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help > RE: z-matrix plot/visualization
Jun 9, 2015 01:06 PM | Fred Uquillas
RE: z-matrix plot/visualization
Hi Alfonso!
This is great, thank you so much. I'll try the hierarchical ordering and see how that turns out.
All the best as always,
Fred
Originally posted by Alfonso Nieto-Castanon:
This is great, thank you so much. I'll try the hierarchical ordering and see how that turns out.
All the best as always,
Fred
Originally posted by Alfonso Nieto-Castanon:
Hi Fred,
Typically, resorting the ROIs (e.g. use imagesc(r(ROIorder,ROIorder)) instead of imagesc(r)) can help organize the resulting connectivity matrix display. There are many ways to resort the ROIs into meaningful clusters. Perhaps a simple approach to get you started would be to use the 'sort ROIs' functionality in CONN ROI-to-ROI results explorer window. If you go to 'results explorer' in the ROI-to-ROI tab, select in 'define connectivity matrix' the ROIs that you want to display, and click on the ROIs menubar and select the option that reads someting like 'sorting: close ROIs are functionally similar (hierarchical clustering)', that will sort and cluster the ROIs so that functionally similar ROIs are close after resorting. You can then use the 'sorting: export ROI order' option to save this ROI order information into a .mat file that you may use for your own displays.
Let me know if that is what you had in mind and if you would like me to give you a more specific example of how to interpret the information in that .mat file (I am away from my computer right now so I am a bit fuzzy about the details).
Best
Alfonso
Originally posted by Fred Uquillas:
Typically, resorting the ROIs (e.g. use imagesc(r(ROIorder,ROIorder)) instead of imagesc(r)) can help organize the resulting connectivity matrix display. There are many ways to resort the ROIs into meaningful clusters. Perhaps a simple approach to get you started would be to use the 'sort ROIs' functionality in CONN ROI-to-ROI results explorer window. If you go to 'results explorer' in the ROI-to-ROI tab, select in 'define connectivity matrix' the ROIs that you want to display, and click on the ROIs menubar and select the option that reads someting like 'sorting: close ROIs are functionally similar (hierarchical clustering)', that will sort and cluster the ROIs so that functionally similar ROIs are close after resorting. You can then use the 'sorting: export ROI order' option to save this ROI order information into a .mat file that you may use for your own displays.
Let me know if that is what you had in mind and if you would like me to give you a more specific example of how to interpret the information in that .mat file (I am away from my computer right now so I am a bit fuzzy about the details).
Best
Alfonso
Originally posted by Fred Uquillas:
Hi Alfonso,
I was wondering if I could get some help with this matrix I'm trying to plot. I would like to organize the association matrix into modules. I've been looking online for a way to do this in MATLAB, but can't seem to have the necessary skills to do this with the ROI.mat file : /
Thank you in advance for any help and advice you may be able to provide.
All the best,
Fred
Originally posted by Fred Uquillas:
I was wondering if I could get some help with this matrix I'm trying to plot. I would like to organize the association matrix into modules. I've been looking online for a way to do this in MATLAB, but can't seem to have the necessary skills to do this with the ROI.mat file : /
Thank you in advance for any help and advice you may be able to provide.
All the best,
Fred
Originally posted by Fred Uquillas:
That's right on the
dot Alfonso. Thank you!
I was able to figure out how to plot two individual's z-matrix from the first-level results folder, one from each group using pcolor in MATLAB (attached). The code you provide (when used to plot a 1 -1 contrast or vice versa) is more what I was going for though!
Thanks again.
Fred
Originally posted by Alfonso Nieto-Castanon:
I was able to figure out how to plot two individual's z-matrix from the first-level results folder, one from each group using pcolor in MATLAB (attached). The code you provide (when used to plot a 1 -1 contrast or vice versa) is more what I was going for though!
Thanks again.
Fred
Originally posted by Alfonso Nieto-Castanon:
Hi Fred,
Not within CONN directly, but you could use some Matlab code like the example below to generate this sort of plots (e.g. when loading the data from a second-level results file)
load /data/conn_project/results/secondlevel/ANALYSIS_01/AllSubjects/rest/ROI.mat;
z = cat(1,ROI.h); % effect-sizes (typically fisher transformed values)
r = tanh(z); % convert to r coefficients
figure
imagesc(r);
axis equal tight
colorbar
Let me know if this is what you had in mind
Best
Alfonso
Originally posted by Fred Uquillas:
Not within CONN directly, but you could use some Matlab code like the example below to generate this sort of plots (e.g. when loading the data from a second-level results file)
load /data/conn_project/results/secondlevel/ANALYSIS_01/AllSubjects/rest/ROI.mat;
z = cat(1,ROI.h); % effect-sizes (typically fisher transformed values)
r = tanh(z); % convert to r coefficients
figure
imagesc(r);
axis equal tight
colorbar
Let me know if this is what you had in mind
Best
Alfonso
Originally posted by Fred Uquillas:
Hi guys,
Anybody out there know how I can plot the z-matrix in a format similar to the attached image?
Thank you so much!!
Fred
Anybody out there know how I can plot the z-matrix in a format similar to the attached image?
Thank you so much!!
Fred
Threaded View
| Title | Author | Date |
|---|---|---|
| Fred Uquillas | Apr 13, 2015 | |
| Alfonso Nieto-Castanon | Apr 14, 2015 | |
| Fred Uquillas | Apr 14, 2015 | |
| Fred Uquillas | Jun 2, 2015 | |
| Alfonso Nieto-Castanon | Jun 4, 2015 | |
| Fred Uquillas | Jun 9, 2015 | |