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;
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It appears I am using the following version:
Version AFNI_19.2.01
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which afni
/Users/ebalde01/abin/afni
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I have added the following to my ‘.afnirc’ file (located at /Users/ebalde01/)
AFNI_PLUGINPATH = /Users/ebalde01/abin/
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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.
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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
- 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
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
Perfect! That worked. Thank you pt!
Cheers,
Edwin