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

Best regards,
Anna

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.

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The export to XLS file in the GUI is made on the group average results. Nevertheless, we keep the results for each subject. To obtain those, you will need to create your own script. Use ‘example_FUN_WU’ as a base, which is located in the Functional folder inside pipelines, and after calculating the analysis use the following…[Read more]

We provide example data for using functional analysis pipelines. And by functional, we understand data that have a time series by region of analysis. In that case, the example data (generated data) provided under “example data FUN (fMRI)” is also valid for EEG.

In order to get started with the software and the analysis of EEG data…[Read more]

In our newest release (https://github.com/softmatterlab/BRAPH-2-Matlab/releases/tag/2.0.0.a3) we added connectivity multiplex pipelines, where the input is an adjacency matrix for each layer per subject.
To understand the structure of the input data, you can check the following tutorial…[Read more]

Could you please let us know which release are you using?
We recommend using our latest one: http://braph.org/2022/11/15/braph-2-0-0-a2-released/

Sometimes parallel computing has problems while using Graphical user interfaces. You could try de-activating it.
Or you could deactivate in the GUI the Memorize Intermediate Results…[Read more]

Best,
Anna

Since you have time series as input, you should use the Functional pipelines, such as Pipeline functional comparison WU/BUD/BUT. In that case, you should arrange the files of each subject in the format 196 (rows) x 111 (columns)
Here you can see how to organize your subjects’ files to use functional pipelines:…[Read more]

As you already mentioned, you should have the same number of ROIS in the atlas and in your matrix. In this case, you should only keep the rows of the 84 regions used for the analysis in the atlas file.

Best,

Anna Canal

1. So far the available multiplex pipelines take the time series (fMRI), connectivity matrices (DWI), or structural values (T1w, PET). In order to directly input your supra-adjacency matrices, you can use braph2 via the command line and create another file similar to MultiplexWU or MultiplexBU removing all the different functions…

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As you have noticed, the functional multiplex pipeline requires the same number of layers per subject. In your case, I understand you are interested to use the different runs as the different layers of a multiplex network. I would suggest taking the common minimum number of runs across subjects or using the functional pipeline (single…[Read more]

To get the coordinates of the FreeSurfer regions, and I suppose also the thalamic subnuclei, you can check the command “mri_segcentroids” in Freesurfer and add the appropriate flags.
In addition, you can also look into the Freesurfer forum for answers related to this topic or post a question yourself in case you have problems when…[Read more]

First of all, sorry for the late response, we are currently focused on the development of the new version of Braph 2.0, which is expected to be released in May, and we forgot to review the questions in braph 1 forum.

We can provide you with the coordinates of these subcortical regions (hippocampus, amygdala, and thalamus) to then you…[Read more]

In order to add atlases or particular regions not provided by our templates, you can add them in excel following the format explained here. You will manually add the regions by adding the label, name, and coordinates (x,y,z). You need to know the coordinates in advance, if you do not know where to find them we can help…[Read more]

Yes, it is possible. In order to prepare your data in the Braph 1.0 format to perform the analysis you can check here under the section “Additional Information”: File formats that can be imported

I hope this will provide you with the necessary information to get started!

Best,
Anna