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help > RE: Error importing SPM.mat file
Jan 3, 2015 01:01 AM | Alfonso Nieto-Castanon - Boston University
RE: Error importing SPM.mat file
Hi Xiaozhen,
Regarding issue #1, thanks for reporting this, to get around this either use the attached patch and/or simply refrain from pushing the tempting 'Ok' button on the "... please wait..." message box.
Regarding issue #2, CONN is complaining there that you have a "NaN" value for one of your second-level covariates. In particular, covariate 'T_BRI' contains a "NaN" (not-a-number) value for subject 83. If that was unintended simply modify that value in Setup.Covariates.SecondLevel. If, on the other hand, the intention was to somehow mark that covariate/subject as a "missing value", please follow instead the steps in here (http://www.nitrc.org/forum/message.php?m...) to disregard specific subjects from your second-level analyses (and enter a 0 or any other valid value, instead of "NaN", for that subject T_BRI covariate value).
Regarding issue #3, as far as I can tell your project looks perfectly fine. Since we had defined all tasks conditions to be session-specific your project contains two first-level covariates for each task (e.g. "Effect of resp_Session1" and "Effect of resp_Session2"). The first covariate will only contain values for the first session (and zero for the second session) and the second covariate will only contain values for the second session (and zero for the first session), which seems to be exactly what the corresponding effects that you included in the Denoising step seem to contain. Let me know if I am misinterpreting your question or where exactly are you failing to find the second-session values that you expected for some of these "Effect of *_Session2" covariates).
Best
Alfonso
Originally posted by Xiaozhen You:
Regarding issue #1, thanks for reporting this, to get around this either use the attached patch and/or simply refrain from pushing the tempting 'Ok' button on the "... please wait..." message box.
Regarding issue #2, CONN is complaining there that you have a "NaN" value for one of your second-level covariates. In particular, covariate 'T_BRI' contains a "NaN" (not-a-number) value for subject 83. If that was unintended simply modify that value in Setup.Covariates.SecondLevel. If, on the other hand, the intention was to somehow mark that covariate/subject as a "missing value", please follow instead the steps in here (http://www.nitrc.org/forum/message.php?m...) to disregard specific subjects from your second-level analyses (and enter a 0 or any other valid value, instead of "NaN", for that subject T_BRI covariate value).
Regarding issue #3, as far as I can tell your project looks perfectly fine. Since we had defined all tasks conditions to be session-specific your project contains two first-level covariates for each task (e.g. "Effect of resp_Session1" and "Effect of resp_Session2"). The first covariate will only contain values for the first session (and zero for the second session) and the second covariate will only contain values for the second session (and zero for the first session), which seems to be exactly what the corresponding effects that you included in the Denoising step seem to contain. Let me know if I am misinterpreting your question or where exactly are you failing to find the second-session values that you expected for some of these "Effect of *_Session2" covariates).
Best
Alfonso
Originally posted by Xiaozhen You:
Thank you Alfonso! Greetings in 2015 now :)
Yes it all works now all the way through, and I can check ROI-ROI 2nd level results, however when I tried to explore graph theory measures, it gives me the following error
ERROR DESCRIPTION:
Error using close (line 93)
Invalid figure handle.
Error in conn_network (line 274)
close(h);
Error in conn_displaynetwork (line 76)
data.Zresults(n1)=conn_network({data.Z(:,:,:,n1),data.names},data.displaytheserois,1,data.Zthrtype-1,Zthr);
Error in conn (line 4710)
conn_displaynetwork('init',CONN_x.Results.xX.nsources);
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.14.p
SPM8 + Anatomy ArtRepair Beamforming DEM FieldMap INRIAlign LI MEEGtools PPPI TOM8 aal marsbar wfupickatlas
Matlab v.2012b
storage: 1227.9Gb available
Warning: art.m overloaded by version in folder /data/apps/spm/8/toolbox/Art_detect
also, when I tried the voxel-voxel result, it gives me the following error:
ERROR DESCRIPTION:
Error using svd
Input to SVD must not contain NaN or Inf.
Error in rank (line 15)
s = svd(A);
Error in conn_glmunivariate (line 9)
Nx=rank(X);
Error in conn (line 4452)
if modeltype==1, [CONN_h.menus.m_results.B,CONN_h.menus.m_results.opt]=conn_glmunivariate('estimate',xf,yf);
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
also the confound viewing for the task conditions still shows all zeros for session 2, while they all look normal in 1st level covariate. is this just some viewing bug or I missed something when I move task conditions to first level covariate then in denoising step add these to confound?
Attached is the conn project file.
Thanks again!
Xiaozhen
Yes it all works now all the way through, and I can check ROI-ROI 2nd level results, however when I tried to explore graph theory measures, it gives me the following error
ERROR DESCRIPTION:
Error using close (line 93)
Invalid figure handle.
Error in conn_network (line 274)
close(h);
Error in conn_displaynetwork (line 76)
data.Zresults(n1)=conn_network({data.Z(:,:,:,n1),data.names},data.displaytheserois,1,data.Zthrtype-1,Zthr);
Error in conn (line 4710)
conn_displaynetwork('init',CONN_x.Results.xX.nsources);
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.14.p
SPM8 + Anatomy ArtRepair Beamforming DEM FieldMap INRIAlign LI MEEGtools PPPI TOM8 aal marsbar wfupickatlas
Matlab v.2012b
storage: 1227.9Gb available
Warning: art.m overloaded by version in folder /data/apps/spm/8/toolbox/Art_detect
also, when I tried the voxel-voxel result, it gives me the following error:
ERROR DESCRIPTION:
Error using svd
Input to SVD must not contain NaN or Inf.
Error in rank (line 15)
s = svd(A);
Error in conn_glmunivariate (line 9)
Nx=rank(X);
Error in conn (line 4452)
if modeltype==1, [CONN_h.menus.m_results.B,CONN_h.menus.m_results.opt]=conn_glmunivariate('estimate',xf,yf);
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
also the confound viewing for the task conditions still shows all zeros for session 2, while they all look normal in 1st level covariate. is this just some viewing bug or I missed something when I move task conditions to first level covariate then in denoising step add these to confound?
Attached is the conn project file.
Thanks again!
Xiaozhen
Threaded View
Title | Author | Date |
---|---|---|
Xiaozhen You | Nov 25, 2014 | |
Xiaozhen You | Nov 26, 2014 | |
Alfonso Nieto-Castanon | Nov 27, 2014 | |
Xiaozhen You | Dec 9, 2014 | |
Alfonso Nieto-Castanon | Dec 10, 2014 | |
Alfonso Nieto-Castanon | Dec 10, 2014 | |
Xiaozhen You | Dec 10, 2014 | |
Alfonso Nieto-Castanon | Dec 12, 2014 | |
Xiaozhen You | Dec 23, 2014 | |
Xiaozhen You | Dec 23, 2014 | |
Alfonso Nieto-Castanon | Dec 24, 2014 | |
Xiaozhen You | Dec 31, 2014 | |
Alfonso Nieto-Castanon | Dec 31, 2014 | |
Xiaozhen You | Jan 1, 2015 | |
Alfonso Nieto-Castanon | Jan 1, 2015 | |
Xiaozhen You | Jan 2, 2015 | |
Alfonso Nieto-Castanon | Jan 3, 2015 | |
Xiaozhen You | Jan 5, 2015 | |
Xiaozhen You | Jan 6, 2015 | |
Alfonso Nieto-Castanon | Jan 15, 2015 | |
Xiaozhen You | Jan 15, 2015 | |
Xiaozhen You | Dec 17, 2014 | |
Xiaozhen You | Nov 27, 2014 | |
Alfonso Nieto-Castanon | Nov 26, 2014 | |