How to preprocess the funtional images of just a part of the brains?

AFNI Message Board
1

Hi,
I used to preprocess the functional images of the whole brain using uber_subject.py. But the functional images I got this time contain only a middle part of the brain. Do I need some extra operations besides the preprocessing steps given by uber_subject? How to align EPI of only a part of brain to anatomy images ?
Thank you!
Yu

2

Hi Yu,

The only special part here should be in aligning the
EPI and anat. For that, pass one of the -partial_*
options to align_epi_anat.py.

Note that you cannot specify this in the GUI (though
you can edit the afni_proc.py command that it
creates in the GUI). It would be better to take the
afni_proc.py command and work from there.

  • rick
3

Hi Rick,
Thanks a lot for your answers! The original EPI contains only a part of the brain because we wanted to increase the spatial resolution of our ROI in the process of collecting data.
But now I would like to know whether the -partial_* option is essential for alignment. Because the preprocess using uber_subject.py has already taken too much time and the alignment without the option -partial_* looks like good:
http://1060.bbs.pinggu.com/forum/201701/14/174044rbq3c3qq7zr5c7ba.jpghttp://1060.bbs.pinggu.com/forum/201701/14/174026jh53ljy5sa3lcsah.jpghttp://1060.bbs.pinggu.com/forum/201701/14/174010488ktvhawry48aoo.jpg
Thank you!

4

Hi Yu,

No, those options are to possibly help registration
when it might be difficult. You might want to
evaluate this more directly using align_epi_anat.py,
before putting the resulting parameters into the
afni_proc.py command.

  • rick