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

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  • filenames: Instead of the scaled_jacobian files, you would instead include the labels for each brain generated by MAGeT.
  • atlas: This argument is NOT USED when each file has its own set of labels. Unfortunately, you still need to specify something or the function will fail. An example of what to specify is the labels for the first file – filenames$labels[1]
  • method: method = "labels" must be specified
  • defs: This is critical if the label definitions for the files you are looking at differ from the standard set of 62, described in Dorr, et. al. This will also need to be specified for users who wish use the set described in Dorr et.al, but are not using the machines at MICe.
  • dropLabels and side can continue to use the defaults.

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Code Block
#anatGetAll call, with slightly different arguments
volumes <- anatGetAll(filenames$labels, filenames$labels[1], method="labels", defs="brain_label_mappings.csv")

#combining structures, anatLm, anatFDR proceed as above:
volumes_combined <- anatCombineStructures(volumes, defs="brain_label_mappings.csv")
anatLm(~ genotype, filenames, volumes_combined)
anatFDR(anatLm(~ genotype, filenames, volumes_combined))


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