library(RMINC)
library(dplyr)
civet_summaries <-
read.csv("/hpf/largeprojects/MICe/chammill/POND/volume_summaries/combined_neuroanatomy20170405.csv"
, stringsAsFactors = FALSE)
civet_files_PND <-
civet.getAllFilenames(
filter(civet_summaries, src == "POND") %>% mutate(scan_np = gsub("-", "_", sub("MR160-", "", scan)))
, idvar = "scan_np", prefix = "MR160_", basedir = "/hpf/largeprojects/MICe/chammill/POND/civetOutputs/pond_2-1_20170227/"
, civetVersion = "2.1.0"
, cnf = yaml::yaml.load_file("/hpf/largeprojects/MICe/chammill/POND/civetOutputs/pond_2-1_20170227/088_0002_01_002/CBRAIN_Colosse-384672-1.params.yml")
)
tvt <-
civet_files_PND %>%
filter(Dx %in% c("CTRL", "ASD")) %>%
group_by(Dx) %>%
slice(1:10) %>%
ungroup
vlm <-
vertexLm(tvt$nativeRMS_RSLtlink_left ~ Dx, data = tvt)
left_surf <- read_obj("/hpf/largeprojects/MICe/chammill/packageSources/CIVET_2.0/CIVET_2.0_icbm_avg_mid_sym_mc_left.obj")
plot(left_surf, colour_map = vlm[,"tvalue-DxCTRL"])
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