10 thoughts on “BRAPH 1.0.0 is now online

  1. Hello,

    I would like to use this software for PET Data but I don’t find how to include an atlas provided by SPM inside the software?

    Could you help me?

    Thanks

    • You have to create a file (txt or xls) containing the names and coordinates of the regions that belong to the atlas you want to use.
      You can then use this file as input in Braph.

      There are detailed instructions on how to create this file in Manual -> Brain Atlas -> Additional information.

      For an example of what your brain atlas should look like, just open the file desikan_atlas.xlsx.

      Once you have prepared it with this specific format, you can import it into Braph, by opening the Brain Atlas interface -> File -> Import.

    • You can find a detailed explanation on how to use Braph for fMRI data in http://braph.org/videos/fmri/

      Please, note that you need to preprocess your data so that you have the time series of the activation of the various brain regions before being able to use Braph.

  2. Very efficient software. I reached the last step of the fMRI Graph Analysis. I am comparing nodal measures between two groups. However, I cannot interpret some results. For example, when fdr (2-tailed)=0, what does this mean? Why not a value? Then anther fdr (2-tailed)=1.0000e-0.4. Two situations happens all through the result table.
    Thank you.

      • If you are using the existed atlas, you can search online to find coordinates in MNI space, which is the center or centroid of each ROI volume. Or you can use some software or write your own code to get the coordinates.
        If you later will not use this to show the figure results, you can put any coordinates, it will not affect graph metrics, just to define where is the ROI. Better idea is graph incudes several atlas, it is easy just use those.
        Maybe the author of Braph will have the tool or other methods.

        • Hi,

          That is right. The positions of the ROIs do not change the network analysis only the visualization, so you could basically use any atlas (in the format of Braph) and you will obtain the same results.

          If you are looking for how to perform ROI analysis from the fMRI images, maybe the following tutorial can help: https://www.fil.ion.ucl.ac.uk/spm/course/usa/Labs/Lab_E_ROImarsbar.pdf

          If there is anything more I could help you with, please let me know.

          Best,
          Mite

          • I have tested ADNI images using SPM 12 TOOL but there is a problem to read its. which data base did you use?

Leave a Reply