Dear Paul,

thanks for your input. In case you will find something out about the data files that I send you, please let me know.

Meanwhile, I changed the following line in my AFNI_proc code:

-align_opts_aea -cost lpc+ZZ -giant_move \
to
-align_opts_aea -cost lpa -giant_move \

This solved the problem. Now, the brain in the file "pb03.Subject_1.r01.volreg+tlrc" is normally aligned as well as in a normal position.
Nonetheless, I am still not sure if the three blocks "align tlrc volreg" do a good job and/or if my raw data is already qualitatively in a bad shape which would require addtional preprocessing even before the "align tlrc volreg" parts of the preprocessing pipeline.

As you suggested, I took a look at comparing the anatomical image as underlay with the functional images as overlay via the AFNI GUI (I am talking about the raw data here). The matching looked okay or even fine to me. For example, the functional images of run 1 are not spatially off the anatomical image.

I would proceed with the regression part of the general linear model now. Later, I would maybe come back to this thread just in case new problems occur which I am unable to solve and that might be related to problems in the preprocessing part of my data. And like I said, in case you already found problems with the raw data files that I send you (e.g. bad quality that could cause problems), please let me know.

Thanks,

Philipp



Edited 1 time(s). Last edit at 08/18/2021 05:52AM by Philipp.