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History of AFNI updates  

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October 01, 2021 03:31PM
Hi, Stef-

The ability to use Alpha+Boxed thresholding with both voxelwise and clusterwise thresholding has now been added to @chauffeur_afni.

If you get the latest version (AFNI_21.2.10 and higher), then you should have this. Here are a couple examples from the help, charmingly both called "E", I now notice... The "trick" with this is that some pieces are specified in specific places---these examples might be the clearest explication of what goes where, but there is also a "Note" in the program's help about it:
[afni.nimh.nih.gov]

E) Included Clusterizing, with Alpha+Boxed on. Also select the Olay
     (idat) and Thr (ithr) volumes descriptively, with subbrick labels.

    @chauffeur_afni                                                 \
        -ulay               anat.nii.gz                             \
        -olay               stats.nii.gz                            \
        -cbar               Reds_and_Blues_Inv                      \
        -clusterize         "-NN 1 -clust_nvox 157"                 \
        -func_range         3                                       \
        -set_subbricks      -1 "vis#0_Coef"  "vis#0_Tstat"          \
        -thr_olay_p2stat    0.001                                   \
        -thr_olay_pside     bisided                                 \
        -olay_alpha         Yes                                     \
        -olay_boxed         Yes                                     \
        -opacity            7                                       \
        -prefix             img_e                                   \
        -montx 3 -monty 3                                           \
        -set_xhairs OFF                                             \
        -label_mode 1 -label_size 4                                 \
        -no_clean


E) Included Clusterizing, with Alpha+Boxed on, similar to above, but
     1sided example.

    @chauffeur_afni                                                 \
        -pbar_posonly                                               \
        -ulay               anat.nii.gz                             \
        -olay               stats.nii.gz                            \
        -cbar               "Spectrum:yellow_to_red"                \
        -clusterize         "-NN 1 -clust_nvox 157"                 \
        -func_range 3                                               \
        -set_subbricks      -1 1 2                                  \
        -thr_olay           3.314300                                \
        -thr_olay_pside     1sided                                  \
        -olay_alpha         Yes                                     \
        -olay_boxed         Yes                                     \
        -opacity            7                                       \
        -prefix             img_f                                   \
        -montx 3 -monty 3                                           \
        -set_xhairs OFF                                             \
        -label_mode 1 -label_size 4                                 \
        -no_clean

Please let me know if anything seems awry.

--pt
Subject Author Posted

Sticky Thoughts about modeling and result reporting

Gang May 11, 2021 07:59AM

Re: Thoughts about modeling and result reporting

munoztd0 May 19, 2021 05:24PM

Re: Thoughts about modeling and result reporting

Gang May 20, 2021 07:05AM

Re: Thoughts about modeling and result reporting

munoztd0 May 20, 2021 08:58AM

Re: Thoughts about modeling and result reporting

Gang May 20, 2021 10:15PM

Re: Thoughts about modeling and result reporting

munoztd0 May 25, 2021 08:51AM

Re: Thoughts about modeling and result reporting

s.meliss September 07, 2021 10:09AM

Re: Thoughts about modeling and result reporting

ptaylor September 07, 2021 10:58AM

Re: Thoughts about modeling and result reporting

s.meliss September 09, 2021 10:25AM

Re: Thoughts about modeling and result reporting

ptaylor September 11, 2021 04:17PM

Re: Thoughts about modeling and result reporting

ptaylor October 01, 2021 03:31PM



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