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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
ptaylor
June 16, 2021 05:51PM
Oh, and regarding how to tell afni_proc.py to tell align_epi_anat.py to use 3dSkullStrip on the EPI, Daniel has provided The Right Answer (as we knew he would).

It should be entered via this AP option: 
-align_epi_strip_method METHOD : specify EPI skull strip method in AEA

        e.g. -align_epi_strip_method 3dSkullStrip
        default: 3dAutomask (changed from 3dSkullStrip, 20 Aug, 2013)

    When align_epi_anat.py is used to align the EPI and anatomy, it
    uses 3dSkullStrip to remove non-brain tissue from the EPI dataset.
    However afni_proc.py changes that to 3dAutomask by default (as of
    August 20, 2013).  This option can be used to specify which method
    to use, one of 3dSkullStrip, 3dAutomask or None.

    This option assumes the 'align' processing block is used.

So, your afni_proc.py command could contain this: 
-align_epi_strip_method 3dSkullStrip                     \
        -align_opts_aea -cost lpc+ZZ -giant_move  \
            -skullstrip_opts -monkey   \
.... and that passes everything along correctly.

-pt
Reply Quote
RSS
Subject Author Posted

-epi_strip in afni_proc.py for monkeys

Doughboys June 14, 2021 08:59PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 16, 2021 03:53PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 16, 2021 05:51PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 01:39PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 17, 2021 02:21PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 03:02PM

Re: -epi_strip in afni_proc.py for monkeys

Pawel June 17, 2021 03:11PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 03:32PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 18, 2021 10:29AM