3 Changes Inspired in China - December 2017


At our recent AFNI bootcamps in Shenzhen and Guangzhou, a few issues came up. Three changes have been implemented this week, inspired by discussions the the students there. Thanks go from me to the 100+ students we had in these cities for interesting discussions and questions. New AFNI binaries are now available with these updates. You can install them with the command

@update.afni.binaries -d

Another way to keep up with information about changes to AFNI is to subscribe to our email “digest”: https://afni.nimh.nih.gov/afni/community/board/read.php?1,154890,154890#msg-154890

  1. A new option “-Tslices” in 3drefit.
    This option allows a user to add slice time offsets directly to a dataset. The purpose of this is to let a user (or script) set the slice timing when the dataset creation process did not do so correctly. AFNI allows arbitrary slice timing to be added to NIFTI files, using the AFNI extension to the NIFTI header. These slice times will be used by the “tshift” processing block in afni_proc.py. Details of how to specify slice time offsets are described in the output of 3drefit -help https://afni.nimh.nih.gov/pub/dist/doc/program_help/3drefit.html .

  2. Fixed “-substatpar” in 3drefit.
    The -substatpar option in 3drefit did not always work properly for some types of datasets. This problem has (hopefully) been fixed, so that the statistical type and parameters associated with a dataset sub-brick can now be changed. The main application for this is when (say) 3dcalc is used to process a dataset: the statistical information is usually removed from the output dataset, since 3dcalc cannot “know” if the calculations affected the statistical distribution. Option -substatpar should usually be combined with option -sublabel to change the label of the same sub-brick, to match the new statistical type (e.g., “Correlation”). Details of how to set statistical parameters and type for a sub-brick are described in 3drefit -help https://afni.nimh.nih.gov/pub/dist/doc/program_help/3drefit.html .

  3. A new AFNI driver command is now available.
    The new command “DATASET#N” drives the Dataset#N “transformation” used in graph viewers to overlay time series plots from more than one dataset. This change allows a script to drive the creation of such overlaid time series graphs and then save them to image files. The details are described in the updated README.driver file https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.driver.html . At this time, this is the only AFNI plugin that can be controlled by driving.

For change 2), I’ll add that you NEED to understand what you are doing to use -substatpar correctly. Otherwise, you will end up with a dataset whose statistical type and/or parameters are wrong, and then will probably be interpreted incorrectly (or worse).

I’m bumping this up (for Christmas!) to help people in China see this report of updates inspired by THEM.