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 14, 2022 11:43AM
Hi-

The path stuff still needs to be sorted in setup, but have you seen the @chauffeur_afni functionality here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/main_toc.html
... and more specifically here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html
?

That would seem to be doing a looot of what you want, and perhaps with a simpler interface. For example, based on your code and this example:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html#ex-4-overlay-beta-coefs-and-threshold-with-stats
I wonder if this is close to what you want (just an easier/more extensible interface):
@chauffeur_afni                                                       \
    -ulay             "${anat}"                                       \
    -olay             "${func_glt}"                                   \
    -set_subbricks    0 8 9                                           \
    -func_range       0.005                                           \
    -cbar             Reds_and_Blues_Inv                              \
    -set_dicom_xyz    0 0 0                                           \
    -delta_slices     14 17 11                                        \
    -opacity          6                                               \
    -thr_olay_p2stat  0.05                                            \
    -thr_olay_pside   bisided                                         \
    -prefix           Aud_Aget_axi_0.005                              \
    -set_xhairs       OFF                                             \
    -montx 3 -monty 3                                                 \
    -blowup           2                                               \
    -label_mode 1 -label_size 4
... though, you could use "-box_focus_slices AMASK_FOCUS_ULAY " to pick a zoomed-in autobox within which to make evenly spaced slices, rather than specifying both "-set_dicom_xyz 0 0 0" and "-delta_slices 14 17 11".

You can also add in the translucent way of thresholding, which I really like, see here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html#ex-5-overlay-beta-coefs-and-threshold-translucently-with-stats

--pt
Subject Author Posted

Saving images with command lines

xiyuezh June 14, 2022 10:58AM

Re: Saving images with command lines

rick reynolds June 14, 2022 11:09AM

Re: Saving images with command lines

ptaylor June 14, 2022 11:43AM

Re: Saving images with command lines

xiyuezh June 20, 2022 04:11PM

Re: Saving images with command lines

xiyuezh June 20, 2022 04:11PM

Re: Saving images with command lines

ptaylor June 20, 2022 05:27PM