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help > RE: importing existing connectivity matrices in CONN
Jul 19, 2022 09:07 PM | Alfonso Nieto-Castanon - Boston University
RE: importing existing connectivity matrices in CONN
Dear Samantha,
That seems to indicate some issue with the ROI labels defined in your matrix NIFTI files, could you check if when creating your nifti files you may have used some syntax like:
conn_mtx_write(filename, Z, ROIlabels);
If so make sure that the ROIlabels variable is a cell array containing one label per row/column of Z, e.g.
ROIlabels = {'ROI1', 'ROI2', 'ROI3'};
(alternatively look at the .json file associated with your matrix NIFTI files to see if that contains non-string elements in the "names" field?)
Hope this helps
Alfonso
Originally posted by Samantha Baldi:
That seems to indicate some issue with the ROI labels defined in your matrix NIFTI files, could you check if when creating your nifti files you may have used some syntax like:
conn_mtx_write(filename, Z, ROIlabels);
If so make sure that the ROIlabels variable is a cell array containing one label per row/column of Z, e.g.
ROIlabels = {'ROI1', 'ROI2', 'ROI3'};
(alternatively look at the .json file associated with your matrix NIFTI files to see if that contains non-string elements in the "names" field?)
Hope this helps
Alfonso
Originally posted by Samantha Baldi:
Dear Alfonso,
I had exactly the same needs so I implemented what you suggested in this post.
This generated an SPM.mat file, together with a spmF_mv.nii, spmF_mv.json and mask.nii files.
I am now trying to load the results with conn_display SPM.mat, however I get the following error:
Loading /rds/user/sb2506/hpc-work/tFMRI_PPI/2ndlevel/dep/SPM.mat
please wait...
Error using regexprep
All cells must be char row vectors.
Error in conn_displayroi (line 204)
data.names=regexprep(data.names,{'_1_1$','^rs\.','^rsREL\.','^aal\.'},'');
Error in conn_display (line 209)
hfigure=conn_displayroi('initspm',fullfile(filepath,[filename,fileext]),varargin{:});
Any idea where this might come from?
I had exactly the same needs so I implemented what you suggested in this post.
This generated an SPM.mat file, together with a spmF_mv.nii, spmF_mv.json and mask.nii files.
I am now trying to load the results with conn_display SPM.mat, however I get the following error:
Loading /rds/user/sb2506/hpc-work/tFMRI_PPI/2ndlevel/dep/SPM.mat
please wait...
Error using regexprep
All cells must be char row vectors.
Error in conn_displayroi (line 204)
data.names=regexprep(data.names,{'_1_1$','^rs\.','^rsREL\.','^aal\.'},'');
Error in conn_display (line 209)
hfigure=conn_displayroi('initspm',fullfile(filepath,[filename,fileext]),varargin{:});
Any idea where this might come from?
Threaded View
| Title | Author | Date |
|---|---|---|
| Jaron Kupers | Jan 7, 2021 | |
| Alfonso Nieto-Castanon | Jan 7, 2021 | |
| chirokoff | Aug 22, 2022 | |
| Alfonso Nieto-Castanon | Aug 29, 2022 | |
| chirokoff | Aug 31, 2022 | |
| Alfonso Nieto-Castanon | Aug 31, 2022 | |
| Samantha Baldi | Jul 14, 2022 | |
| Alfonso Nieto-Castanon | Jul 19, 2022 | |
| Jaron Kupers | Jan 8, 2021 | |
| Alfonso Nieto-Castanon | Jan 15, 2021 | |
| Jaron Kupers | Jan 21, 2021 | |
| Alfonso Nieto-Castanon | Jan 11, 2021 | |
| Jaron Kupers | Jan 14, 2021 | |