Tagged: connectivity; PLV; EEG
October 3, 2017 at 7:40 pm #1005
I have question regarding the results returned by Braph of my EEG graph analysis. Looking at the nodal measures (after clicking at comparision), in this window there are columns like –> difference, p(1 tailed), fdr(1 -tailed)… and so on.
I am wondering that do we still have to apply fdr if this column has zero values. Sometime it has value like 1e-3 (fdr-1 tail). Does it show the value of false discovery?
Also if I have repeated measure design, do I have to define some other parameters or by selecting longitudinal study will work?
AmnaOctober 10, 2017 at 10:39 am #1007
We are very happy you chose to use Braph for your analysis and I hope everything is going well with it.
The table on the Nodal measures panel contains the information on the calculated parameters outputted from the permutation test. The fdr part of this table works in the following way:
To calculate the false discovery rate (corrected by using the Benjamini-Hochberg procedure, http://braph.org/manual/brain-graphs/) the p-values are ranked in ascending order and compared with their false corrected values. Once the largest p-value that is smaller than the corresponding false-rate-corrected value is identified, all the p-values smaller than this value are considered significant. These multiple comparisons are performed at a particular density for a given measure across all of the regions in the brain atlas.
Therefore, if you have a zero in the fdr column this means that none of the regions show a significant differences at that particular density value once their corresponding p-values are fdr corrected. Conversely, a non-zero p-value in the fdr column is the largest p-value discussed earlier (this value can be for any region but it is calculated at the particular density). In other words, if the p-value that is shown in the p-value column is smaller than the corresponding fdr value shown in the fdr column, that region is significant at this density. Please note that as you change the regions from the popup menu, the fdr value does not change since for a given measure it depends only on the density.
For your second question, yes, the longitudinal study will work.
If you need further help, please do not hesitate to contact me.
MiteOctober 11, 2017 at 6:33 pm #1008
Thanks for your detailed answer. I would like to ask about connectivity matrix calculation.
I have already calculated connectivity matrices using phase locking values (PLV). For that reason I would like to bypass the connectivity matrices calculation option and start graph theoretical analysis on matrices that I already got using PLV algorithm. However, I can see that one has to select different measures (spearman, pearson etc) in braph. The question is how can I eliminate this option in Braph? Cause changing this option is effecting my already calculated connectivity matrices. Is it possible or do I have to measure connectivities again using time series of EEG data?
AmnaOctober 16, 2017 at 1:21 pm #1017
Currently you cannot enter the adjacency matrix directly from the graphical user interface. However, you could still perform the analysis with a pre-calculated adjacency matrix from the command line while using all functionalities of Braph (like calculation of graph measures).
If, on the other hand, you would still like to use the graphical interface you would need to modify the code a bit in order to allow for the adjacency matrix to be inputted.
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.
If you instead have a ready Matlab code that will calculate the adjacency matrix with the PLV method 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 PLV instead of the standard correlation methods.
After these modifications, all other features of BRAPH will work as in the original case.
I really hope this was helpful. If you need any more information, or further help about these modifications, please do not hesitate to ask me.