Visualizing DBM results on Mouse Average

### visualizing results of mincLM model####
library(grid)
library(MRIcrotome)

#use the [pipeline-name]-nlin-3.mnc output file from your MBM run to display the results
anatFile <- "/data/chamal/projects/stephanie/Tau35-collab-Vernon/derivatives/mbm_20190910/TAU20190910_nlin/TAU20190910-nlin-3.mnc"
anatVol <- mincArray(mincGetVolume(anatFile))

tFDR5 = 2.4
tmax = 5.8

mincPlotSliceSeries(anatVol,
                    mincArray(mincLmModel, "tvalue-genotypeWT"),    # specify which column of the mincLM model you want to display
                    anatLow=700, anatHigh=1400,                     #intensity threshold of anatomical volume that you will be displaying the results on
                    low=tFDR5geno, high=tmaxgeno, symmetric = T,    # t score range; symmetric = T means show positive and negative t values
                    begin=25, end=-50,                              #slice sequence to display stats; starting at end (most anterior slice) and begin (most posterior slice)
                    legend="t-statistics")

For other ways to visualize the data, please see: https://htmlpreview.github.io/?https://github.com/Mouse-Imaging-Centre/MRIcrotome/blob/master/vignettes/figures.html