Activity

Hi Shrikanth,

Thank you for using Braph. Braph uses an FDR correction, which can indicate which edges remain significant after correcting for multiple comparisons. Additionally, one could visualize the subject matrices and check which edges have the strongest weight.

However, as there are many different methods published in the literature…[Read more]

Hi Jo-Hsin,

Many thanks! Please don’t hesitate to reach out if you have any questions or need assistance.

Thank you.The way you guided me has been very helpful.
It has inspired me to seek more information in a similar manner.
I look forward to asking questions in the future as I come across them.

Hi Jo-Hsin,

Thank you for your feedback in suing BRAPH 2.

Absolutely, it is possible to extract the learned parameters from a trained neural network model.

Let me to guide you through the process using the “example_NN_CON_WU_Classification_AdjacencyMatrix.m” script as an illustration. After line 69, kindly integrate the following code…[Read more]

Thank you.

Thanks! that’s what I wanted to know.

Hi Nabin,

Yes, if you select partial Pearson correlation, the covariates are considered then. So, before measures are calculated.

Best regards,
Anna

Hi Anna,

Thank you for your response. Yes, I select the Pearson with covariates. My question was rather when exactly during the processing the covariates are applied when I select this option. So, is the process as follows true ?

1. The pearson correlation matrices for each group is created considering the covariates (or using residual).
2. These…

[Read more]

Hi Nabin,

If you are using a structural pipeline, you can adjust for covariates by selecting the partial Pearson correlation or partial Spearman correlation when creating the graph/network. If you do not select one of these options, covariates won’t be used in the analysis.

Thank you for choosing BRAPH 2. I’m here to help you with visualizing matrices at different densities using the GUI. Here are the steps:

1. Right-click on the graph measure panel and a list will pop out. You can refer to the following screenshot.
   http://braph.org/wp-content/uploads/2023/07/plot_graph_forum_answer-2.png
2. Click on “Plot Graph” in the…

[Read more]

Thanks Emiliano for your help on this.

This question was solved with the following example of code:

*Note***
In Nabin’s case the saved b2 file was a Comparison of Structural groups.

[file, path, filterindex] = uigetfile(BRAPH2.EXT_ELEMENT, [‘Select the .b2 file.’]);
tmp = load(filename, ‘-mat’, ‘el’);
filename = fullfile(path, file);
tmp = load(filename, ‘-mat’, ‘el’);
comparison =…[Read more]

Dear Keivan,

Thank you for contacting us and for using Braph for your analysis.

The betweenness centrality in Braph has to option to provide both normalized and unnormalized values when used from the command line. However, if you are using the GUIs provided by Braph, then the default value is the normalized version.

The measure is normalized by…[Read more]