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This page provides a history of the Tips and Tricks presented at MICe Meetings and Computing Meetings.

September 1, 2016: dplyr and %>% (pipes) in R

The presentation that Chris gave on September 1, 2016 can be found here: 

September 20, 2012: sge tips

October 4, 2012: anatGetAll

anatGetAll is part of the RMINC package and is a useful way to calculate volumes of different brain regions. A typical anatGetAll call might look like this:

vols <- anatGetAll(gf$scaled_jacobians, "resampled_atlas.mnc")

However, by not specifying any additional arguments, this call will use the defaults for the volume calculation type or atlas labels. These defaults are set for 56 micron brain-in-the-basket studies, so if this is what you are doing, you're fine.

> anatGetAll
function (filenames, atlas, method = "jacobians", defs = "/projects/mice/jlerch/cortex-label/c57_brain_atlas_labels.csv", 
 dropLabels = FALSE, side = "both")

If you wish to use MAGeT to calculate structure volumes or want to use an atlas with an alternate set of label definitions, additional arguments must be specified.

vols <- anatGetAll(gf$labels, gf$labels[0], method="labels", defs="in-vivo-t2_mapping_of_labels.csv")
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