Latest version of AFNI from instructions at https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu.html
To run an interactive session, try:
docker run -i -t \
-v /local/path/to/raw/data:/raw_data:ro \
-v /local/path/to/data/derivatives:/data_derivatives \
jflournoy/dockerfile_afni_17
The -v option allows you to specify a file-system mount of the form /local:/container:options. We mount the raw data directory read-only with ro.
Once you have a command line prompt, check the afni version with afni -ver. If you're interested in trying to get a GUI, see this stackoverflow post. Command-line utilities work well -- e.g., 3dFWHMx:
root@473443dbc162:/# 3dFWHMx -acf NULL /raw_data/bold4d.nii.gz
++ 3dFWHMx: AFNI version=AFNI_17.0.16 (Mar 21 2017) [64-bit]
++ Authored by: The Bob
** AFNI converts NIFTI_datatype=512 (UINT16) in file /raw_data/bold4d.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /raw_data/bold4d.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/raw_data/bold4d.nii.gz is 7.596907 degrees from plumb.
*+ WARNING: removed 7724 voxels from mask because they are constant in time
*+ WARNING: Suggestion: use the '-detrend' option:
+ 728410 (out of 795053) voxel time series have significant means
++ start FWHM calculations
+ FWHM done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 35.68 mm
+ ACF done (0.00 CPU s thus far)
10.3174 13.5028 12.0841 11.8961
0.724423 38.668 13.4381 70.2055