Intro to stats
Load the data and prepare the environment
First, read in the file that contains the description of all the scans in the irradiation study that we will be using as our example dataset.
gf <- read.csv("/hpf/largeprojects/MICe/jason/MISS2017/intro-stats/fixed_datatable_IRdose.csv")Take a look at the data in that file:
names(gf)## [1] "X" "MouseID" "Sex"
## [4] "Dose" "Litter" "Coil"
## [7] "ScanDate" "original_mnc" "Jacobfile_scaled"
## [10] "Jacobfile_scaled0.2" "Jacobfile_scaled0.5"The last three columns contain the filenames for the Jacobian determinants, either with or without blurring. Sex and Dose are the most interesting covariates here.
table(gf$Dose, gf$Sex)##
## F M
## 0 6 4
## 3 6 5
## 5 5 5
## 7 5 5So about 5 males and 5 females for each irradiation dose.
Exploring the highest dose data
Starting simple, let’s just look at a dose of 0 vs 7, for now.
d7vsd0 <- subset(gf, Dose %in% c(0, 7))
table(d7vsd0$Dose, d7vsd0$Sex)##
## F M
## 0 6 4
## 7 5 5To do further analyses and see the results, we need to load two more bits of data: the background non-linear average on which we will display results, and the labels for computing volumes.
library(RMINC)## Loading required package: BatchJobs## Loading required package: BBmisc## Sourcing configuration file: '/axiom2/projects/software/arch/linux-xenial-xerus/RMINC/1.5.0.0/BatchJobs/etc/BatchJobs_global_config.R'## BatchJobs configuration:
## cluster functions: Interactive
## mail.from:
## mail.to:
## mail.start: none
## mail.done: none
## mail.error: none
## default.resources:
## debug: FALSE
## raise.warnings: FALSE
## staged.queries: TRUE
## max.concurrent.jobs: Inf
## fs.timeout: NA## Sourcing configuration file: '/micehome/chammill/R/x86_64-pc-linux-gnu-library/3.3/RMINC/parallel/sge_BatchJobs.R'anatFile <- "/projects/moush/lbernas/Irradiation_behaviour_project/fixed_build_masked_23mar13_nlin/nlin-3.mnc"
labelFile <-
paste0("/hpf/largeprojects/MICe/jason/MISS2017/intro-stats/atlas-registration/"
, "pipeline-18-08-2017-at-07-08-48_processed/nlin-3/voted.mnc")
defsFile <-
paste0("/hpf/largeprojects/MICe/tools/atlases/"
, "Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/"
, "mappings/DSURQE_40micron_R_mapping.csv")Linear model at every voxel
vs <- mincLm(Jacobfile_scaled0.2 ~ Dose, d7vsd0, mask=labelFile)## Method: lm
## Number of volumes: 20
## Volume sizes: 152 320 225
## N: 20 P: 2
## In slice
## 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151
## DoneLet’s explore the data. First, get a sense of the background range for the anatomical volume, after reading it in, of course.
anatVolume <- mincArray(mincGetVolume(anatFile))
hist(anatVolume)
d7vsd0$DoseFactor <- as.factor(d7vsd0$Dose)
launch_shinyRMINC(vs, anatVolume, anatLow=9, anatHigh=15, plotcolumns = d7vsd0)And plot the data with an n of 41 in my sample.
mincPlotSliceSeries(anatVolume, mincArray(vs, "tvalue-Dose"), anatLow=9, anatHigh=15, low=2, high=7, symmetric=T, begin=50, end=-40, legend="t-statistic", plottitle = "Dose (7 vs 0 only)")
Now, use the False Discovery Rate to correct for multiple comparisons
qvs <- mincFDR(vs, mask=labelFile)##
## Computing FDR threshold for all columns
## Computing threshold for F-statistic
## Computing threshold for tvalue-(Intercept)
## Computing threshold for tvalue-DoseLet’s see the thresholds:
qvs## Multidimensional MINC volume
## Columns: F-statistic tvalue-(Intercept) tvalue-Dose
## [1] "/projects/moush/lbernas/Irradiation_behaviour_project/fixed_build_masked_23mar13_processed/fixed_03dec12.1.jan2011_distortion_corrected/stats-volumes/fixed_03dec12.1.jan2011_distortion_corrected-log-determinant-scaled-fwhm0.2.mnc"
## Degrees of Freedom: c(1, 18) 18 18
## FDR Thresholds:
## F-statistic tvalue-(Intercept) tvalue-Dose
## 0.01 20.662246 NA 4.545574
## 0.05 11.740098 6.539125 3.426383
## 0.1 8.367236 5.160173 2.892617
## 0.15 6.470188 4.248727 2.543657
## 0.2 5.170516 3.805525 2.273877And plot at that threshold
mincPlotSliceSeries(anatVolume, mincArray(vs, "tvalue-Dose"), anatLow=9, anatHigh=15, low=3.42, high=7, symmetric=T, begin=50, end=-40, legend="t-statistic", plottitle = "Dose (7 vs 0 only)")
Or plot the q values directly
mincPlotSliceSeries(anatVolume, -log10(mincArray(qvs, "tvalue-Dose")), anatLow=9, anatHigh=15, low=1.3, high=3, symmetric=F, begin=50, end=-40, legend="-log10 q value", plottitle = "Dose (7 vs 0 only)")
Or the same, but with direction added again:
mincPlotSliceSeries(anatVolume, -log10(mincArray(qvs, "tvalue-Dose"))*sign(mincArray(vs, "tvalue-Dose")), anatLow=9, anatHigh=15, low=1.3, high=3, symmetric=T, begin=50, end=-40, legend="log10 q value", plottitle = "Dose (7 vs 0 only)")
Linear model across volumes
Now compute the volumes. There are several ways of doing so; in this case, we’ll integrate the Jacobian determinants, since that is what we have for this particular pipeline. Takes a few minutes to run.
library(RMINC)
allvols <- anatGetAll(d7vsd0$Jacobfile_scaled, atlas=labelFile,
defs=defsFile,method="jacobians")And we have to put anatomy and hierarchical definitions together. This takes a few minutes to run
AllenDefs <- "/hpf/largeprojects/MICe/tools/atlases/Allen_Brain/Allen_hierarchy_definitions.json"
hdefs <- makeMICeDefsHierachical(defsFile, AllenDefs)Next, add the volumes from this dataset into the hierarchy.
hanatd7vsd0 <- addVolumesToHierarchy(hdefs, allvols)Run a simple linear model
hVs <- hanatLm(~Dose, d7vsd0, hanatd7vsd0)## N: 20 P: 2
## Beginning vertex loop: 590 3
## Done with vertex loophanatView(hVs, "tvalue.Dose", low=2, high=6, symmetric=T)Print them to the screen
print(hVs, "tvalue.Dose", limit=NULL)## levelName
## 1 root2
## 2 ¦--Basic cell groups and regions
## 3 ¦ ¦--Cerebrum
## 4 ¦ ¦ ¦--Cerebral cortex
## 5 ¦ ¦ ¦ ¦--Cortical subplate
## 6 ¦ ¦ ¦ ¦ ¦--Cortical subplate-other
## 7 ¦ ¦ ¦ ¦ ¦ ¦--left Cortical subplate-other
## 8 ¦ ¦ ¦ ¦ ¦ °--right Cortical subplate-other
## 9 ¦ ¦ ¦ ¦ ¦--Claustrum
## 10 ¦ ¦ ¦ ¦ ¦ ¦--Claustrum-other
## 11 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Claustrum-other
## 12 ¦ ¦ ¦ ¦ ¦ ¦ °--right Claustrum-other
## 13 ¦ ¦ ¦ ¦ ¦ ¦--Claustrum: dorsal part
## 14 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Claustrum: dorsal part
## 15 ¦ ¦ ¦ ¦ ¦ ¦ °--right Claustrum: dorsal part
## 16 ¦ ¦ ¦ ¦ ¦ °--Claustrum: ventral part
## 17 ¦ ¦ ¦ ¦ ¦ ¦--left Claustrum: ventral part
## 18 ¦ ¦ ¦ ¦ ¦ °--right Claustrum: ventral part
## 19 ¦ ¦ ¦ ¦ °--Endopiriform nucleus
## 20 ¦ ¦ ¦ ¦ ¦--Endopiriform nucleus, dorsal part
## 21 ¦ ¦ ¦ ¦ ¦ ¦--Dorsal nucleus of the endopiriform
## 22 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Dorsal nucleus of the endopiriform
## 23 ¦ ¦ ¦ ¦ ¦ ¦ °--right Dorsal nucleus of the endopiriform
## 24 ¦ ¦ ¦ ¦ ¦ °--Intermediate nucleus of the endopiriform claustrum
## 25 ¦ ¦ ¦ ¦ ¦ ¦--left Intermediate nucleus of the endopiriform claustrum
## 26 ¦ ¦ ¦ ¦ ¦ °--right Intermediate nucleus of the endopiriform claustrum
## 27 ¦ ¦ ¦ ¦ °--Endopiriform nucleus, ventral part
## 28 ¦ ¦ ¦ ¦ ¦--left Endopiriform nucleus, ventral part
## 29 ¦ ¦ ¦ ¦ °--right Endopiriform nucleus, ventral part
## 30 ¦ ¦ ¦ °--Cortical plate
## 31 ¦ ¦ ¦ ¦--Olfactory areas
## 32 ¦ ¦ ¦ ¦ ¦--Olfactory areas-other
## 33 ¦ ¦ ¦ ¦ ¦ ¦--left Olfactory areas-other
## 34 ¦ ¦ ¦ ¦ ¦ °--right Olfactory areas-other
## 35 ¦ ¦ ¦ ¦ ¦--Postpiriform transition area
## 36 ¦ ¦ ¦ ¦ ¦ ¦--left Postpiriform transition area
## 37 ¦ ¦ ¦ ¦ ¦ °--right Postpiriform transition area
## 38 ¦ ¦ ¦ ¦ ¦--Piriform area
## 39 ¦ ¦ ¦ ¦ ¦ ¦--Cortex-amygdala transition zones
## 40 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Cortex-amygdala transition zones
## 41 ¦ ¦ ¦ ¦ ¦ ¦ °--right Cortex-amygdala transition zones
## 42 ¦ ¦ ¦ ¦ ¦ °--Piriform cortex
## 43 ¦ ¦ ¦ ¦ ¦ ¦--left Piriform cortex
## 44 ¦ ¦ ¦ ¦ ¦ °--right Piriform cortex
## 45 ¦ ¦ ¦ ¦ ¦--Taenia tecta
## 46 ¦ ¦ ¦ ¦ ¦ ¦--Taenia tecta, dorsal part
## 47 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Taenia tecta, dorsal part
## 48 ¦ ¦ ¦ ¦ ¦ ¦ °--right Taenia tecta, dorsal part
## 49 ¦ ¦ ¦ ¦ ¦ °--Taenia tecta, ventral part
## 50 ¦ ¦ ¦ ¦ ¦ ¦--left Taenia tecta, ventral part
## 51 ¦ ¦ ¦ ¦ ¦ °--right Taenia tecta, ventral part
## 52 ¦ ¦ ¦ ¦ ¦--Cortical amygdalar area
## 53 ¦ ¦ ¦ ¦ ¦ °--Cortical amygdalar area, posterior part
## 54 ¦ ¦ ¦ ¦ ¦ ¦--Cortical amygdalar area, posterior part, lateral zone
## 55 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Cortical amygdalar area, posterior part, lateral zone
## 56 ¦ ¦ ¦ ¦ ¦ ¦ °--right Cortical amygdalar area, posterior part, lateral zone
## 57 ¦ ¦ ¦ ¦ ¦ °--Cortical amygdalar area, posterior part, medial zone
## 58 ¦ ¦ ¦ ¦ ¦ ¦--left Cortical amygdalar area, posterior part, medial zone
## 59 ¦ ¦ ¦ ¦ ¦ °--right Cortical amygdalar area, posterior part, medial zone
## 60 ¦ ¦ ¦ ¦ ¦--Piriform-amygdalar area
## 61 ¦ ¦ ¦ ¦ ¦ ¦--left Piriform-amygdalar area
## 62 ¦ ¦ ¦ ¦ ¦ °--right Piriform-amygdalar area
## 63 ¦ ¦ ¦ ¦ ¦--Main olfactory bulb
## 64 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, glomerular layer
## 65 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Main olfactory bulb, glomerular layer
## 66 ¦ ¦ ¦ ¦ ¦ ¦ °--right Main olfactory bulb, glomerular layer
## 67 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, outer plexiform layer
## 68 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Main olfactory bulb, outer plexiform layer
## 69 ¦ ¦ ¦ ¦ ¦ ¦ °--right Main olfactory bulb, outer plexiform layer
## 70 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, mitral layer
## 71 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Main olfactory bulb, mitral layer
## 72 ¦ ¦ ¦ ¦ ¦ ¦ °--right Main olfactory bulb, mitral layer
## 73 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, inner plexiform layer
## 74 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Main olfactory bulb, inner plexiform layer
## 75 ¦ ¦ ¦ ¦ ¦ ¦ °--right Main olfactory bulb, inner plexiform layer
## 76 ¦ ¦ ¦ ¦ ¦ °--Main olfactory bulb, granule layer
## 77 ¦ ¦ ¦ ¦ ¦ ¦--left Main olfactory bulb, granule layer
## 78 ¦ ¦ ¦ ¦ ¦ °--right Main olfactory bulb, granule layer
## 79 ¦ ¦ ¦ ¦ ¦--Accessory olfactory bulb
## 80 ¦ ¦ ¦ ¦ ¦ ¦--Accessory olfactory bulb, glomerular layer
## 81 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Accessory olfactory bulb, glomerular layer
## 82 ¦ ¦ ¦ ¦ ¦ ¦ °--right Accessory olfactory bulb, glomerular layer
## 83 ¦ ¦ ¦ ¦ ¦ °--Accessory olfactory bulb, granular layer
## 84 ¦ ¦ ¦ ¦ ¦ ¦--left Accessory olfactory bulb, granular layer
## 85 ¦ ¦ ¦ ¦ ¦ °--right Accessory olfactory bulb, granular layer
## 86 ¦ ¦ ¦ ¦ °--Anterior olfactory nucleus
## 87 ¦ ¦ ¦ ¦ ¦--left Anterior olfactory nucleus
## 88 ¦ ¦ ¦ ¦ °--right Anterior olfactory nucleus
## 89 ¦ ¦ ¦ ¦--Hippocampal formation
## 90 ¦ ¦ ¦ ¦ ¦--Retrohippocampal region
## 91 ¦ ¦ ¦ ¦ ¦ ¦--Subiculum
## 92 ¦ ¦ ¦ ¦ ¦ ¦ ¦--pre-para subiculum
## 93 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left pre-para subiculum
## 94 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right pre-para subiculum
## 95 ¦ ¦ ¦ ¦ ¦ ¦ °--subiculum
## 96 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left subiculum
## 97 ¦ ¦ ¦ ¦ ¦ ¦ °--right subiculum
## 98 ¦ ¦ ¦ ¦ ¦ °--Entorhinal area
## 99 ¦ ¦ ¦ ¦ ¦ ¦--Entorhinal area, medial part, dorsal zone
## 100 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Entorhinal area, medial part, dorsal zone
## 101 ¦ ¦ ¦ ¦ ¦ ¦ °--right Entorhinal area, medial part, dorsal zone
## 102 ¦ ¦ ¦ ¦ ¦ ¦--Entorhinal area, lateral part
## 103 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Dorsal intermediate entorhinal cortex
## 104 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Dorsal intermediate entorhinal cortex
## 105 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Dorsal intermediate entorhinal cortex
## 106 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Dorsolateral entorhinal cortex
## 107 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Dorsolateral entorhinal cortex
## 108 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Dorsolateral entorhinal cortex
## 109 ¦ ¦ ¦ ¦ ¦ ¦ °--Ventral intermediate entorhinal cortex
## 110 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Ventral intermediate entorhinal cortex
## 111 ¦ ¦ ¦ ¦ ¦ ¦ °--right Ventral intermediate entorhinal cortex
## 112 ¦ ¦ ¦ ¦ ¦ °--Entorhinal area, medial part, ventral zone
## 113 ¦ ¦ ¦ ¦ ¦ ¦--left Entorhinal area, medial part, ventral zone
## 114 ¦ ¦ ¦ ¦ ¦ °--right Entorhinal area, medial part, ventral zone
## 115 ¦ ¦ ¦ ¦ °--Hippocampal region
## 116 ¦ ¦ ¦ ¦ ¦--Ammon's horn
## 117 ¦ ¦ ¦ ¦ ¦ ¦--Field CA1
## 118 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA1, stratum oriens
## 119 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA1, stratum oriens
## 120 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA1, stratum oriens
## 121 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA1, stratum lacunosum-moleculare
## 122 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA1, stratum lacunosum-moleculare
## 123 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA1, stratum lacunosum-moleculare
## 124 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA1, stratum radiatum
## 125 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA1, stratum radiatum
## 126 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA1, stratum radiatum
## 127 ¦ ¦ ¦ ¦ ¦ ¦ °--Field CA1, pyramidal layer
## 128 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA1, pyramidal layer
## 129 ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA1, pyramidal layer
## 130 ¦ ¦ ¦ ¦ ¦ ¦--Field CA2
## 131 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA2, pyramidal layer
## 132 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA2, pyramidal layer
## 133 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA2, pyramidal layer
## 134 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA2, stratum oriens
## 135 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA2, stratum oriens
## 136 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA2, stratum oriens
## 137 ¦ ¦ ¦ ¦ ¦ ¦ °--Field CA2, stratum radiatum
## 138 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA2, stratum radiatum
## 139 ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA2, stratum radiatum
## 140 ¦ ¦ ¦ ¦ ¦ °--Field CA3
## 141 ¦ ¦ ¦ ¦ ¦ ¦--Field CA3, pyramidal layer
## 142 ¦ ¦ ¦ ¦ ¦ ¦ ¦--CA3Py Inner
## 143 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left CA3Py Inner
## 144 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right CA3Py Inner
## 145 ¦ ¦ ¦ ¦ ¦ ¦ °--CA3Py Outer
## 146 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left CA3Py Outer
## 147 ¦ ¦ ¦ ¦ ¦ ¦ °--right CA3Py Outer
## 148 ¦ ¦ ¦ ¦ ¦ ¦--Field CA3, stratum oriens
## 149 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA3, stratum oriens
## 150 ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA3, stratum oriens
## 151 ¦ ¦ ¦ ¦ ¦ ¦--Field CA3, stratum radiatum
## 152 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Field CA3, stratum radiatum
## 153 ¦ ¦ ¦ ¦ ¦ ¦ °--right Field CA3, stratum radiatum
## 154 ¦ ¦ ¦ ¦ ¦ °--Field CA3, stratum lucidum
## 155 ¦ ¦ ¦ ¦ ¦ ¦--left Field CA3, stratum lucidum
## 156 ¦ ¦ ¦ ¦ ¦ °--right Field CA3, stratum lucidum
## 157 ¦ ¦ ¦ ¦ °--Dentate gyrus
## 158 ¦ ¦ ¦ ¦ ¦--Dentate gyrus, molecular layer
## 159 ¦ ¦ ¦ ¦ ¦ ¦--left Dentate gyrus, molecular layer
## 160 ¦ ¦ ¦ ¦ ¦ °--right Dentate gyrus, molecular layer
## 161 ¦ ¦ ¦ ¦ °--Dentate gyrus, granule cell layer
## 162 ¦ ¦ ¦ ¦ ¦--GrDG
## 163 ¦ ¦ ¦ ¦ ¦ ¦--left GrDG
## 164 ¦ ¦ ¦ ¦ ¦ °--right GrDG
## 165 ¦ ¦ ¦ ¦ °--PoDG
## 166 ¦ ¦ ¦ ¦ ¦--left PoDG
## 167 ¦ ¦ ¦ ¦ °--right PoDG
## 168 ¦ ¦ ¦ °--Isocortex
## 169 ¦ ¦ ¦ ¦--Anterior cingulate area
## 170 ¦ ¦ ¦ ¦ ¦--Anterior cingulate area, ventral part
## 171 ¦ ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 24a
## 172 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 24a
## 173 ¦ ¦ ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 24a
## 174 ¦ ¦ ¦ ¦ ¦ °--Cingulate cortex: area 24a'
## 175 ¦ ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 24a'
## 176 ¦ ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 24a'
## 177 ¦ ¦ ¦ ¦ °--Anterior cingulate area, dorsal part
## 178 ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 24b
## 179 ¦ ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 24b
## 180 ¦ ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 24b
## 181 ¦ ¦ ¦ ¦ °--Cingulate cortex: area 24b'
## 182 ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 24b'
## 183 ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 24b'
## 184 ¦ ¦ ¦ ¦--Infralimbic area
## 185 ¦ ¦ ¦ ¦ ¦--left Infralimbic area
## 186 ¦ ¦ ¦ ¦ °--right Infralimbic area
## 187 ¦ ¦ ¦ ¦--Retrosplenial area
## 188 ¦ ¦ ¦ ¦ ¦--Retrosplenial area, ventral part
## 189 ¦ ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 29a
## 190 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 29a
## 191 ¦ ¦ ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 29a
## 192 ¦ ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 29b
## 193 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 29b
## 194 ¦ ¦ ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 29b
## 195 ¦ ¦ ¦ ¦ ¦ °--Cingulate cortex: area 29c
## 196 ¦ ¦ ¦ ¦ ¦ ¦--left Cingulate cortex: area 29c
## 197 ¦ ¦ ¦ ¦ ¦ °--right Cingulate cortex: area 29c
## 198 ¦ ¦ ¦ ¦ °--Retrosplenial area, dorsal part
## 199 ¦ ¦ ¦ ¦ ¦--left Retrosplenial area, dorsal part
## 200 ¦ ¦ ¦ ¦ °--right Retrosplenial area, dorsal part
## 201 ¦ ¦ ¦ ¦--Prelimbic area
## 202 ¦ ¦ ¦ ¦ ¦--left Prelimbic area
## 203 ¦ ¦ ¦ ¦ °--right Prelimbic area
## 204 ¦ ¦ ¦ ¦--Auditory areas
## 205 ¦ ¦ ¦ ¦ ¦--Primary auditory area
## 206 ¦ ¦ ¦ ¦ ¦ ¦--left Primary auditory area
## 207 ¦ ¦ ¦ ¦ ¦ °--right Primary auditory area
## 208 ¦ ¦ ¦ ¦ ¦--Dorsal auditory area
## 209 ¦ ¦ ¦ ¦ ¦ ¦--left Dorsal auditory area
## 210 ¦ ¦ ¦ ¦ ¦ °--right Dorsal auditory area
## 211 ¦ ¦ ¦ ¦ °--Ventral auditory area
## 212 ¦ ¦ ¦ ¦ ¦--left Ventral auditory area
## 213 ¦ ¦ ¦ ¦ °--right Ventral auditory area
## 214 ¦ ¦ ¦ ¦--Agranular insular area
## 215 ¦ ¦ ¦ ¦ °--Agranular insular area, dorsal part
## 216 ¦ ¦ ¦ ¦ ¦--left Agranular insular area, dorsal part
## 217 ¦ ¦ ¦ ¦ °--right Agranular insular area, dorsal part
## 218 ¦ ¦ ¦ ¦--Ectorhinal area
## 219 ¦ ¦ ¦ ¦ ¦--Ectorhinal cortex
## 220 ¦ ¦ ¦ ¦ ¦ ¦--left Ectorhinal cortex
## 221 ¦ ¦ ¦ ¦ ¦ °--right Ectorhinal cortex
## 222 ¦ ¦ ¦ ¦ °--Insular region: not subdivided
## 223 ¦ ¦ ¦ ¦ ¦--left Insular region: not subdivided
## 224 ¦ ¦ ¦ ¦ °--right Insular region: not subdivided
## 225 ¦ ¦ ¦ ¦--Somatomotor areas
## 226 ¦ ¦ ¦ ¦ ¦--Primary motor area
## 227 ¦ ¦ ¦ ¦ ¦ ¦--Frontal cortex: area 3
## 228 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Frontal cortex: area 3
## 229 ¦ ¦ ¦ ¦ ¦ ¦ °--right Frontal cortex: area 3
## 230 ¦ ¦ ¦ ¦ ¦ °--Primary motor cortex
## 231 ¦ ¦ ¦ ¦ ¦ ¦--left Primary motor cortex
## 232 ¦ ¦ ¦ ¦ ¦ °--right Primary motor cortex
## 233 ¦ ¦ ¦ ¦ °--Secondary motor area
## 234 ¦ ¦ ¦ ¦ ¦--left Secondary motor area
## 235 ¦ ¦ ¦ ¦ °--right Secondary motor area
## 236 ¦ ¦ ¦ ¦--Frontal pole, cerebral cortex
## 237 ¦ ¦ ¦ ¦ ¦--left Frontal pole, cerebral cortex
## 238 ¦ ¦ ¦ ¦ °--right Frontal pole, cerebral cortex
## 239 ¦ ¦ ¦ ¦--Orbital area
## 240 ¦ ¦ ¦ ¦ ¦--Orbital area, lateral part
## 241 ¦ ¦ ¦ ¦ ¦ ¦--left Orbital area, lateral part
## 242 ¦ ¦ ¦ ¦ ¦ °--right Orbital area, lateral part
## 243 ¦ ¦ ¦ ¦ ¦--Orbital area, medial part
## 244 ¦ ¦ ¦ ¦ ¦ ¦--left Orbital area, medial part
## 245 ¦ ¦ ¦ ¦ ¦ °--right Orbital area, medial part
## 246 ¦ ¦ ¦ ¦ °--Orbital area, ventrolateral part
## 247 ¦ ¦ ¦ ¦ ¦--left Orbital area, ventrolateral part
## 248 ¦ ¦ ¦ ¦ °--right Orbital area, ventrolateral part
## 249 ¦ ¦ ¦ ¦--Posterior parietal association areas
## 250 ¦ ¦ ¦ ¦ ¦--Lateral parietal association cortex
## 251 ¦ ¦ ¦ ¦ ¦ ¦--left Lateral parietal association cortex
## 252 ¦ ¦ ¦ ¦ ¦ °--right Lateral parietal association cortex
## 253 ¦ ¦ ¦ ¦ ¦--Medial parietal association cortex
## 254 ¦ ¦ ¦ ¦ ¦ ¦--left Medial parietal association cortex
## 255 ¦ ¦ ¦ ¦ ¦ °--right Medial parietal association cortex
## 256 ¦ ¦ ¦ ¦ ¦--Parietal cortex: posterior area: rostral part
## 257 ¦ ¦ ¦ ¦ ¦ ¦--left Parietal cortex: posterior area: rostral part
## 258 ¦ ¦ ¦ ¦ ¦ °--right Parietal cortex: posterior area: rostral part
## 259 ¦ ¦ ¦ ¦ °--Secondary visual cortex: mediomedial area
## 260 ¦ ¦ ¦ ¦ ¦--left Secondary visual cortex: mediomedial area
## 261 ¦ ¦ ¦ ¦ °--right Secondary visual cortex: mediomedial area
## 262 ¦ ¦ ¦ ¦--Perirhinal area
## 263 ¦ ¦ ¦ ¦ ¦--left Perirhinal area
## 264 ¦ ¦ ¦ ¦ °--right Perirhinal area
## 265 ¦ ¦ ¦ ¦--Somatosensory areas
## 266 ¦ ¦ ¦ ¦ ¦--Primary somatosensory area
## 267 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area-other
## 268 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory area-other
## 269 ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory area-other
## 270 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, barrel field
## 271 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory area, barrel field
## 272 ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory area, barrel field
## 273 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, trunk
## 274 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory cortex: dysgranular zone
## 275 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory cortex: dysgranular zone
## 276 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory cortex: dysgranular zone
## 277 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory cortex: shoulder region
## 278 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory cortex: shoulder region
## 279 ¦ ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory cortex: shoulder region
## 280 ¦ ¦ ¦ ¦ ¦ ¦ °--Primary somatosensory cortex: trunk region
## 281 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory cortex: trunk region
## 282 ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory cortex: trunk region
## 283 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, upper limb
## 284 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory area, upper limb
## 285 ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory area, upper limb
## 286 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, lower limb
## 287 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory area, lower limb
## 288 ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory area, lower limb
## 289 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, mouth
## 290 ¦ ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory area, mouth
## 291 ¦ ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory area, mouth
## 292 ¦ ¦ ¦ ¦ ¦ °--Primary somatosensory area, nose
## 293 ¦ ¦ ¦ ¦ ¦ ¦--left Primary somatosensory area, nose
## 294 ¦ ¦ ¦ ¦ ¦ °--right Primary somatosensory area, nose
## 295 ¦ ¦ ¦ ¦ °--Supplemental somatosensory area
## 296 ¦ ¦ ¦ ¦ ¦--left Supplemental somatosensory area
## 297 ¦ ¦ ¦ ¦ °--right Supplemental somatosensory area
## 298 ¦ ¦ ¦ ¦--Temporal association areas
## 299 ¦ ¦ ¦ ¦ ¦--left Temporal association areas
## 300 ¦ ¦ ¦ ¦ °--right Temporal association areas
## 301 ¦ ¦ ¦ °--Visual areas
## 302 ¦ ¦ ¦ ¦--Primary visual area
## 303 ¦ ¦ ¦ ¦ ¦--left Primary visual area
## 304 ¦ ¦ ¦ ¦ °--right Primary visual area
## 305 ¦ ¦ ¦ ¦--Lateral visual area
## 306 ¦ ¦ ¦ ¦ ¦--left Lateral visual area
## 307 ¦ ¦ ¦ ¦ °--right Lateral visual area
## 308 ¦ ¦ ¦ ¦--posteromedial visual area
## 309 ¦ ¦ ¦ ¦ ¦--left posteromedial visual area
## 310 ¦ ¦ ¦ ¦ °--right posteromedial visual area
## 311 ¦ ¦ ¦ ¦--Anterolateral visual area
## 312 ¦ ¦ ¦ ¦ ¦--left Anterolateral visual area
## 313 ¦ ¦ ¦ ¦ °--right Anterolateral visual area
## 314 ¦ ¦ ¦ °--Anteromedial visual area
## 315 ¦ ¦ ¦ ¦--left Anteromedial visual area
## 316 ¦ ¦ ¦ °--right Anteromedial visual area
## 317 ¦ ¦ °--Cerebral nuclei
## 318 ¦ ¦ ¦--Pallidum
## 319 ¦ ¦ ¦ ¦--Pallidum, ventral region
## 320 ¦ ¦ ¦ ¦ ¦--left Pallidum, ventral region
## 321 ¦ ¦ ¦ ¦ °--right Pallidum, ventral region
## 322 ¦ ¦ ¦ ¦--Pallidum, caudal region
## 323 ¦ ¦ ¦ ¦ °--Bed nuclei of the stria terminalis
## 324 ¦ ¦ ¦ ¦ ¦--left Bed nuclei of the stria terminalis
## 325 ¦ ¦ ¦ ¦ °--right Bed nuclei of the stria terminalis
## 326 ¦ ¦ ¦ ¦--Pallidum, dorsal region
## 327 ¦ ¦ ¦ ¦ ¦--left Pallidum, dorsal region
## 328 ¦ ¦ ¦ ¦ °--right Pallidum, dorsal region
## 329 ¦ ¦ ¦ °--Pallidum, medial region
## 330 ¦ ¦ ¦ °--Medial septal complex
## 331 ¦ ¦ ¦ ¦--left Medial septal complex
## 332 ¦ ¦ ¦ °--right Medial septal complex
## 333 ¦ ¦ °--Striatum
## 334 ¦ ¦ ¦--Striatum ventral region
## 335 ¦ ¦ ¦ ¦--Fundus of striatum
## 336 ¦ ¦ ¦ ¦ ¦--left Fundus of striatum
## 337 ¦ ¦ ¦ ¦ °--right Fundus of striatum
## 338 ¦ ¦ ¦ ¦--Nucleus accumbens
## 339 ¦ ¦ ¦ ¦ ¦--left Nucleus accumbens
## 340 ¦ ¦ ¦ ¦ °--right Nucleus accumbens
## 341 ¦ ¦ ¦ °--Olfactory tubercle
## 342 ¦ ¦ ¦ ¦--left Olfactory tubercle
## 343 ¦ ¦ ¦ °--right Olfactory tubercle
## 344 ¦ ¦ ¦--Lateral septal complex
## 345 ¦ ¦ ¦ ¦--left Lateral septal complex
## 346 ¦ ¦ ¦ °--right Lateral septal complex
## 347 ¦ ¦ ¦--Striatum dorsal region
## 348 ¦ ¦ ¦ °--Caudoputamen
## 349 ¦ ¦ ¦ ¦--left Caudoputamen
## 350 ¦ ¦ ¦ °--right Caudoputamen
## 351 ¦ ¦ °--Striatum-like amygdalar nuclei
## 352 ¦ ¦ °--Medial amygdalar nucleus
## 353 ¦ ¦ ¦--left Medial amygdalar nucleus
## 354 ¦ ¦ °--right Medial amygdalar nucleus
## 355 ¦ ¦--Brain stem
## 356 ¦ ¦ ¦--Midbrain
## 357 ¦ ¦ ¦ ¦--Midbrain, sensory related
## 358 ¦ ¦ ¦ ¦ ¦--Inferior colliculus
## 359 ¦ ¦ ¦ ¦ ¦ ¦--left Inferior colliculus
## 360 ¦ ¦ ¦ ¦ ¦ °--right Inferior colliculus
## 361 ¦ ¦ ¦ ¦ °--Superior colliculus, sensory related
## 362 ¦ ¦ ¦ ¦ ¦--left Superior colliculus, sensory related
## 363 ¦ ¦ ¦ ¦ °--right Superior colliculus, sensory related
## 364 ¦ ¦ ¦ ¦--Midbrain, behavioral state related
## 365 ¦ ¦ ¦ ¦ °--Midbrain raphe nuclei
## 366 ¦ ¦ ¦ ¦ °--Interpeduncular nucleus
## 367 ¦ ¦ ¦ ¦--Midbrain-other
## 368 ¦ ¦ ¦ °--Midbrain, motor related
## 369 ¦ ¦ ¦ °--Periaqueductal gray
## 370 ¦ ¦ ¦--Hindbrain
## 371 ¦ ¦ ¦ ¦--Medulla
## 372 ¦ ¦ ¦ ¦ ¦--Medulla, sensory related
## 373 ¦ ¦ ¦ ¦ ¦ °--Dorsal column nuclei
## 374 ¦ ¦ ¦ ¦ ¦ °--Cuneate nucleus
## 375 ¦ ¦ ¦ ¦ ¦ ¦--left Cuneate nucleus
## 376 ¦ ¦ ¦ ¦ ¦ °--right Cuneate nucleus
## 377 ¦ ¦ ¦ ¦ ¦--Medulla, motor related
## 378 ¦ ¦ ¦ ¦ ¦ °--Inferior olivary complex
## 379 ¦ ¦ ¦ ¦ ¦ ¦--left Inferior olivary complex
## 380 ¦ ¦ ¦ ¦ ¦ °--right Inferior olivary complex
## 381 ¦ ¦ ¦ ¦ °--Medulla-other
## 382 ¦ ¦ ¦ °--Pons
## 383 ¦ ¦ ¦ ¦--Pons-other
## 384 ¦ ¦ ¦ ¦--Pons, behavioral state related
## 385 ¦ ¦ ¦ ¦ °--Pontine reticular nucleus
## 386 ¦ ¦ ¦ ¦ ¦--left Pontine reticular nucleus
## 387 ¦ ¦ ¦ ¦ °--right Pontine reticular nucleus
## 388 ¦ ¦ ¦ °--Pons, sensory related
## 389 ¦ ¦ ¦ °--Superior olivary complex
## 390 ¦ ¦ ¦ ¦--left Superior olivary complex
## 391 ¦ ¦ ¦ °--right Superior olivary complex
## 392 ¦ ¦ °--Interbrain
## 393 ¦ ¦ ¦--Hypothalamus
## 394 ¦ ¦ ¦ ¦--Hypothalamus-other
## 395 ¦ ¦ ¦ ¦ ¦--left Hypothalamus-other
## 396 ¦ ¦ ¦ ¦ °--right Hypothalamus-other
## 397 ¦ ¦ ¦ °--Hypothalamic medial zone
## 398 ¦ ¦ ¦ ¦--Mammillary body
## 399 ¦ ¦ ¦ ¦ ¦--left Mammillary body
## 400 ¦ ¦ ¦ ¦ °--right Mammillary body
## 401 ¦ ¦ ¦ °--Medial preoptic nucleus
## 402 ¦ ¦ ¦ ¦--left Medial preoptic nucleus
## 403 ¦ ¦ ¦ °--right Medial preoptic nucleus
## 404 ¦ ¦ °--Thalamus
## 405 ¦ ¦ ¦--left Thalamus
## 406 ¦ ¦ °--right Thalamus
## 407 ¦ °--Cerebellum
## 408 ¦ ¦--Cerebellar cortex
## 409 ¦ ¦ ¦--Vermal regions
## 410 ¦ ¦ ¦ ¦--Lingula (I)
## 411 ¦ ¦ ¦ ¦--Central lobule
## 412 ¦ ¦ ¦ ¦--Culmen
## 413 ¦ ¦ ¦ ¦ ¦--Culmen-other
## 414 ¦ ¦ ¦ ¦ °--Lobules IV-V
## 415 ¦ ¦ ¦ ¦ ¦--left Lobules IV-V
## 416 ¦ ¦ ¦ ¦ °--right Lobules IV-V
## 417 ¦ ¦ ¦ ¦--Declive (VI)
## 418 ¦ ¦ ¦ ¦--Folium-tuber vermis (VII)
## 419 ¦ ¦ ¦ ¦--Pyramus (VIII)
## 420 ¦ ¦ ¦ ¦--Uvula (IX)
## 421 ¦ ¦ ¦ °--Nodulus (X)
## 422 ¦ ¦ °--Hemispheric regions
## 423 ¦ ¦ ¦--Simple lobule
## 424 ¦ ¦ ¦ ¦--left Simple lobule
## 425 ¦ ¦ ¦ °--right Simple lobule
## 426 ¦ ¦ ¦--Ansiform lobule
## 427 ¦ ¦ ¦ ¦--Crus 1
## 428 ¦ ¦ ¦ ¦ ¦--left Crus 1
## 429 ¦ ¦ ¦ ¦ °--right Crus 1
## 430 ¦ ¦ ¦ °--Crus 2
## 431 ¦ ¦ ¦ ¦--left Crus 2
## 432 ¦ ¦ ¦ °--right Crus 2
## 433 ¦ ¦ ¦--Paramedian lobule
## 434 ¦ ¦ ¦ ¦--left Paramedian lobule
## 435 ¦ ¦ ¦ °--right Paramedian lobule
## 436 ¦ ¦ ¦--Copula pyramidis
## 437 ¦ ¦ ¦ ¦--left Copula pyramidis
## 438 ¦ ¦ ¦ °--right Copula pyramidis
## 439 ¦ ¦ ¦--Flocculus
## 440 ¦ ¦ ¦ ¦--left Flocculus
## 441 ¦ ¦ ¦ °--right Flocculus
## 442 ¦ ¦ °--Paraflocculus
## 443 ¦ ¦ ¦--left Paraflocculus
## 444 ¦ ¦ °--right Paraflocculus
## 445 ¦ °--Cerebellar nuclei
## 446 ¦ ¦--Dentate nucleus
## 447 ¦ ¦ ¦--left Dentate nucleus
## 448 ¦ ¦ °--right Dentate nucleus
## 449 ¦ ¦--Interposed nucleus
## 450 ¦ ¦ ¦--left Interposed nucleus
## 451 ¦ ¦ °--right Interposed nucleus
## 452 ¦ °--Fastigial nucleus
## 453 ¦ ¦--left Fastigial nucleus
## 454 ¦ °--right Fastigial nucleus
## 455 ¦--fiber tracts
## 456 ¦ ¦--cranial nerves
## 457 ¦ ¦ ¦--olfactory nerve
## 458 ¦ ¦ ¦ ¦--anterior commissure, olfactory limb
## 459 ¦ ¦ ¦ ¦ ¦--left anterior commissure, olfactory limb
## 460 ¦ ¦ ¦ ¦ °--right anterior commissure, olfactory limb
## 461 ¦ ¦ ¦ °--lateral olfactory tract, general
## 462 ¦ ¦ ¦ ¦--left lateral olfactory tract, general
## 463 ¦ ¦ ¦ °--right lateral olfactory tract, general
## 464 ¦ ¦ ¦--facial nerve
## 465 ¦ ¦ ¦ ¦--left facial nerve
## 466 ¦ ¦ ¦ °--right facial nerve
## 467 ¦ ¦ ¦--dorsal roots
## 468 ¦ ¦ ¦ °--cervicothalamic tract
## 469 ¦ ¦ ¦ °--medial lemniscus
## 470 ¦ ¦ ¦ ¦--left medial lemniscus
## 471 ¦ ¦ ¦ °--right medial lemniscus
## 472 ¦ ¦ ¦--optic nerve
## 473 ¦ ¦ ¦ °--optic tract
## 474 ¦ ¦ ¦ ¦--left optic tract
## 475 ¦ ¦ ¦ °--right optic tract
## 476 ¦ ¦ °--oculomotor nerve
## 477 ¦ ¦ °--posterior commissure
## 478 ¦ ¦--medial forebrain bundle system
## 479 ¦ ¦ ¦--cerebrum related
## 480 ¦ ¦ ¦ ¦--anterior commissure, temporal limb
## 481 ¦ ¦ ¦ ¦ ¦--left anterior commissure, temporal limb
## 482 ¦ ¦ ¦ ¦ °--right anterior commissure, temporal limb
## 483 ¦ ¦ ¦ ¦--fornix system
## 484 ¦ ¦ ¦ ¦ ¦--fimbria
## 485 ¦ ¦ ¦ ¦ ¦ ¦--left fimbria
## 486 ¦ ¦ ¦ ¦ ¦ °--right fimbria
## 487 ¦ ¦ ¦ ¦ °--dorsal fornix
## 488 ¦ ¦ ¦ ¦ ¦--left dorsal fornix
## 489 ¦ ¦ ¦ ¦ °--right dorsal fornix
## 490 ¦ ¦ ¦ ¦--stria terminalis
## 491 ¦ ¦ ¦ ¦ ¦--left stria terminalis
## 492 ¦ ¦ ¦ ¦ °--right stria terminalis
## 493 ¦ ¦ ¦ °--cingulum bundle
## 494 ¦ ¦ ¦ ¦--left cingulum bundle
## 495 ¦ ¦ ¦ °--right cingulum bundle
## 496 ¦ ¦ °--hypothalamus related
## 497 ¦ ¦ ¦--epithalamus related
## 498 ¦ ¦ ¦ ¦--fasciculus retroflexus
## 499 ¦ ¦ ¦ ¦ ¦--left fasciculus retroflexus
## 500 ¦ ¦ ¦ ¦ °--right fasciculus retroflexus
## 501 ¦ ¦ ¦ ¦--habenular commissure
## 502 ¦ ¦ ¦ ¦ ¦--left habenular commissure
## 503 ¦ ¦ ¦ ¦ °--right habenular commissure
## 504 ¦ ¦ ¦ °--stria medullaris
## 505 ¦ ¦ ¦ ¦--left stria medullaris
## 506 ¦ ¦ ¦ °--right stria medullaris
## 507 ¦ ¦ °--mammillary related
## 508 ¦ ¦ °--mammilothalmic tract
## 509 ¦ ¦ ¦--left mammilothalmic tract
## 510 ¦ ¦ °--right mammilothalmic tract
## 511 ¦ ¦--cerebellum related fiber tracts
## 512 ¦ ¦ ¦--cerebellar peduncles
## 513 ¦ ¦ ¦ ¦--inferior cerebellar peduncle
## 514 ¦ ¦ ¦ ¦ ¦--left inferior cerebellar peduncle
## 515 ¦ ¦ ¦ ¦ °--right inferior cerebellar peduncle
## 516 ¦ ¦ ¦ ¦--middle cerebellar peduncle
## 517 ¦ ¦ ¦ ¦ ¦--left middle cerebellar peduncle
## 518 ¦ ¦ ¦ ¦ °--right middle cerebellar peduncle
## 519 ¦ ¦ ¦ °--superior cerebelar peduncles
## 520 ¦ ¦ ¦ ¦--left superior cerebelar peduncles
## 521 ¦ ¦ ¦ °--right superior cerebelar peduncles
## 522 ¦ ¦ °--arbor vitae
## 523 ¦ ¦ ¦--trunk of arbor vita
## 524 ¦ ¦ ¦--lobule 1-2 white matter
## 525 ¦ ¦ ¦--lobule 3 white matter
## 526 ¦ ¦ ¦--trunk of lobules 1-3 white matter
## 527 ¦ ¦ ¦--lobules 4-5 white matter
## 528 ¦ ¦ ¦--lobules 6-7 white matter
## 529 ¦ ¦ ¦--lobule 8 white matter
## 530 ¦ ¦ ¦--trunk of lobules 6-8 white matter
## 531 ¦ ¦ ¦--lobule 9 white matter
## 532 ¦ ¦ ¦--lobule 10 white matter
## 533 ¦ ¦ ¦--anterior lobule white matter
## 534 ¦ ¦ ¦ ¦--left anterior lobule white matter
## 535 ¦ ¦ ¦ °--right anterior lobule white matter
## 536 ¦ ¦ ¦--simple lobule white matter
## 537 ¦ ¦ ¦ ¦--left simple lobule white matter
## 538 ¦ ¦ ¦ °--right simple lobule white matter
## 539 ¦ ¦ ¦--crus 1 white matter
## 540 ¦ ¦ ¦ ¦--left crus 1 white matter
## 541 ¦ ¦ ¦ °--right crus 1 white matter
## 542 ¦ ¦ ¦--trunk of simple and crus 1 white matter
## 543 ¦ ¦ ¦ ¦--left trunk of simple and crus 1 white matter
## 544 ¦ ¦ ¦ °--right trunk of simple and crus 1 white matter
## 545 ¦ ¦ ¦--crus 2 white matter
## 546 ¦ ¦ ¦ ¦--left crus 2 white matter
## 547 ¦ ¦ ¦ °--right crus 2 white matter
## 548 ¦ ¦ ¦--paramedian lobule
## 549 ¦ ¦ ¦ ¦--left paramedian lobule
## 550 ¦ ¦ ¦ °--right paramedian lobule
## 551 ¦ ¦ ¦--trunk of crus 2 and paramedian white matter
## 552 ¦ ¦ ¦ ¦--left trunk of crus 2 and paramedian white matter
## 553 ¦ ¦ ¦ °--right trunk of crus 2 and paramedian white matter
## 554 ¦ ¦ ¦--copula white matter
## 555 ¦ ¦ ¦ ¦--left copula white matter
## 556 ¦ ¦ ¦ °--right copula white matter
## 557 ¦ ¦ ¦--paraflocculus white matter
## 558 ¦ ¦ ¦ ¦--left paraflocculus white matter
## 559 ¦ ¦ ¦ °--right paraflocculus white matter
## 560 ¦ ¦ °--flocculus white matter
## 561 ¦ ¦ ¦--left flocculus white matter
## 562 ¦ ¦ °--right flocculus white matter
## 563 ¦ ¦--lateral forebrain bundle system
## 564 ¦ ¦ ¦--corticospinal tract
## 565 ¦ ¦ ¦ ¦--cerebal peduncle
## 566 ¦ ¦ ¦ ¦ ¦--left cerebal peduncle
## 567 ¦ ¦ ¦ ¦ °--right cerebal peduncle
## 568 ¦ ¦ ¦ ¦--corticospinal tract-other
## 569 ¦ ¦ ¦ ¦ ¦--left corticospinal tract-other
## 570 ¦ ¦ ¦ ¦ °--right corticospinal tract-other
## 571 ¦ ¦ ¦ °--internal capsule
## 572 ¦ ¦ ¦ ¦--left internal capsule
## 573 ¦ ¦ ¦ °--right internal capsule
## 574 ¦ ¦ °--corpus callosum
## 575 ¦ ¦ ¦--left corpus callosum
## 576 ¦ ¦ °--right corpus callosum
## 577 ¦ °--extrapyramidal fiber systems
## 578 ¦ °--rubrospinal tract
## 579 ¦ °--ventral tegmental decussation
## 580 °--ventricular systems
## 581 ¦--cerebral aqueduct
## 582 ¦--fourth ventricle
## 583 ¦--lateral ventricle
## 584 ¦ ¦--lateral ventricle-other
## 585 ¦ ¦ ¦--left lateral ventricle-other
## 586 ¦ ¦ °--right lateral ventricle-other
## 587 ¦ °--subependymal zone
## 588 ¦ ¦--left subependymal zone
## 589 ¦ °--right subependymal zone
## 590 °--third ventricle
## tvalue.Dose
## 1 -2.90474829
## 2 -2.78485148
## 3 -2.79664057
## 4 -2.92924691
## 5 -1.12188998
## 6 -1.00040816
## 7 -0.37505336
## 8 -1.62418088
## 9 0.03867171
## 10 -1.00607751
## 11 -1.03292406
## 12 -0.64071804
## 13 0.71175225
## 14 0.50154584
## 15 0.75596208
## 16 0.67735049
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## 18 0.70063177
## 19 -1.61713168
## 20 -1.57973782
## 21 -1.19236304
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## 23 -1.26473766
## 24 -2.29228880
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## 27 -1.33489038
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## 31 -5.50979145
## 32 -3.12448434
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## 90 -1.59251912
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## 130 -2.06148403
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## 134 -2.57019524
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## 165 -6.75270536
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## 168 -1.65502924
## 169 -0.17993942
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## 172 -1.15274756
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## 590 -0.80282067And display the results as images.
labelVolume <- mincArray(mincGetVolume(labelFile))
vol <- hanatToVolume(hVs, labelVolume, "tvalue.Dose")
mincPlotSliceSeries(anatVolume, vol, low=2, high=6, symmetric=T, anatLow=9, anatHigh=15)
Now, let’s correct for multiple comparisons here too:
hVs <- hanatFDR(hVs)##
## Computing FDR threshold for all columns
## Computing threshold for F-statistic
## Computing threshold for tvalue-(Intercept)
## Computing threshold for tvalue-Dosethresholds(hVs)## F-statistic tvalue-(Intercept) tvalue-Dose
## 0.01 24.48279 16.74523 4.948008
## 0.05 16.97169 16.74523 4.119671
## 0.1 13.33255 16.74523 3.651377
## 0.15 11.85484 16.74523 3.443086
## 0.2 10.83568 16.74523 3.291759hanatView(hVs, "tvalue.Dose", low=4.12, high=8, symmetric=T, fontsize = 40, levelSeparation = 1000)vol <- hanatToVolume(hVs, labelVolume, "tvalue.Dose")
mincPlotSliceSeries(anatVolume, vol, low=4.12, high=8, symmetric=T, anatLow=9, anatHigh=15)
Let’s do the anatomical analysis only on merged left and right variants of each structure.
library(data.tree)
hVsSymmetric <- Clone(hVs)
Prune(hVsSymmetric, function(x) !(startsWith(x$name, "right") | startsWith(x$name, "left")))## [1] 308print(hVsSymmetric, "tvalue.Dose", limit=NULL)## levelName
## 1 root2
## 2 ¦--Basic cell groups and regions
## 3 ¦ ¦--Cerebrum
## 4 ¦ ¦ ¦--Cerebral cortex
## 5 ¦ ¦ ¦ ¦--Cortical subplate
## 6 ¦ ¦ ¦ ¦ ¦--Cortical subplate-other
## 7 ¦ ¦ ¦ ¦ ¦--Claustrum
## 8 ¦ ¦ ¦ ¦ ¦ ¦--Claustrum-other
## 9 ¦ ¦ ¦ ¦ ¦ ¦--Claustrum: dorsal part
## 10 ¦ ¦ ¦ ¦ ¦ °--Claustrum: ventral part
## 11 ¦ ¦ ¦ ¦ °--Endopiriform nucleus
## 12 ¦ ¦ ¦ ¦ ¦--Endopiriform nucleus, dorsal part
## 13 ¦ ¦ ¦ ¦ ¦ ¦--Dorsal nucleus of the endopiriform
## 14 ¦ ¦ ¦ ¦ ¦ °--Intermediate nucleus of the endopiriform claustrum
## 15 ¦ ¦ ¦ ¦ °--Endopiriform nucleus, ventral part
## 16 ¦ ¦ ¦ °--Cortical plate
## 17 ¦ ¦ ¦ ¦--Olfactory areas
## 18 ¦ ¦ ¦ ¦ ¦--Olfactory areas-other
## 19 ¦ ¦ ¦ ¦ ¦--Postpiriform transition area
## 20 ¦ ¦ ¦ ¦ ¦--Piriform area
## 21 ¦ ¦ ¦ ¦ ¦ ¦--Cortex-amygdala transition zones
## 22 ¦ ¦ ¦ ¦ ¦ °--Piriform cortex
## 23 ¦ ¦ ¦ ¦ ¦--Taenia tecta
## 24 ¦ ¦ ¦ ¦ ¦ ¦--Taenia tecta, dorsal part
## 25 ¦ ¦ ¦ ¦ ¦ °--Taenia tecta, ventral part
## 26 ¦ ¦ ¦ ¦ ¦--Cortical amygdalar area
## 27 ¦ ¦ ¦ ¦ ¦ °--Cortical amygdalar area, posterior part
## 28 ¦ ¦ ¦ ¦ ¦ ¦--Cortical amygdalar area, posterior part, lateral zone
## 29 ¦ ¦ ¦ ¦ ¦ °--Cortical amygdalar area, posterior part, medial zone
## 30 ¦ ¦ ¦ ¦ ¦--Piriform-amygdalar area
## 31 ¦ ¦ ¦ ¦ ¦--Main olfactory bulb
## 32 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, glomerular layer
## 33 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, outer plexiform layer
## 34 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, mitral layer
## 35 ¦ ¦ ¦ ¦ ¦ ¦--Main olfactory bulb, inner plexiform layer
## 36 ¦ ¦ ¦ ¦ ¦ °--Main olfactory bulb, granule layer
## 37 ¦ ¦ ¦ ¦ ¦--Accessory olfactory bulb
## 38 ¦ ¦ ¦ ¦ ¦ ¦--Accessory olfactory bulb, glomerular layer
## 39 ¦ ¦ ¦ ¦ ¦ °--Accessory olfactory bulb, granular layer
## 40 ¦ ¦ ¦ ¦ °--Anterior olfactory nucleus
## 41 ¦ ¦ ¦ ¦--Hippocampal formation
## 42 ¦ ¦ ¦ ¦ ¦--Retrohippocampal region
## 43 ¦ ¦ ¦ ¦ ¦ ¦--Subiculum
## 44 ¦ ¦ ¦ ¦ ¦ ¦ ¦--pre-para subiculum
## 45 ¦ ¦ ¦ ¦ ¦ ¦ °--subiculum
## 46 ¦ ¦ ¦ ¦ ¦ °--Entorhinal area
## 47 ¦ ¦ ¦ ¦ ¦ ¦--Entorhinal area, medial part, dorsal zone
## 48 ¦ ¦ ¦ ¦ ¦ ¦--Entorhinal area, lateral part
## 49 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Dorsal intermediate entorhinal cortex
## 50 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Dorsolateral entorhinal cortex
## 51 ¦ ¦ ¦ ¦ ¦ ¦ °--Ventral intermediate entorhinal cortex
## 52 ¦ ¦ ¦ ¦ ¦ °--Entorhinal area, medial part, ventral zone
## 53 ¦ ¦ ¦ ¦ °--Hippocampal region
## 54 ¦ ¦ ¦ ¦ ¦--Ammon's horn
## 55 ¦ ¦ ¦ ¦ ¦ ¦--Field CA1
## 56 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA1, stratum oriens
## 57 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA1, stratum lacunosum-moleculare
## 58 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA1, stratum radiatum
## 59 ¦ ¦ ¦ ¦ ¦ ¦ °--Field CA1, pyramidal layer
## 60 ¦ ¦ ¦ ¦ ¦ ¦--Field CA2
## 61 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA2, pyramidal layer
## 62 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Field CA2, stratum oriens
## 63 ¦ ¦ ¦ ¦ ¦ ¦ °--Field CA2, stratum radiatum
## 64 ¦ ¦ ¦ ¦ ¦ °--Field CA3
## 65 ¦ ¦ ¦ ¦ ¦ ¦--Field CA3, pyramidal layer
## 66 ¦ ¦ ¦ ¦ ¦ ¦ ¦--CA3Py Inner
## 67 ¦ ¦ ¦ ¦ ¦ ¦ °--CA3Py Outer
## 68 ¦ ¦ ¦ ¦ ¦ ¦--Field CA3, stratum oriens
## 69 ¦ ¦ ¦ ¦ ¦ ¦--Field CA3, stratum radiatum
## 70 ¦ ¦ ¦ ¦ ¦ °--Field CA3, stratum lucidum
## 71 ¦ ¦ ¦ ¦ °--Dentate gyrus
## 72 ¦ ¦ ¦ ¦ ¦--Dentate gyrus, molecular layer
## 73 ¦ ¦ ¦ ¦ °--Dentate gyrus, granule cell layer
## 74 ¦ ¦ ¦ ¦ ¦--GrDG
## 75 ¦ ¦ ¦ ¦ °--PoDG
## 76 ¦ ¦ ¦ °--Isocortex
## 77 ¦ ¦ ¦ ¦--Anterior cingulate area
## 78 ¦ ¦ ¦ ¦ ¦--Anterior cingulate area, ventral part
## 79 ¦ ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 24a
## 80 ¦ ¦ ¦ ¦ ¦ °--Cingulate cortex: area 24a'
## 81 ¦ ¦ ¦ ¦ °--Anterior cingulate area, dorsal part
## 82 ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 24b
## 83 ¦ ¦ ¦ ¦ °--Cingulate cortex: area 24b'
## 84 ¦ ¦ ¦ ¦--Infralimbic area
## 85 ¦ ¦ ¦ ¦--Retrosplenial area
## 86 ¦ ¦ ¦ ¦ ¦--Retrosplenial area, ventral part
## 87 ¦ ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 29a
## 88 ¦ ¦ ¦ ¦ ¦ ¦--Cingulate cortex: area 29b
## 89 ¦ ¦ ¦ ¦ ¦ °--Cingulate cortex: area 29c
## 90 ¦ ¦ ¦ ¦ °--Retrosplenial area, dorsal part
## 91 ¦ ¦ ¦ ¦--Prelimbic area
## 92 ¦ ¦ ¦ ¦--Auditory areas
## 93 ¦ ¦ ¦ ¦ ¦--Primary auditory area
## 94 ¦ ¦ ¦ ¦ ¦--Dorsal auditory area
## 95 ¦ ¦ ¦ ¦ °--Ventral auditory area
## 96 ¦ ¦ ¦ ¦--Agranular insular area
## 97 ¦ ¦ ¦ ¦ °--Agranular insular area, dorsal part
## 98 ¦ ¦ ¦ ¦--Ectorhinal area
## 99 ¦ ¦ ¦ ¦ ¦--Ectorhinal cortex
## 100 ¦ ¦ ¦ ¦ °--Insular region: not subdivided
## 101 ¦ ¦ ¦ ¦--Somatomotor areas
## 102 ¦ ¦ ¦ ¦ ¦--Primary motor area
## 103 ¦ ¦ ¦ ¦ ¦ ¦--Frontal cortex: area 3
## 104 ¦ ¦ ¦ ¦ ¦ °--Primary motor cortex
## 105 ¦ ¦ ¦ ¦ °--Secondary motor area
## 106 ¦ ¦ ¦ ¦--Frontal pole, cerebral cortex
## 107 ¦ ¦ ¦ ¦--Orbital area
## 108 ¦ ¦ ¦ ¦ ¦--Orbital area, lateral part
## 109 ¦ ¦ ¦ ¦ ¦--Orbital area, medial part
## 110 ¦ ¦ ¦ ¦ °--Orbital area, ventrolateral part
## 111 ¦ ¦ ¦ ¦--Posterior parietal association areas
## 112 ¦ ¦ ¦ ¦ ¦--Lateral parietal association cortex
## 113 ¦ ¦ ¦ ¦ ¦--Medial parietal association cortex
## 114 ¦ ¦ ¦ ¦ ¦--Parietal cortex: posterior area: rostral part
## 115 ¦ ¦ ¦ ¦ °--Secondary visual cortex: mediomedial area
## 116 ¦ ¦ ¦ ¦--Perirhinal area
## 117 ¦ ¦ ¦ ¦--Somatosensory areas
## 118 ¦ ¦ ¦ ¦ ¦--Primary somatosensory area
## 119 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area-other
## 120 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, barrel field
## 121 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, trunk
## 122 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory cortex: dysgranular zone
## 123 ¦ ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory cortex: shoulder region
## 124 ¦ ¦ ¦ ¦ ¦ ¦ °--Primary somatosensory cortex: trunk region
## 125 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, upper limb
## 126 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, lower limb
## 127 ¦ ¦ ¦ ¦ ¦ ¦--Primary somatosensory area, mouth
## 128 ¦ ¦ ¦ ¦ ¦ °--Primary somatosensory area, nose
## 129 ¦ ¦ ¦ ¦ °--Supplemental somatosensory area
## 130 ¦ ¦ ¦ ¦--Temporal association areas
## 131 ¦ ¦ ¦ °--Visual areas
## 132 ¦ ¦ ¦ ¦--Primary visual area
## 133 ¦ ¦ ¦ ¦--Lateral visual area
## 134 ¦ ¦ ¦ ¦--posteromedial visual area
## 135 ¦ ¦ ¦ ¦--Anterolateral visual area
## 136 ¦ ¦ ¦ °--Anteromedial visual area
## 137 ¦ ¦ °--Cerebral nuclei
## 138 ¦ ¦ ¦--Pallidum
## 139 ¦ ¦ ¦ ¦--Pallidum, ventral region
## 140 ¦ ¦ ¦ ¦--Pallidum, caudal region
## 141 ¦ ¦ ¦ ¦ °--Bed nuclei of the stria terminalis
## 142 ¦ ¦ ¦ ¦--Pallidum, dorsal region
## 143 ¦ ¦ ¦ °--Pallidum, medial region
## 144 ¦ ¦ ¦ °--Medial septal complex
## 145 ¦ ¦ °--Striatum
## 146 ¦ ¦ ¦--Striatum ventral region
## 147 ¦ ¦ ¦ ¦--Fundus of striatum
## 148 ¦ ¦ ¦ ¦--Nucleus accumbens
## 149 ¦ ¦ ¦ °--Olfactory tubercle
## 150 ¦ ¦ ¦--Lateral septal complex
## 151 ¦ ¦ ¦--Striatum dorsal region
## 152 ¦ ¦ ¦ °--Caudoputamen
## 153 ¦ ¦ °--Striatum-like amygdalar nuclei
## 154 ¦ ¦ °--Medial amygdalar nucleus
## 155 ¦ ¦--Brain stem
## 156 ¦ ¦ ¦--Midbrain
## 157 ¦ ¦ ¦ ¦--Midbrain, sensory related
## 158 ¦ ¦ ¦ ¦ ¦--Inferior colliculus
## 159 ¦ ¦ ¦ ¦ °--Superior colliculus, sensory related
## 160 ¦ ¦ ¦ ¦--Midbrain, behavioral state related
## 161 ¦ ¦ ¦ ¦ °--Midbrain raphe nuclei
## 162 ¦ ¦ ¦ ¦ °--Interpeduncular nucleus
## 163 ¦ ¦ ¦ ¦--Midbrain-other
## 164 ¦ ¦ ¦ °--Midbrain, motor related
## 165 ¦ ¦ ¦ °--Periaqueductal gray
## 166 ¦ ¦ ¦--Hindbrain
## 167 ¦ ¦ ¦ ¦--Medulla
## 168 ¦ ¦ ¦ ¦ ¦--Medulla, sensory related
## 169 ¦ ¦ ¦ ¦ ¦ °--Dorsal column nuclei
## 170 ¦ ¦ ¦ ¦ ¦ °--Cuneate nucleus
## 171 ¦ ¦ ¦ ¦ ¦--Medulla, motor related
## 172 ¦ ¦ ¦ ¦ ¦ °--Inferior olivary complex
## 173 ¦ ¦ ¦ ¦ °--Medulla-other
## 174 ¦ ¦ ¦ °--Pons
## 175 ¦ ¦ ¦ ¦--Pons-other
## 176 ¦ ¦ ¦ ¦--Pons, behavioral state related
## 177 ¦ ¦ ¦ ¦ °--Pontine reticular nucleus
## 178 ¦ ¦ ¦ °--Pons, sensory related
## 179 ¦ ¦ ¦ °--Superior olivary complex
## 180 ¦ ¦ °--Interbrain
## 181 ¦ ¦ ¦--Hypothalamus
## 182 ¦ ¦ ¦ ¦--Hypothalamus-other
## 183 ¦ ¦ ¦ °--Hypothalamic medial zone
## 184 ¦ ¦ ¦ ¦--Mammillary body
## 185 ¦ ¦ ¦ °--Medial preoptic nucleus
## 186 ¦ ¦ °--Thalamus
## 187 ¦ °--Cerebellum
## 188 ¦ ¦--Cerebellar cortex
## 189 ¦ ¦ ¦--Vermal regions
## 190 ¦ ¦ ¦ ¦--Lingula (I)
## 191 ¦ ¦ ¦ ¦--Central lobule
## 192 ¦ ¦ ¦ ¦--Culmen
## 193 ¦ ¦ ¦ ¦ ¦--Culmen-other
## 194 ¦ ¦ ¦ ¦ °--Lobules IV-V
## 195 ¦ ¦ ¦ ¦--Declive (VI)
## 196 ¦ ¦ ¦ ¦--Folium-tuber vermis (VII)
## 197 ¦ ¦ ¦ ¦--Pyramus (VIII)
## 198 ¦ ¦ ¦ ¦--Uvula (IX)
## 199 ¦ ¦ ¦ °--Nodulus (X)
## 200 ¦ ¦ °--Hemispheric regions
## 201 ¦ ¦ ¦--Simple lobule
## 202 ¦ ¦ ¦--Ansiform lobule
## 203 ¦ ¦ ¦ ¦--Crus 1
## 204 ¦ ¦ ¦ °--Crus 2
## 205 ¦ ¦ ¦--Paramedian lobule
## 206 ¦ ¦ ¦--Copula pyramidis
## 207 ¦ ¦ ¦--Flocculus
## 208 ¦ ¦ °--Paraflocculus
## 209 ¦ °--Cerebellar nuclei
## 210 ¦ ¦--Dentate nucleus
## 211 ¦ ¦--Interposed nucleus
## 212 ¦ °--Fastigial nucleus
## 213 ¦--fiber tracts
## 214 ¦ ¦--cranial nerves
## 215 ¦ ¦ ¦--olfactory nerve
## 216 ¦ ¦ ¦ ¦--anterior commissure, olfactory limb
## 217 ¦ ¦ ¦ °--lateral olfactory tract, general
## 218 ¦ ¦ ¦--facial nerve
## 219 ¦ ¦ ¦--dorsal roots
## 220 ¦ ¦ ¦ °--cervicothalamic tract
## 221 ¦ ¦ ¦ °--medial lemniscus
## 222 ¦ ¦ ¦--optic nerve
## 223 ¦ ¦ ¦ °--optic tract
## 224 ¦ ¦ °--oculomotor nerve
## 225 ¦ ¦ °--posterior commissure
## 226 ¦ ¦--medial forebrain bundle system
## 227 ¦ ¦ ¦--cerebrum related
## 228 ¦ ¦ ¦ ¦--anterior commissure, temporal limb
## 229 ¦ ¦ ¦ ¦--fornix system
## 230 ¦ ¦ ¦ ¦ ¦--fimbria
## 231 ¦ ¦ ¦ ¦ °--dorsal fornix
## 232 ¦ ¦ ¦ ¦--stria terminalis
## 233 ¦ ¦ ¦ °--cingulum bundle
## 234 ¦ ¦ °--hypothalamus related
## 235 ¦ ¦ ¦--epithalamus related
## 236 ¦ ¦ ¦ ¦--fasciculus retroflexus
## 237 ¦ ¦ ¦ ¦--habenular commissure
## 238 ¦ ¦ ¦ °--stria medullaris
## 239 ¦ ¦ °--mammillary related
## 240 ¦ ¦ °--mammilothalmic tract
## 241 ¦ ¦--cerebellum related fiber tracts
## 242 ¦ ¦ ¦--cerebellar peduncles
## 243 ¦ ¦ ¦ ¦--inferior cerebellar peduncle
## 244 ¦ ¦ ¦ ¦--middle cerebellar peduncle
## 245 ¦ ¦ ¦ °--superior cerebelar peduncles
## 246 ¦ ¦ °--arbor vitae
## 247 ¦ ¦ ¦--trunk of arbor vita
## 248 ¦ ¦ ¦--lobule 1-2 white matter
## 249 ¦ ¦ ¦--lobule 3 white matter
## 250 ¦ ¦ ¦--trunk of lobules 1-3 white matter
## 251 ¦ ¦ ¦--lobules 4-5 white matter
## 252 ¦ ¦ ¦--lobules 6-7 white matter
## 253 ¦ ¦ ¦--lobule 8 white matter
## 254 ¦ ¦ ¦--trunk of lobules 6-8 white matter
## 255 ¦ ¦ ¦--lobule 9 white matter
## 256 ¦ ¦ ¦--lobule 10 white matter
## 257 ¦ ¦ ¦--anterior lobule white matter
## 258 ¦ ¦ ¦--simple lobule white matter
## 259 ¦ ¦ ¦--crus 1 white matter
## 260 ¦ ¦ ¦--trunk of simple and crus 1 white matter
## 261 ¦ ¦ ¦--crus 2 white matter
## 262 ¦ ¦ ¦--paramedian lobule
## 263 ¦ ¦ ¦--trunk of crus 2 and paramedian white matter
## 264 ¦ ¦ ¦--copula white matter
## 265 ¦ ¦ ¦--paraflocculus white matter
## 266 ¦ ¦ °--flocculus white matter
## 267 ¦ ¦--lateral forebrain bundle system
## 268 ¦ ¦ ¦--corticospinal tract
## 269 ¦ ¦ ¦ ¦--cerebal peduncle
## 270 ¦ ¦ ¦ ¦--corticospinal tract-other
## 271 ¦ ¦ ¦ °--internal capsule
## 272 ¦ ¦ °--corpus callosum
## 273 ¦ °--extrapyramidal fiber systems
## 274 ¦ °--rubrospinal tract
## 275 ¦ °--ventral tegmental decussation
## 276 °--ventricular systems
## 277 ¦--cerebral aqueduct
## 278 ¦--fourth ventricle
## 279 ¦--lateral ventricle
## 280 ¦ ¦--lateral ventricle-other
## 281 ¦ °--subependymal zone
## 282 °--third ventricle
## tvalue.Dose
## 1 -2.90474829
## 2 -2.78485148
## 3 -2.79664057
## 4 -2.92924691
## 5 -1.12188998
## 6 -1.00040816
## 7 0.03867171
## 8 -1.00607751
## 9 0.71175225
## 10 0.67735049
## 11 -1.61713168
## 12 -1.57973782
## 13 -1.19236304
## 14 -2.29228880
## 15 -1.33489038
## 16 -3.03738351
## 17 -5.50979145
## 18 -3.12448434
## 19 -1.48860105
## 20 -2.45908071
## 21 -0.55411946
## 22 -2.61744527
## 23 -1.52106996
## 24 -1.57138747
## 25 -0.66665496
## 26 -0.87180247
## 27 -0.87180247
## 28 -0.77818943
## 29 -0.75092342
## 30 -1.59609470
## 31 -7.07808038
## 32 -6.19054061
## 33 -6.98535502
## 34 -7.07337567
## 35 -7.29966864
## 36 -7.39934482
## 37 -5.68206967
## 38 -4.04568899
## 39 -6.37355703
## 40 -2.20394380
## 41 -3.34048107
## 42 -1.59251912
## 43 -1.39233463
## 44 -1.06725148
## 45 -1.57860583
## 46 -1.55133428
## 47 0.10059419
## 48 -2.91438918
## 49 -3.01041644
## 50 -2.19592179
## 51 -2.36219292
## 52 -1.84840716
## 53 -4.33961855
## 54 -2.91498719
## 55 -2.72736617
## 56 -3.03898815
## 57 -3.34754717
## 58 -1.91770300
## 59 -1.93237246
## 60 -2.06148403
## 61 -2.10682875
## 62 -2.57019524
## 63 -0.77791321
## 64 -2.73776126
## 65 -3.01300047
## 66 -3.61672058
## 67 -2.75559729
## 68 -2.71292528
## 69 -1.93336539
## 70 -2.59823728
## 71 -7.91698039
## 72 -6.86708751
## 73 -8.73480635
## 74 -9.22598326
## 75 -6.75270536
## 76 -1.65502924
## 77 -0.17993942
## 78 -0.79206567
## 79 -0.87563597
## 80 -0.17353608
## 81 0.66341524
## 82 0.52133080
## 83 0.81946000
## 84 -1.23187835
## 85 -1.87504853
## 86 -1.17283836
## 87 -1.20723839
## 88 -1.34961614
## 89 -0.95191676
## 90 -2.39032598
## 91 0.55572122
## 92 -0.81617054
## 93 -0.86503918
## 94 -0.45259323
## 95 -0.90888965
## 96 -0.96475786
## 97 -0.96475786
## 98 -0.98580616
## 99 -2.07899916
## 100 -0.55126286
## 101 -1.72656332
## 102 -2.01603904
## 103 -1.21052271
## 104 -2.06974357
## 105 -1.26692675
## 106 -0.70295209
## 107 -1.30244612
## 108 -1.78814643
## 109 -0.05682619
## 110 -1.68275598
## 111 -1.76946313
## 112 -1.07634014
## 113 -1.10908443
## 114 -1.42012251
## 115 -1.90465482
## 116 -2.60901353
## 117 -2.13051732
## 118 -2.48105449
## 119 -0.97213031
## 120 -2.83848723
## 121 -1.97984100
## 122 -3.82384277
## 123 -0.69391053
## 124 -1.03984348
## 125 -2.40537179
## 126 -1.76849659
## 127 -3.21369877
## 128 -2.20848183
## 129 -0.97371062
## 130 -1.89632960
## 131 -1.75575359
## 132 -1.54629654
## 133 -1.73742722
## 134 -1.45439448
## 135 -1.86724040
## 136 -1.52092750
## 137 -1.97447924
## 138 -2.47212156
## 139 -1.39697382
## 140 -1.82675460
## 141 -1.82675460
## 142 -3.76012208
## 143 -0.72932371
## 144 -0.72932371
## 145 -1.76840468
## 146 -2.12639384
## 147 -1.89881231
## 148 -2.22420209
## 149 -1.09460587
## 150 -0.88800174
## 151 -1.56241447
## 152 -1.56241447
## 153 0.42304887
## 154 0.42304887
## 155 -2.49092886
## 156 -2.08976288
## 157 -1.82923748
## 158 -2.33735115
## 159 -1.47701932
## 160 -0.93459784
## 161 -0.93459784
## 162 -0.93459784
## 163 -2.51827499
## 164 -1.51908776
## 165 -1.51908776
## 166 -1.87183760
## 167 -1.89172847
## 168 -0.38120788
## 169 -0.38120788
## 170 -0.38120788
## 171 -2.39857174
## 172 -2.39857174
## 173 -1.88924461
## 174 -1.65687216
## 175 -1.71141555
## 176 -1.02446188
## 177 -1.02446188
## 178 -0.41138918
## 179 -0.41138918
## 180 -2.11781936
## 181 -2.10367888
## 182 -2.03567535
## 183 -2.05053989
## 184 -2.23436232
## 185 -0.18153128
## 186 -1.86872396
## 187 -1.81228544
## 188 -1.77715868
## 189 -1.63464683
## 190 -1.83658549
## 191 -0.81596496
## 192 -1.07895050
## 193 -1.01841020
## 194 -1.01459243
## 195 -2.26284821
## 196 -0.84425605
## 197 -1.08290784
## 198 -0.88685446
## 199 -1.77132002
## 200 -1.83499600
## 201 -1.90266007
## 202 -2.29768654
## 203 -1.93079797
## 204 -2.63747886
## 205 -1.85972406
## 206 -1.18607441
## 207 -2.13109744
## 208 -0.35240413
## 209 -2.04896209
## 210 -2.17481239
## 211 -1.79766943
## 212 -2.00168440
## 213 -3.76695299
## 214 -5.49010091
## 215 -5.79116574
## 216 -5.04437831
## 217 -5.90575606
## 218 -2.32823843
## 219 -4.24154255
## 220 -4.24154255
## 221 -4.24154255
## 222 -3.15828707
## 223 -3.15828707
## 224 -2.02746322
## 225 -2.02746322
## 226 -3.48454591
## 227 -3.69223406
## 228 -3.82427933
## 229 -3.25709281
## 230 -3.05297922
## 231 -4.17790740
## 232 -4.36921460
## 233 -3.44873725
## 234 -2.05711340
## 235 -1.96377570
## 236 -3.02649659
## 237 -0.02279210
## 238 -1.68163184
## 239 -2.24701461
## 240 -2.24701461
## 241 -1.75029153
## 242 -2.45133213
## 243 -0.81792867
## 244 -2.29355347
## 245 -2.22645579
## 246 -1.50832626
## 247 -1.75409922
## 248 -1.07419509
## 249 -0.96582924
## 250 -0.83477784
## 251 -0.36491410
## 252 -1.14600155
## 253 -0.63046880
## 254 0.32609041
## 255 -0.61658333
## 256 -1.83287142
## 257 -0.82689617
## 258 -0.83668055
## 259 -1.37632853
## 260 -1.11946374
## 261 -2.74197063
## 262 -1.28071945
## 263 -0.84870347
## 264 -1.14794098
## 265 -0.77782781
## 266 -1.84638454
## 267 -4.11967100
## 268 -5.01170878
## 269 -4.94800833
## 270 -3.14058451
## 271 -4.13917564
## 272 -3.46924945
## 273 -1.38433427
## 274 -1.38433427
## 275 -1.38433427
## 276 -2.15114699
## 277 -2.41301840
## 278 -0.56288958
## 279 -2.18580771
## 280 -2.16313499
## 281 -3.90357390
## 282 -0.80282067vol <- hanatToVolume(hVsSymmetric, labelVolume, "tvalue.Dose")
mincPlotSliceSeries(anatVolume, vol, low=4.12, high=8, symmetric=T, anatLow=9, anatHigh=15,
begin=50, end=-50)
We can also look at just a subset of the tree:
print(FindNode(hVsSymmetric, "Hippocampal region"), "tvalue.Dose", limit=NULL)## levelName tvalue.Dose
## 1 Hippocampal region -4.3396185
## 2 ¦--Ammon's horn -2.9149872
## 3 ¦ ¦--Field CA1 -2.7273662
## 4 ¦ ¦ ¦--Field CA1, stratum oriens -3.0389881
## 5 ¦ ¦ ¦--Field CA1, stratum lacunosum-moleculare -3.3475472
## 6 ¦ ¦ ¦--Field CA1, stratum radiatum -1.9177030
## 7 ¦ ¦ °--Field CA1, pyramidal layer -1.9323725
## 8 ¦ ¦--Field CA2 -2.0614840
## 9 ¦ ¦ ¦--Field CA2, pyramidal layer -2.1068287
## 10 ¦ ¦ ¦--Field CA2, stratum oriens -2.5701952
## 11 ¦ ¦ °--Field CA2, stratum radiatum -0.7779132
## 12 ¦ °--Field CA3 -2.7377613
## 13 ¦ ¦--Field CA3, pyramidal layer -3.0130005
## 14 ¦ ¦ ¦--CA3Py Inner -3.6167206
## 15 ¦ ¦ °--CA3Py Outer -2.7555973
## 16 ¦ ¦--Field CA3, stratum oriens -2.7129253
## 17 ¦ ¦--Field CA3, stratum radiatum -1.9333654
## 18 ¦ °--Field CA3, stratum lucidum -2.5982373
## 19 °--Dentate gyrus -7.9169804
## 20 ¦--Dentate gyrus, molecular layer -6.8670875
## 21 °--Dentate gyrus, granule cell layer -8.7348064
## 22 ¦--GrDG -9.2259833
## 23 °--PoDG -6.7527054vol <- hanatToVolume(FindNode(hVsSymmetric, "Hippocampal region"), labelVolume, "tvalue.Dose")
mincPlotSliceSeries(anatVolume, vol, low=4.12, high=8, symmetric=T, anatLow=9, anatHigh=15,
begin=120, end=-170, plottitle = "Dose, Hippocampal region", legend="t-statistic",
mfrow = c(3,3))
library(ggplot2)
d7vsd0$volume <- FindNode(hanatd7vsd0, "Dentate gyrus")$volumes
qplot(as.factor(Dose), volume, data=d7vsd0, geom="boxplot")
library(RMINC)
allvols <- anatGetAll(gf$Jacobfile_scaled, atlas=labelFile,
defs=defsFile,method="jacobians")
hanat <- addVolumesToHierarchy(hdefs, allvols)