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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ptaylor
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
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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