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  

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June 13, 2022 02:13PM
Hi Doug,
Which tedana version would you like to use? If you want to use the tedana packaged in abin/, you'll probably need to use a python 2 environment as it's python 2. In order to use a more modern tedana (which would be my current recommendation), you'll want to, in your current environment, run:

pip install tedana

to get the latest version. Then, in your afni_proc script, change the line
-combine_method OC_tedort \

to

-combine_method m_tedana_m_tedort \

Relevant excerpt of the afni_proc help text:

Quote

---- combine methods that use Prantik's "original" tedana.py ----

Prantik's tedana.py is run using the 'tedana*' combine methods.

Prantik's tedana.py requires python 2.7.

By default, tedana.py will be applied from the AFNI
installation directory.

Alternatively, one can specify the location of a different
tedana.py using -combine_tedana_path. And if it is
preferable to run it as an executable (as opposed to running
it via 'python PATH/TO/tedana.py'), one can tell this to
tedana_wrapper.py by applying:
-combine_opts_tedwrap -tedana_is_exec

methods
-------
OC_tedort : OC, and pass tedana orts to regression
tedana : run tedana.py, using output dn_ts_OC.nii
tedana_OC : run tedana.py, using output ts_OC.nii
(i.e. use tedana.py for optimally combined)
tedana_OC_tedort : tedana_OC, and include tedana orts


---- combine methods that use tedana from the MEICA group ----

The MEICA group tedana is specified with 'm_tedana*' methods.

This tedana requires python 3.6+.

AFNI does not distribute this version of tedana, so it must
be in the PATH. For installation details, please see:

[tedana.readthedocs.io]

methods
-------
m_tedana : tedana from MEICA group (dn_ts_OC.nii.gz)
m_tedana_OC : tedana OC from MEICA group (ts_OC.nii.gz)
m_tedana_m_tedort: tedana from MEICA group (dn_ts_OC.nii.gz)
"tedort" from MEICA group
(--tedort: "good" projected from "bad")

Please feel free to ask me more questions as I'm one of the tedana developers.
Subject Author Posted

Using Tedana via AFNI_proc.py

dhschultz June 13, 2022 12:12PM

Re: Using Tedana via AFNI_proc.py

jbteves June 13, 2022 02:13PM

Re: Using Tedana via AFNI_proc.py

rick reynolds June 13, 2022 02:21PM

Re: Using Tedana via AFNI_proc.py

dhschultz June 14, 2022 11:10AM

Re: Using Tedana via AFNI_proc.py

rick reynolds June 14, 2022 11:21AM

Re: Using Tedana via AFNI_proc.py

dhschultz June 20, 2022 05:46PM

Re: Using Tedana via AFNI_proc.py

rick reynolds June 20, 2022 10:32PM

Re: Using Tedana via AFNI_proc.py

dhschultz June 14, 2022 11:00AM