Graph FC fMRI

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This topic contains 1 reply, has 2 voices, and was last updated by  Mite Mijalkov 1 year ago.

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    Dear all,

    I would like to perform fMRI graph analysis. I see that there is no possibility to import preprocessed (NIfTI) data into BRAPH/ or to create correlation matrix within toolbox. Therefore I would like to know whether my first step should be to make correlation matrix based on choosen atlas (AAL) let’s say in DPABI, and importing the matrix inside BRAPH and choose same atlas (or choosen part’s of the brain) in order to perform graph analysis?

    Thank you in advance,

    #17465 Reply

    Mite Mijalkov

    Dear Bartosz,

    Thank you for your interest in Braph. I hope it proves useful to you and allows you to perform your analysis with ease.

    Currently, Braph does not allow the import of NIfTI data. Instead, if you have the time series of each brain region extracted, you can input those time series (while also inputting the brain atlas you extracted them with) and then Braph will calculate the adjacency matrix based on the most frequently used correlation types. For detailed information about how the fMRI Cohort is formed in Braph, you could check the video: Moreover, the steps involved into uploading a brain atlas are detailed at:

    On the other hand, if you would like to calculate the adjacency matrix by an external software and then perform the graph analysis in Braph, you would need to do your analysis from the command line as Braph currently does not allow the adjacency matrix to be entered directly from the graphical interface. In order to be able to input an adjacency matrix into Braph using the graphical interface, you would need to modify the code as outlined below.

    Assuming that you have an adjacency matrix already calculated for each subject you would need to modify two things:
    1. Modify the input to the GUIfMRICohort / fMRICohort so that instead of time series for each brain region, you will be able to import matrices.
    2. Modify the fMRIGraphAnalysis object (in the method adjmatrix either add one case in the switch function or modify an existing case that you would not use) so that instead of reading the object data and calculating the matrix, it reads the adjacency matrix from each subject and accepts it without doing any calculation.

    Additionally, if you have a ready Matlab code that will calculate the adjacency matrix provided the time series of the subject, you could just modify the fMRIGraphAnalysis object. In this case, you would add another case in the switch function (the method adjmatrix) that would execute your code instead of the standard correlation methods.

    After these modifications, all other features of BRAPH will work as in the unmodified case.

    I really hope you find this information helpful. If you need any more help about these modifications, please do not hesitate to ask me.


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