition name, both should fix this issue.
To clarify, all of the condition-specific files that CONN creates during the processing steps are associated with a condition "name". If you change the name of a condition, it is understood as an entirely new condition and you need to run that new condition through the Denoising/first-level analysis steps to have that available at the second-level analysis tab.
Hope this helps
Alfonso
ps. to further clarify, in your case you have only a single condition "resting" in your project, but the record there shows three other conditions named "game", "rest", and "resting state" that have been defined before and run through at least some of the processing steps, so I imagine perhaps the new "resting" condition may have not gone through the first-level analysis step, even if some of the previously-defined conditions had?
Originally posted by Sanja Nedic:
Could you please check in the folder .../phase1_resting_project_001_01/results/firstlevel/ANALYSIS_01 for files named resultsROI_Condition*.mat? If you do not find there a file named resultsROI_Condition004.mat (but you potentially find files named resultsROI_Condition001.mat through resultsROI_Condition003.mat) then the most likely reason for this issue would be if you have changed the name of your condition in Setup.Conditions but you have not yet re-run the denoising or first-level analysis step for this newly defined condition. If that is the case then, either re-naming the condition to its old name (the name that was used when running the denoising and first-level analysis steps), or re-running the denoising and first-level analysis steps under this new condition name, both should fix this issue.
To clarify, all of the condition-specific files that CONN creates during the processing steps are associated with a condition "name". If you change the name of a condition, it is understood as an entirely new condition and you need to run that new condition through the Denoising/first-level analysis steps to have that available at the second-level analysis tab.
Hope this helps
Alfonso
ps. to further clarify, in your case you have only a single condition "resting" in your project, but the record there shows three other conditions named "game", "rest", and "resting state" that have been defined before and run through at least some of the processing steps, so I imagine perhaps the new "resting" condition may have not gone through the first-level analysis step, even if some of the previously-defined conditions had?
Originally posted by Sanja Nedic:
Dear
Alfonso,
As of recently, I am having the same issue as Jami. I am analyzing resting-state data, so there is one condition only, with infinite duration (I have tried using both 'Inf' and 600 (10 minutes) for the duration) . I have rerun this a few times, using SPM8 and SPM12, and Conn 14p and 15a. I use Matlab 2014b.
Everything seems perfectly fine until the 2nd level analysis when I get the error below. The condition appears in the 1st level analysis tab, but not in the 2nd level analysis. The Conn file is attached. Help would be greatly appreciated. Thank you.
ERROR DESCRIPTION:
Attempted to access CONN_h.menus.m_results.shownconditions(0); index must be a positive integer or logical.
Error in conn (line 4493)
nconditions=CONN_h.menus.m_results.shownconditions(nconditions);
Error in conn (line 3712)
conn gui_results;
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
Hi Jami,
This message typically indicates that there are no valid conditions ready for second-level analyses. I would suggest re-running your first-level analysis step (make sure you select "all conditions" when prompted). If that does not work please send me your conn_*.mat file to see if I can figure out what might be the problem there.
Best
Alfonso
Originally posted by jami andy:
As of recently, I am having the same issue as Jami. I am analyzing resting-state data, so there is one condition only, with infinite duration (I have tried using both 'Inf' and 600 (10 minutes) for the duration) . I have rerun this a few times, using SPM8 and SPM12, and Conn 14p and 15a. I use Matlab 2014b.
Everything seems perfectly fine until the 2nd level analysis when I get the error below. The condition appears in the 1st level analysis tab, but not in the 2nd level analysis. The Conn file is attached. Help would be greatly appreciated. Thank you.
ERROR DESCRIPTION:
Attempted to access CONN_h.menus.m_results.shownconditions(0); index must be a positive integer or logical.
Error in conn (line 4493)
nconditions=CONN_h.menus.m_results.shownconditions(nconditions);
Error in conn (line 3712)
conn gui_results;
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
Hi Jami,
This message typically indicates that there are no valid conditions ready for second-level analyses. I would suggest re-running your first-level analysis step (make sure you select "all conditions" when prompted). If that does not work please send me your conn_*.mat file to see if I can figure out what might be the problem there.
Best
Alfonso
Originally posted by jami andy:
Hi
I have matlab2013 and CONN v14p. I got the following error in the 2nd level analysis.
I checked many times my conditions and the 2nd level covariates.. They all look ok. I don't know what else to do.. Any help will be greatly appreciated.
thanks
J.
"ERROR DESCRIPTION:
Attempted to access CONN_h.menus.m_results.shownconditions(0); index must be a positive integer or logical.
Error in conn (line 4436)
nconditions=CONN_h.menus.m_results.shownconditions(nconditions);
CONN v.14.p
SPM8 + Beamforming DEM FieldMap MEEGtools
Matlab v.2013a
storage: 709.8Gb available
I have matlab2013 and CONN v14p. I got the following error in the 2nd level analysis.
I checked many times my conditions and the 2nd level covariates.. They all look ok. I don't know what else to do.. Any help will be greatly appreciated.
thanks
J.
"ERROR DESCRIPTION:
Attempted to access CONN_h.menus.m_results.shownconditions(0); index must be a positive integer or logical.
Error in conn (line 4436)
nconditions=CONN_h.menus.m_results.shownconditions(nconditions);
CONN v.14.p
SPM8 + Beamforming DEM FieldMap MEEGtools
Matlab v.2013a
storage: 709.8Gb available
Threaded View
| Title | Author | Date |
|---|---|---|
| Janani Raveendran | Feb 23, 2012 | |
| Alfonso Nieto-Castanon | Feb 23, 2012 | |
| jami andy | Mar 17, 2015 | |
| Alfonso Nieto-Castanon | Mar 22, 2015 | |
| sanja2012 | Apr 15, 2015 | |
| Alfonso Nieto-Castanon | Apr 17, 2015 | |
| sanja2012 | Apr 17, 2015 | |
| Alfonso Nieto-Castanon | Apr 17, 2015 | |
| sanja2012 | Apr 17, 2015 | |
| jami andy | Mar 17, 2015 | |
| Janani Raveendran | Feb 23, 2012 | |
| Alfonso Nieto-Castanon | Feb 24, 2012 | |
| Janani Raveendran | Feb 24, 2012 | |
| Janani Raveendran | Mar 1, 2012 | |
| Alfonso Nieto-Castanon | Mar 1, 2012 | |
| Janani Raveendran | Mar 1, 2012 | |