Plugins

AFNI Message Board
1

Hi All,

From previous searches I understand this might be a bit of exasperating topic, so I apologize in advance. But I just got a new computer and attempting to install AFNI on it and the plugins available after installation appear to be incomplete compared to my previous installation of it. To give you some background;

  1. It appears I am using the following version:
    Version AFNI_19.2.01

which afni
/Users/ebalde01/abin/afni

I have added the following to my ‘.afnirc’ file (located at /Users/ebalde01/)

AFNI_PLUGINPATH = /Users/ebalde01/abin/

  1. I have attempted to install AFNI using both the ‘Setup Instructions’ as well as the App and both appear to lead to the same outcome.

  2. In the final system check it always responds with the following ‘fix’. Both of which I am not sure how to remediate
    ========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
  1. When starting AFNI it does say ‘Plugins = 51 libraries read’ BUT only 15 appear in the ‘Define Datamode → Plugins’

Any help into this will be greatly appreciated.

Thank you.
Edwin

2

Hi, Edwin-

The default list size got reduced a while ago for readability, but full functionality do exist. You can set an environment variable in your ~/.afnirc to do this:


AFNI_ALLOW_ALL_PLUGINS = YES

See the more full description(s) of this and related env variables, excerpting from here:
https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html


--------------------------------
Variable: AFNI_ALLOW_ALL_PLUGINS
--------------------------------
Setting this variable to YES will allow all defined plugins to
be loaded. Otherwise, little-used plugins must be allowed one
at a time, using the next set of variable names.

-------------------------------------
Variables: AFNI_ALLOW_somename_PLUGIN
-------------------------------------
Some plugins distributed with AFNI are not commonly used, and are
disabled by default. If you wish to turn one of these plugins
back on, set the corresponding environment variable to YES.
The list of these plugins is:
  --- somename ---     --- name in menu ---
  2DREGISTRATION       2D Registration
  3DCLUSTER            3D Cluster
  3DCORRELATION        3D Correlation
  3DDUMP98             3D Dump98
  3DEDIT               3D Edit
  3DEXTRACT            3D+t Extract
  3DREGISTRATION       3D Registration
  3DSTATISTIC          3D+t Statistic
  4DDUMP               4D Dump
  ASL                  ASL a3/d3
  BRIKCOMPRESSOR       BRIK Compressor
  COORDORDER           Coord Order
  DATASETCOPY          Dataset Copy
  DATASETDUP           Dataset Dup
  DATASETRENAME        Dataset Rename
  DECONVOLVE           Deconvolution
  DSETZEROPAD          Dset Zeropad
  FOURIER              Fourier
  GYRUSFINDER          Gyrus Finder
  HEMISUBTRACT         Hemi-subtract
  HILBERTDELAY98       Hilbert Delay98
  HISTOGRAMBFIT        Histogram: BFit
  L1FIT                L1_Fit & Dtr
  L2FIT                LSqFit & Dtr
  MASKCALC             maskcalc
  PERMUTATIONTEST      Permutation Test
  POWERSPECTRUM        Power Spectrum
  REORDER              Reorder
  RETROICOR            RETROICOR
  ROIAVERAGE           ROI Average
  ROIPLOT              ROI Plot
  SINGLETRIALAVG       SingleTrial Avg
  THRESHOLD            Threshold
  TSGENERATE           TS Generate
  WAVELETS             Wavelets

–pt

3

Perfect! That worked. Thank you pt!

Cheers,
Edwin

4

Rockin’.

–pt