Hi again :)

I am running the preprocessing with FM to compare it with my previous (published) results using default pipeline, just to make sure that we can use it for future analysis in our working group.

I ran the preprocessing using FM and it went good but the results changed drastically! I lost the significant cluster totally even with lowering the threshold.  I am afraid there is something wrong in the steps I did. Althought it worked fine without errors, I checked the registration of the FM on the structural images and it is not well registered, is there a step missing?
And the preprocessing pipeline is different from the default one in the order of the steps, and there is no structural segmentation, could this affect that much the results?
Last thing, my images resolutions are 1x1x1 for T1 and 1.8x1.8x2 for functional. When choosing the default tissue probability maps I keep the input as default, do I have to change something at this stage? what is bounding box?

Thanks a lot!

Best,
Dayana