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
April 10, 2023 03:27PM
Hi, Colm-

I suspect that using @chauffeur_afni:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html
would simplify your life here. It automatically makes sets of axial, coronal and sagittal images. It can make montages, and/or you can specify slice locations. You can specify ulay and olay ranges at the command line. You can combine it with 2dcat:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_2dcat.html
too.

This is a wrapper for making movies of a single slice---it will make 3 movies, one of axial, sagittal and coronal---which you might find useful, and in fact it might do what you want directly? 
@djunct_4d_imager                 \
        -inset  4D_DSET        \
        -prefix PREFIX           \
        -do_movie AGIF
... which will produce these outputs: 
+ an image of the same central slice across volumes along the time
      axis, with the brightness range constant across volume
      ("*onescl*" images); that is, the same grayscale in each panel
      corresponds to the same numerical value.  
    + an image of the same central slice across volumes along the time
      axis, with the brightness range possibly *varying* for each
      panel across volume ("*sepscl*" images); that is, the grayscale
      value in each panel can (and likely will) correspond to *a
      different* numerical value.  Useful, for example, for checking
      details in DWIs, where the expected scale of values can change
      dramatically across volumes.
    + (with option flag) a movie version of the "onescl" images,
      showing one slice at a time.
    + (with option flag) a movie version of the "sepscl" images,
      showing one slice at a time.

--pt
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Subject Author Posted

replicating AFNI GUI's brightness reduction for each of three echos using plugout_drive

Colm Connolly April 10, 2023 03:04PM

Re: replicating AFNI GUI's brightness reduction for each of three echos using plugout_drive

ptaylor April 10, 2023 03:27PM