Dear Florian,

Thank you for getting back to me - apologies if some of my questions were a little vague.

When you say you run melodic, does that mean you run melodic with the same mask, same resolution and smoothing you use in the toolbox? Or do you mean an unmasked ICA? In the latter case it would not be surprising to get completely different results because of different intrinsic dimensionalities of the different brain regions. Unfortunately, we had to remove that part of the results from our toolbox paper prior to publication.

Yes I ran melodic with and without the toolbox in exactly the same way (i.e. with a mask etc). In fact the components I get out are the same but I only get the convergence error when I use the toolbox. In fact the output with the toolbox is all there if I run the groupICA but in the tmp_log I do get the convergence error although it doesn't seem to affect anything. The only reason I noticed was because of the error in the reproducibility analysis.

To understand this problem, I need more information. Are you running split-half or test-retest reproducibility analysis? If the first, how many repetitions did you choose? if it was only one, this may explain the crash since there is nothing to calculate the correlation coefficients from. Try running more repetitions then. The ICA should not have convergence problems for all samplings. The no_convergence_error.png file should then be in the top folder of the analysis (together with an output "corr_mean.png" that is essentially the figure 2A of our paper). If it is not there, that means that the analysis did not finish properly.

I ran the split-half method using the parameters in the attached file. I chose 50 repetitions. My corr_dim.txt files are in the first sample_0001 folder, however I do not get the .png files so I guess something is not working properly. I will definitely try running the last step as you have suggested.


Let me know what you think and thanks again for the help!
Sara