It's a long story how I got here. I was studying MRIs on AFNI and noticed that with some of my scans, the resting and functional alignment was very, very bad. I worked with Rick Reynolds to revise the processing script, and that worked for a while, but most of our last few scans have terrible alignment and the new script doesn't fix it. I noticed the following error messages in the badly aligned data runs:

Center of mass shifts (-cmass) are turned off, but would be large
-at least one is more than 20% of search range
Cmass xyz shifts = [numbers varied depending on the dataset]
Shift search range is +/- = [numbers varied]
Center of mass shifts turned off, but would be TERRIBLY large!
At least 1 is more than 50% of search range
Cmass xyz shifts = [numbers varied depending on the dataset]
Shift search range is +/- = [numbers varied]
Cmass was turned off, but might have been needed :(
Please check your results – PLEASE PLEASE PLEASE
No output dataset will be calculated

I also saw multiple messages about considering running “3dWarp -deoblique” if I am “performing spatial transformations on an oblique dset or viewing/combining it with volumes of differing obliquity.”
My colleague suggested I run uber_subject.py, which would allow me to insert the suggested lines, e.g. -cmass. But when I tried to run uber_subject.py, I was told I need python-qt4.

Relevant information, perhaps: the patients range from infant to 13 years old, male and female. My work involves finding connectivity networks, so I open resting and anatomical data in AFNI and they should overlap more or less exactly. I didn't write the processing scripts.

I tried using anaconda to install python-qt4, and that didn't work.

Is there an updated version of python-qt4? How do I work around this? Or, more simply, is there a way to fix this alignment?