Dear Alfonso,
thank you very much for your last answer. It made me feel a lot more confident about my data-extraction approach.

As you suggested I checked the approach and now got a correlation coefficient of 1, at least if I unchecked the "despiking"-option in the preprocessing step.

The time-series still do not exactly match for a scaling problem which I assume is due to a scaling within the ROI vs. scaling with the entire ROI. If this is true the difference is meaningless for further work with data extracted from the niftiDATA_Subject001_Condition001.nii-file.

The next thing I encountered is that the correlation for the time courses (my extracted mean) vs. the ROI-mean shown by conn and contained in the ROI_Subject001_Condition001.mat-file is 1 if the desping option in the preprocessing step is unchecked whereas is it is slightly less if the "despiking"-option is checked.
Is it correct that the despinking procedure is also done seperately for ROI-Data and whole-brain-Data? This would again mean that inspite of the slight differences with the conn-output I could proceed.

Again I would like to mention how grateful I am for your last answers!
Kind regards
Tobias