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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rick reynolds
March 20, 2023 03:44PM
Indeed, afni_proc.py can be used with "-combine_method m_tedana" to run the MEICA group's tedana as part of the step to combine echoes. See
APMULTI_Demo1_rest/scripts_desktop/do_26_ap_me_bT.tcsh for an afni_proc.py command script, including use of that combine method.

In any case, tedana creates the NIFTI datasets generally using nibabel, which writes an sform_code of 2, which has an ambiguous space (orig vs standard). AFNI can be told to interpret that as being in orig space by setting AFNI_NIFTI_VIEW to "orig" (in the command, the shell environment or the ~/.afnirc file). If you continue to run afni_proc.py only after tedana, it would be reasonable to set it at the top of that command script (or in your .afnirc).

- rick
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Subject Author Posted

proc.py on tlrc data

MayaSa March 19, 2023 07:59AM

Re: proc.py on tlrc data

ptaylor March 19, 2023 11:42AM

Re: proc.py on tlrc data

rick reynolds March 20, 2023 03:44PM