AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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kittyzxu
December 16, 2014 12:32AM
Hi AFNI friends,

I was trying to use uber_subject.py for running my analysis and I ran into a problem with volume registration.
uber_subject.py offers three options: volreg base string (first/third/last) . However, I don't know how to apply this to my specific case because I have 6 functional run plus one structural run. The structural one is in the middle, that is, i have 3 functional runs, then one structural run, then the remaining 3 functional run. Each of my functional run TR = 232.

in conventional afni_proc.py scripting, i can just do this----> -volreg_base_dset 'MyFileName+orig[231]', but I don't know how to use this in uber_subject.py... any ideas?

Second question:
I do NOT need AFNI to perform skull stripping for me in uber_subject.py because I do this using fsl_anat in FSL beforehand and would like to feed the skull stripped image in uber_subject.py. How can I do this in uber_subject.py?

In conventional afni_proc.py scripting, I can just do this ----> -copy_anat MyFileName_T1_biascorr_brain+orig (FSL gives "T1_biascorr_brain+orig" by defaulyt, i think. ) -anat_has_skull no

Can someone answer my two questions?

Thank you!

Kitty
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Subject Author Posted

How to NOT using Uber_subject.py default option for -volreg_base and NOT using uber_subject.py to do skull stripping?

kittyzxu December 16, 2014 12:32AM

Re: How to NOT using Uber_subject.py default option for -volreg_base and NOT using uber_subject.py to do skull stripping?

rick reynolds December 23, 2014 07:14PM