June 28, 2021 03:13PM | |
Moderator Registered: 11 years ago Posts: 2,321 |
-blur_size SIZE_MM : specify the size, in millimeters e.g. -blur_size 6.0 default: 4 This option allows the user to specify the size of the blur used by 3dmerge (or another applied smoothing program). It is applied as the 'bmm' parameter in the filter option (such as -1blur_fwhm) in 3dmerge. Note the relationship between blur sizes, as used in 3dmerge: sigma = 0.57735027 * rms = 0.42466090 * fwhm (implying fwhm = 1.359556 * rms) Programs 3dmerge and 3dBlurInMask apply -blur_size as an additional gaussian blur. Therefore smoothing estimates should be computed per subject for the correction for multiple comparisons. Programs 3dBlurToFWHM and SurfSmooth apply -blur_size as the resulting blur, and so do not requre blur estimation. Please see '3dmerge -help' for more information. Please see '3dBlurInMask -help' for more information. Please see '3dBlurToFWHM -help' for more information. Please see 'SurfSmooth -help' for more information. See also -blur_filter.
-regress_run_clustsim yes(and check afni_proc.py's help for more about that).
[-GOFORIT [g]] Use this to proceed even if the matrix has bad problems (e.g., duplicate columns, large condition number, etc.). *N.B.: Warnings that you should particularly heed have the string '!!' somewhere in their text. *N.B.: Error and Warning messages go to stderr and also to file 3dDeconvolve.err. ++ You can disable the creation of this .err file by setting environment variable AFNI_USE_ERROR_FILE to NO before running this program. *N.B.: The optional number 'g' that appears is the number of warnings that can be ignored. That is, if you use -GOFORIT 7 and 9 '!!' matrix warnings appear, then the program will not run. If 'g' is not present, 1 is used.3dREMLfit's help also warns about making sure you can justify using this opt.
-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. Please see '3dDeconvolve -help' for more informationBasically, there is a rule-of-thumb based on the EPI duration (which appears to be 437.5 s in your case here---you can see what value of polort that gives in the formulation noted in the above help). Because you didn't specify anything wtih this opt, the script generates its own choice.
-regress_censor_outliers 0.1\ -regress_censor_motion 0.5\Did your subjects move a lot, and/or is this a "difficult" scanning population? For standard human FMRI acquisitions (voxels about 2-3mm), we might recommend starting with:
-regress_censor_outliers 0.05 \ -regress_censor_motion 0.3 \The tradeoff is: lower values mean harsher thresholding and therefore fewer time points left in the data; however, higher values mean potentially leaving in more motion-contaminated data, throwing off results. Motion tends to be of larger concern in resting state FMRI, because you don't have task stimuli to try to model, but it is worth seeing if you can lower these thresholds and still process your data.
-regress_apply_mot_types demean deriv\Normally, the "deriv" part is just included for resting state processing, and not for task. As noted above, resting state data is more sensitive to motion than task-based data. The "sacrifice" you make by including "deriv" is that 6 more degrees of freedom get used up in your model (because you are adding 6 more regressors to your model).
-regress_motion_per_run \
-mask_epi_anat yes \... to calculate the stricter mask, for either later use or for QC estimates.
-html_review_style pythonic... to get the fuller QC HTML output. It just requires you having Python and matplotlib on your OS.
Subject | Author | Posted |
---|---|---|
Proc Py Message |
grangers | June 15, 2021 03:15PM |
Re: Proc Py Message |
ptaylor | June 28, 2021 03:13PM |