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help > RE: Extract Sorted 2nd Level ROI-ROI Matrix
Aug 3, 2021 01:08 PM | Alfonso Nieto-Castanon - Boston University
RE: Extract Sorted 2nd Level ROI-ROI Matrix
Hi Spencer,
Thanks for the clarification, I see what you mean now. The summary.results.RRC_F variable contains the matrix of individual connection-level statistics (T or F statistic associated with your second-level model hypothesis for each individual connection; this is the same info as what you would obtain when using the 'export mask' button, but before thresholding). The summary.results.RRC_p field contains the matrix of associated p-values (just the uncorrected connection-level p-values), and the summary.results_RRC_P field contains the matrix of associated corrected p-values (FDR-corrected connection-level p-values). All of these fields are computed when running 2nd-level analyses, they are independent-of / not-informed-by your choice of thresholding method (to be precise, these p/P values would be relevant only/mainly in the context of connection-level inferences, i.e. when choosing the thresholding option "alternative settings for connection-based inferences: parametric univariate statistics")
Regarding (2), if you click on the 'export data' button, that will create a NIFTI file (e.g. data.nii) that contains the Fisher transformed correlation coefficient matrices for each individual subject and condition in your analysis. You can read that data using the same syntax as before, e.g. :
[rZ, roinames] = conn_mtx_read( '/my2ndlevelfolder/data.nii');
where now rZ will be a [132 x 132 x #subjects] 3D matrix containing the original data. note: if your analysis contains multiple conditions per subject, rZ will still be a 3D matrix now with size [132 x 132 x #subjects*#conditions]; you may use the syntax "[rZ, roinames, roicoords, samples] = conn_mtx_read( '/my2ndlevelfolder/data.nii');" when reading the data file to get a "samples" variable describing the subject and condition number associated with each element of this 3D matrix.
Hope this helps
Alfonso
Originally posted by Spencer Upton:
Thanks for the clarification, I see what you mean now. The summary.results.RRC_F variable contains the matrix of individual connection-level statistics (T or F statistic associated with your second-level model hypothesis for each individual connection; this is the same info as what you would obtain when using the 'export mask' button, but before thresholding). The summary.results.RRC_p field contains the matrix of associated p-values (just the uncorrected connection-level p-values), and the summary.results_RRC_P field contains the matrix of associated corrected p-values (FDR-corrected connection-level p-values). All of these fields are computed when running 2nd-level analyses, they are independent-of / not-informed-by your choice of thresholding method (to be precise, these p/P values would be relevant only/mainly in the context of connection-level inferences, i.e. when choosing the thresholding option "alternative settings for connection-based inferences: parametric univariate statistics")
Regarding (2), if you click on the 'export data' button, that will create a NIFTI file (e.g. data.nii) that contains the Fisher transformed correlation coefficient matrices for each individual subject and condition in your analysis. You can read that data using the same syntax as before, e.g. :
[rZ, roinames] = conn_mtx_read( '/my2ndlevelfolder/data.nii');
where now rZ will be a [132 x 132 x #subjects] 3D matrix containing the original data. note: if your analysis contains multiple conditions per subject, rZ will still be a 3D matrix now with size [132 x 132 x #subjects*#conditions]; you may use the syntax "[rZ, roinames, roicoords, samples] = conn_mtx_read( '/my2ndlevelfolder/data.nii');" when reading the data file to get a "samples" variable describing the subject and condition number associated with each element of this 3D matrix.
Hope this helps
Alfonso
Originally posted by Spencer Upton:
Hi Alfonso,
Thank you for the prompt responses.
(1) I did and ROI to ROI bivariate correlation on resting state data using the default CONN atlas (132 x 132). I have 5 sessions of data. For example, when I make generate a second level results for say baseline [1 0 0 0 0], I go to results-->2ndlevel-->my model -->Baseline, I get an ROI.mat file. In the mat file, I can choose ROI or summary.
In ROI there is a column listed 'p'. (i.e., ROI p).
In Summary, you can select 'results' and this gives you 'RRC_F', 'RRC_p', "RRC_P'.
I understand what the RRC_F refers to, but the others all are different. For example, if I grab data from the same cell for all, I get different numbers:
1. ROI p (e.g., p=0.0127)
2. RRC p (e.g., p=0.0255)
3. RRC P (e.g., p=0.0397)
Do you know what these are all referring to?
(2) Another follow up question.
The other day you gave me this command '[stats, roinames] = conn_mtx_read( '/my2ndlevelfolder/results.nii')" so that I could extract data as it is sorted in the 2nd level gui. This worked great for getting the T/F/Zscore values, but I also need to get the rZ fisher correlation coefficients in this order as well. Is there a command for that? Thanks!
-Spencer
Thank you for the prompt responses.
(1) I did and ROI to ROI bivariate correlation on resting state data using the default CONN atlas (132 x 132). I have 5 sessions of data. For example, when I make generate a second level results for say baseline [1 0 0 0 0], I go to results-->2ndlevel-->my model -->Baseline, I get an ROI.mat file. In the mat file, I can choose ROI or summary.
In ROI there is a column listed 'p'. (i.e., ROI p).
In Summary, you can select 'results' and this gives you 'RRC_F', 'RRC_p', "RRC_P'.
I understand what the RRC_F refers to, but the others all are different. For example, if I grab data from the same cell for all, I get different numbers:
1. ROI p (e.g., p=0.0127)
2. RRC p (e.g., p=0.0255)
3. RRC P (e.g., p=0.0397)
Do you know what these are all referring to?
(2) Another follow up question.
The other day you gave me this command '[stats, roinames] = conn_mtx_read( '/my2ndlevelfolder/results.nii')" so that I could extract data as it is sorted in the 2nd level gui. This worked great for getting the T/F/Zscore values, but I also need to get the rZ fisher correlation coefficients in this order as well. Is there a command for that? Thanks!
-Spencer
Threaded View
Title | Author | Date |
---|---|---|
Spencer Upton | Jul 28, 2021 | |
Alfonso Nieto-Castanon | Jul 30, 2021 | |
Spencer Upton | Aug 2, 2021 | |
Alfonso Nieto-Castanon | Aug 2, 2021 | |
Spencer Upton | Aug 3, 2021 | |
Alfonso Nieto-Castanon | Aug 3, 2021 | |
Spencer Upton | Aug 3, 2021 | |
Dione Q | Oct 6, 2021 | |
Spencer Upton | Aug 3, 2021 | |
Spencer Upton | Aug 4, 2021 | |
Spencer Upton | Aug 3, 2021 | |