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braph-software / BRAPH-2

BRAPH 2.0 is a comprehensive software package for the analysis and visualization of brain connectivity data, offering flexible customization, rich visualization capabilities, and a platform for collaboration in neuroscience research.
http://braph.org
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Notes from Joana #1057

Closed Joana70 closed 2 years ago

Joana70 commented 2 years ago

I tried to run some analyses in the new version of Braph without reading any tutorials/videos. This is what I noticed so far:

——————————————————— Issue 1) Installation of braph2genesis -> Takes approx. 1 hour, which is fine but there is not a clear message showing that the installation is proceeding well and no clear message showing the installation is done, which the users might find confusing. Also, this warning came out:

Warning: Deep Learning Toolboxs are not installed. Please refer to Deep Learning Toolbox and Deep Learning Toolbox Converter for ONNX Model Format

In braph2 (line 55) In braph2genesis (line 30)

——————————————————— Issue 2) The names of the workflows do not make much sense in the brain connectivity field. They should be renamed.

ANNA: please add suggerences ——————————————————— Issue 3) The brain atlas "human" - I do not know what this is, it looks like an inflated brain with some subcortical information but it's definitively not standard or recognisable (see link)

Screenshot 2021-10-14 at 18 27 31

Also, when I change to other surfaces it opens the same one and another empty window appears in the back. I think the default color should be changed from rainbow to grey.

——————————————————— Issue 4) I tried running nodal degree calculations and then plotted the graph, which showed a strange matrix:

Screenshot 2021-10-14 at 19 24 09

——————————————————— Issue 5) The windows need to be closed one by one, and there are quite a few windows after an analysis so it's not very efficient

——————————————————— Issue 6) I ran a structural BUD analysis but I didn’t find how to change the 6 densities that are written on the table (also I didn't understand why those specific ones are the default ones or how to specify more densities)

——————————————————— Issue 7) I think its confusing to have so many windows, which have to be slided up and down + enlarged sometimes. Also, new small windows appear when calculating each measure and they disappear when a measure is calculated so unless the user is not doing other things in the computer, he/she will not realize the calculations are done (I checked my email in the meantime for example and didn't know that the analysis was done).

For the multiple windows, I would suggest changing this to something like FSL (one GUI with different layers), otherwise the users will have multiple windows that will get mixed up when running different analyses

——————————————————— Issue 8) Structural BUD: I calculated clustering for group 1 and group 2, and then calculated the group difference - why is it not possible to do directly the group comparison like before (I understand that it needs to calculate each group measure first)?

Now there are different plots for CI up, CI down, etc - why are these provided/useful? I also saw that in the table it is written layers rather than densities, for a moment I thought I was running multilayer analyses but then realised this was just a mistake

——————————————————— Issue 9) What are the values highlighted in green in the ComparisonGroup tables for nodal measures?

mitemijalkov commented 2 years ago

Regarding the Issue 1) of Joana. For comparison, in my system it takes around 5-10 min to run braph2genesis.