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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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May 19, 2023 09:34AM
Howdy-

OK, that is a long time series. The option for controlling the degree of polynomial in the regression model is this, which explains the default degree chosen (based on the run_length value, which is the total time of the EPIs), as well as how to adjust it and use the "-regress_bandpass .." option to do some baseline capturing, itself:
-regress_polort DEGREE  : specify the polynomial degree of baseline

        e.g. -regress_polort 2
        default: 1 + floor(run_length / 150.0)

    3dDeconvolve models the baseline for each run separately, using
    Legendre polynomials (by default).  This option specifies the
    degree of polynomial.  Note that this will create DEGREE * NRUNS
    regressors.

    The default is computed from the length of a run, in seconds, as
    shown above.  For example, if each run were 320 seconds, then the
    default polort would be 3 (cubic).

  * It is also possible to use a high-pass filter to model baseline
    drift (using sinusoids).  Since sinusoids do not model quadratic
    drift well, one could consider using both, as in:

        -regress_polort 2         \
        -regress_bandpass 0.01 1

    Here, the sinusoids allow every frequency from 0.01 on up to pass
    (assuming the Nyquist frequency is <= 1), modeling the lower
    frequencies as regressors of no interest, along with 3 terms for
    polort 2.

So, for your resting state analysis, you could put in these options to your AP command:
  -regress_polort 2         \
  -regress_bandpass 0.01 1 \
as a reasonable starting point.

--pt
Subject Author Posted

MACAQUE afni_proc.py failed Attachments

Jewel May 18, 2023 05:29AM

Re: MACAQUE afni_proc.py failed

ptaylor May 18, 2023 09:41AM

Re: MACAQUE afni_proc.py failed

Jewel May 19, 2023 03:19AM

Re: MACAQUE afni_proc.py failed

ptaylor May 19, 2023 09:34AM

Re: MACAQUE afni_proc.py failed

rick reynolds May 19, 2023 10:20AM

Re: MACAQUE afni_proc.py failed

Jewel May 21, 2023 10:52PM