NITRC BrainNet Viewer Forum: open-discussion

.edge file creation

celiavic — Fri, 06 Dec 2024 21:05:09 GMT

Hello everyone!
I have an M matrix of size 448x448 on matlab (attached here in M.xlsx document).
I'm trying to convert it to a .edge text file so I can represent the connections between my nodes (data.node). 
1) I've tried the fprintf function: for i = 1:size(M, 1)     fprintf(fid, '%f ', M(i, :)); % Writes each element with a space as separator     fprintf(fid, '\n'); % Adds a line feed at the end of each line end
The result is attached as frprint_file.edge
 2) I've also tried save('m.edge','M','-ascii'). 
The result is attached as Save_file.edge
 
In both cases, a file is created and I can represent the connections (see illustration), but I have the data is being transformed or the recording isn't being done correctly, as only positive connection values are represented and the maximum value corresponds to the minimum value in my original matrix, as if there were a problem in the sign management...
Do you have a simple and reliable method for transforming a matrix into the format desired by BrainNet (on matlab or directly from excel)? 
Thank you in advance for you help!
Célia

Can it work for regions other than brain?

Anirban Sengupta — Sat, 02 Oct 2021 17:37:20 GMT

Hi,
I am a new user for this s/w. My requirement is to use it as a tool for visualizing the network obtained from connectivity matrix of spinal cord (not brain). So, I would not require any volume/surface panel of brain to overlay the network on. I would just require the network visualization based on the nodes and their edges i.e connectivity values and don't need any surface (brain/spinal cord) to overlay it on. Is that possible to perform in this s/w?

I have encountered other s/w like Gephi which performs similar function but they are not customized for fMRI data. It will be really helpful if someone can let me know whether BrainNet viewer can create network visualization for regions other than brain? Thanks..

RE: Can't find Destrieux Atlas .nii file

Andrea Cometa — Tue, 08 Jun 2021 12:25:45 GMT

[i]Originally posted by Molly Rowlands:[/i][quote]Hello,

I am looking for a .nii file for the Destrieux atlas so that I can add it as an atlas within MRIcron/MRIcroGL. I know how to add atlases, the issue instead is that I cannot find where to access the Destrieux Atlas .nii file, e.g. the equivalent of the default all.nii atlas. Does anyone know where I can download this?; Is there a website with all of the available atlases that I am missing?

Thanks in advance!

Molly[/quote][color=#000000]Hi Molly,[/color]

I could find only this: [url=https://www.nitrc.org/frs/download.php/11942/destrieux2009.tgz]https://www.nitrc.org/frs/download.php/11942/[/url][url=https://www.nitrc.org/frs/download.php/11942/destrieux2009.tgz]destrieux2009.tgz[/url]. You can download and uncompress it using 7zip or similar.
Alternatively, if you are familiar with python, you could try to use the 'datasets.fetch_atlas_destrieux_2009' or 'datasets.fetch_atlas_surf_destrieux' functions from the nilearn package.

Can't find Destrieux Atlas .nii file

Molly Rowlands — Fri, 02 Apr 2021 9:52:46 GMT

Hello,

I am looking for a .nii file for the Destrieux atlas so that I can add it as an atlas within MRIcron/MRIcroGL. I know how to add atlases, the issue instead is that I cannot find where to access the Destrieux Atlas .nii file, e.g. the equivalent of the default all.nii atlas. Does anyone know where I can download this?; Is there a website with all of the available atlases that I am missing?

Thanks in advance!

Molly

Matlab Script for Automated Visualization and Saving Imaging

Janzaib Masood — Sat, 16 Nov 2019 4:10:28 GMT

Dear Community,

I am working with a very large number of connectivity matrices and it is very difficult to visualize and save the brain networks with the graphical interface of BrainNet Viewer.

Could anyone please share some example script that can help read surface, node and edge files for the visualization and save the results.

Thank You,
Janzaib Masood

Creating Node File

src — Mon, 17 Jun 2019 14:28:32 GMT

I am unable to understand how exactly does one create a node file? If we wish to create nodes for say, Desikan-Killany 112 nodes, how should we go about it? Any pointers will be very helpful as I am new to this.
Thanks
src

Volume mapping

Fabien Cignetti — Sun, 17 Mar 2019 16:35:54 GMT

Hello

Is there a way when mapping a volume to make it transparent and only display the border?
Otherwise, software very useful and user-friendly ... thanks!

Best
Fabien

Options not accessible.

Thomas Alderson — Thu, 24 Aug 2017 8:05:29 GMT

Moved to help.

Setting my own modular colors

Alessandro Crimi — Wed, 09 Aug 2017 2:52:43 GMT

Hi,
I would like to show my custom modules (partitioning or clustering or whatever you want to call them).
Is there a way?
It seems that the modular option in the option panel is setting different colors according to the internal algorithm of Brainnet viewer and this cannot be customized.
For example I don't want it to show the horizontal clusters green you see in the pictures with the same color, or specify myself each node which color should be.

Welcome to Open-Discussion

Christian Haselgrove — Thu, 07 Jul 2011 17:38:30 GMT

Welcome to Open-Discussion