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help > RE: First-level analysis after adding new ROIs
Mar 10, 2022 10:03 PM | Alfonso Nieto-Castanon - Boston University
RE: First-level analysis after adding new ROIs
Dear Mary,
Not sure what this error may indicate, it may possibly mean that at least for some subject there were not brain voxels within the ROI mask (?). Without really fixing this issue one possible "hack" to have that second-level analysis run would be to look at the design matrix to check the name of the subject-5 'pre' file that is missing and create a "fake" file for that subject/condition copying the data from a different subject condition (and of course then make sure that your second-level analysis does NOT include that subject in the analysis).
That said, the combination of Matlab 2011b, SPM8, and CONN16b really needs an upgrade on all three fronts if possible (ideally Matlab 2021, SPM12, and CONN21?). If trying other combinations please keep in mind that many parts of the newer CONN releases -and probably also SPM12- will simply not work on Matlab releases older than 2013. I would probably suggest to create a back-up copy of your entire project just to be safe, and then try to see if you can load your project and everything looks still fine after installing newer versions (the back-up copy is necessary because upgrading an old CONN project to a newer CONN version is a non-reversible operation)
Best
Alfonso
Originally posted by Mary Newsome:
Not sure what this error may indicate, it may possibly mean that at least for some subject there were not brain voxels within the ROI mask (?). Without really fixing this issue one possible "hack" to have that second-level analysis run would be to look at the design matrix to check the name of the subject-5 'pre' file that is missing and create a "fake" file for that subject/condition copying the data from a different subject condition (and of course then make sure that your second-level analysis does NOT include that subject in the analysis).
That said, the combination of Matlab 2011b, SPM8, and CONN16b really needs an upgrade on all three fronts if possible (ideally Matlab 2021, SPM12, and CONN21?). If trying other combinations please keep in mind that many parts of the newer CONN releases -and probably also SPM12- will simply not work on Matlab releases older than 2013. I would probably suggest to create a back-up copy of your entire project just to be safe, and then try to see if you can load your project and everything looks still fine after installing newer versions (the back-up copy is necessary because upgrading an old CONN project to a newer CONN version is a non-reversible operation)
Best
Alfonso
Originally posted by Mary Newsome:
Dear Alfonso,
Hope you're well! I've been trying to figure out why I am having an error message pop up when trying to add new ROIs to an analysis. It's the old "matrix dimensions must agree" error haha (pasted below). I double checked things and for sure the x,y,z are the same as the other ROIs, and as the images, and all are normalized in MNI space. The error message seems to pop up for Subject 5. Subject 5 isn't in the group analysis I'm trying to do, so I tried skipping that subject when adding the ROIs to the first level (everything goes well during Setup and Denoising when adding them), but during second level I get an error message that data are missing for Pre.(It's a Pre-Post design). I tried updating to both versions 17f (the one right after the one I'm using, which is 16b) and to the latest version of 20, but 17f logs me out when I load the .mat file, and 20 gives me an error message when starting.
Thanks for any help : )
Mary
ERROR DESCRIPTION:
Error using .*
Matrix dimensions must agree.
Error in conn_wdemean (line 4)
y=conn_bsxfun(@minus,x,sum(x.*repmat(w,[1,size(x,2)]),1)./max(eps,sum(w)));
Error in conn_process (line 1889)
y=conn_wdemean(y,wx);
Error in conn_process (line 38)
case 'analyses_gui_seed',disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10,11,15],CONN_x.Analysis);
Error in conn (line 4529)
else conn_process('analyses_gui_seed',CONN_x.Analysis);
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.16.b
SPM8 + Anatomy Beamforming DEM FieldMap MEEGtools aal conn marsbar
Matlab v.2011b
storage: 18047.8Gb available
Warning: Contents.m overloaded by version in folder /usr/local/spm8/toolbox/SnPM13
Hope you're well! I've been trying to figure out why I am having an error message pop up when trying to add new ROIs to an analysis. It's the old "matrix dimensions must agree" error haha (pasted below). I double checked things and for sure the x,y,z are the same as the other ROIs, and as the images, and all are normalized in MNI space. The error message seems to pop up for Subject 5. Subject 5 isn't in the group analysis I'm trying to do, so I tried skipping that subject when adding the ROIs to the first level (everything goes well during Setup and Denoising when adding them), but during second level I get an error message that data are missing for Pre.(It's a Pre-Post design). I tried updating to both versions 17f (the one right after the one I'm using, which is 16b) and to the latest version of 20, but 17f logs me out when I load the .mat file, and 20 gives me an error message when starting.
Thanks for any help : )
Mary
ERROR DESCRIPTION:
Error using .*
Matrix dimensions must agree.
Error in conn_wdemean (line 4)
y=conn_bsxfun(@minus,x,sum(x.*repmat(w,[1,size(x,2)]),1)./max(eps,sum(w)));
Error in conn_process (line 1889)
y=conn_wdemean(y,wx);
Error in conn_process (line 38)
case 'analyses_gui_seed',disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10,11,15],CONN_x.Analysis);
Error in conn (line 4529)
else conn_process('analyses_gui_seed',CONN_x.Analysis);
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.16.b
SPM8 + Anatomy Beamforming DEM FieldMap MEEGtools aal conn marsbar
Matlab v.2011b
storage: 18047.8Gb available
Warning: Contents.m overloaded by version in folder /usr/local/spm8/toolbox/SnPM13
Threaded View
| Title | Author | Date |
|---|---|---|
| Mary Newsome | Feb 24, 2022 | |
| Alfonso Nieto-Castanon | Mar 10, 2022 | |