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Anna Canal-Garcia replied to the topic Export graph metric values in the forum General Help (Braph 2.0) 1 year, 1 month ago
Dear Sai Prasanna,
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]
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Sai Prasanna started the topic Export graph metric values in the forum General Help (Braph 2.0) 1 year, 2 months ago
Hi,
When I run the Functional analysis pipeline, is there anyway I can obtain the graph metrics values for individual subject and not just the group average. I need these values subject-wise and store them in a xls file.Thanks.
Sai Prasanna -
Anna Canal-Garcia replied to the topic Analysis of EEG data in the forum General Help (Braph 2.0) 1 year, 4 months ago
Dear Sergio,
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]
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Sergio Blanco Trejo started the topic Analysis of EEG data in the forum General Help (Braph 2.0) 1 year, 4 months ago
Good evening,
I would like to use your software for analyzing EEG data. Could you please provide me some EEG data (the same way that is provided for fMRI and MRI) and give me some advices for getting started? I will really appreciate it.
Thank you in advance,
Sergio -
Avalon Campbell-Cousins replied to the topic Construction of fMRI multiplex adjacency matrices in the forum General Help (Braph 2.0) 1 year, 5 months ago
Dear Anna,
Thank you very much for the update!
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Anna Canal-Garcia replied to the topic Construction of fMRI multiplex adjacency matrices in the forum General Help (Braph 2.0) 1 year, 5 months ago
Dear Avalon,
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] -
Anna Canal-Garcia replied to the topic Out of memory issue in the forum General Help (Braph 2.0) 1 year, 5 months ago
Dear Sai Prasanna,
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] -
Sai Prasanna started the topic Out of memory issue in the forum General Help (Braph 2.0) 1 year, 5 months ago
I am doing the group comparison on Functional Comparision BUT pipeline and getting the following error:
Error using ComparisonEnsemble/calculate_results (line 1220)
Out of Memory during deserializationError in ComparisonEnsemble/calculateValue (line 1121)
[cp.diff, cp.p1, cp.p2, cp.ci_lower, cp.ci_upper] = calculate_results(cp);Error in…[Read more]
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Anna Canal-Garcia replied to the topic Plotting results of connectivity study in the forum General Help (Braph 2.0) 1 year, 5 months ago
You can just create your own atlas in XLS, following the same structure 🙂
And then make sure you have the same brain regions included in the atlas and in your subject’s dataBest,
Anna -
Rene Andrade replied to the topic Plotting results of connectivity study in the forum General Help (Braph 2.0) 1 year, 5 months ago
My follow up question is that I don’t find a match between my data and any atlas. I have a mix of desikan with some other subcortical data like this
35 L.CER Left-Cerebellum-Cortex 230 148 34 255
36 L.TH Left-Thalamus 0 118 14 255
36 L.TH Left-Thalamus-Proper 0 118 14 255
37 L.CA…[Read more] -
Rene Andrade replied to the topic Plotting results of connectivity study in the forum General Help (Braph 2.0) 1 year, 5 months ago
thank you!
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Sai Prasanna replied to the topic Error while uploading files from xls in the forum General Help (Braph 2.0) 1 year, 5 months ago
Thanks, I realised that immediately after posting here. My bad.
Thank you for your quick response. Much appreciated.
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Anna Canal-Garcia replied to the topic Error while uploading files from xls in the forum General Help (Braph 2.0) 1 year, 5 months ago
Dear Sai Prasanna,
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] -
Sai Prasanna started the topic Error while uploading files from xls in the forum General Help (Braph 2.0) 1 year, 5 months ago
Hi,
I am using Pipeline connectivity comparison wu. My atlas has 111 regions and each subject has 196 time-series values. The data is arranged in xls files in the format 111*196.However, I am getting the error that says the following:
BRAPH2:SubjectCON:WrongInput The value num[111 196][-4.671351 -6.610331 6.539966 19.08763 …. is not a valid…[Read more] -
Anna Canal-Garcia replied to the topic Plotting results of connectivity study in the forum General Help (Braph 2.0) 1 year, 5 months ago
Dear Rene,
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
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Rene Andrade started the topic Plotting results of connectivity study in the forum General Help (Braph 2.0) 1 year, 5 months ago
I don’t know how to plot the results of my group analysis. Of the brain graph measures of a connectivity study. I do click right and try to plot but nothing appears. I don’t know if this is related to my connectivity matrix having 84×84 dimensions and the atlas 148 ROIs.
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Sai Prasanna replied to the topic Import correlation matrices in BRAPH in the forum General Help (Braph 2.0) 1 year, 6 months ago
Hi,
Thanks so much for your quick response. Feel motivated by active moderators like you.- The dataset I have started with is the ABIDE-I Preprocessed data. The time-series values are already available for various Atlases in text files for each subject. Is there any way I could generate the connectivity matrix using the data in this format?
- I…
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Mite Mijalkov replied to the topic Import correlation matrices in BRAPH in the forum General Help (Braph 2.0) 1 year, 6 months ago
Hi,
Thank you for considering BRAPH for your research and I am sorry to hear you are experiencing problems with your analysis. We would be very happy to assist you with this issue and we can do so in 2 ways:
1) You could upload your data directly in BRAPH and generate the correlation matrices within the software. If you would like to calculate…[Read more]
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Mite Mijalkov replied to the topic Question on MRISubject in the forum General Help (Braph 1.0) 1 year, 6 months ago
Hi Aaron,
The run time on the MRIComparisonWU would depend on the size of your network, number of measures and which measures you will calculate, but it will also be highly dependent on the number of permutations that you choose to perform.
This issue arises due to the methods used to calculate the null distributions for the MRI covariance…[Read more]
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Sai Prasanna started the topic Import correlation matrices in BRAPH in the forum General Help (Braph 2.0) 1 year, 6 months ago
Hi,
I have a set of correlation matrices generated using GraphVar toolbox. I wish to do a graph analysis on them using BRAPH. Could you please let me know how to go about it?
I am new to this area. Your help is much appreciated.
Thanks
Sai Prasanna - Load More