how to present the statistical results on the brain template

Forums Forums Surface and Volume Registration (SVReg) how to present the statistical results on the brain template

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    • #2045
      glf19780301
      Participant

      After processing the data of brain area volume, surface area and cortical thickness, how to present the statistical results on the brain template for use in the paper?

    • #2049
      Anand Joshi
      Moderator

      The visualization is described here:
      http://brainsuite.org/wp-content/uploads/2017/06/BrainSuite_Workshop_2017_BSSR_Shantanu_Joshi.pdf
      Please let me know how it goes.

    • #2050
      glf19780301
      Participant

      Thank you.We’re dealing with the surface area of the brain, how do we deal with that? I didn’t see any relevant content in the document you gave me.

    • #2051
      Anand Joshi
      Moderator

      Are you running ROI wise analysis? You can check slides 43-45.

    • #2052
      glf19780301
      Participant

      Thank you.

      “Volumetric analysis – sMRI” and “volumetric analysis – dMRI” how do I calculate?

    • #2053
      Anand Joshi
      Moderator

      There are slides in the link on diffusion analysis (FA). sMRI analysis (T1) can be done using tensor based morphometry (TBM). Please check slides on those.

    • #2054
      glf19780301
      Participant

      I want to compare the surface and area of each area of the whole brain. How do I do that?I didn’t see it in “slides 43-45.”
      Thank you.

    • #2055
      shjoshi
      Moderator

      Thanks Anand for pointing to the right slides.
      As Anand replied,
      volumetric MRI analysis can be found starting at slide 33.
      volumetric diffusion analysis (analysis of diffusion parameters such as FA, MD, RD) can be found from slide 38 onwards.

      Have you installed bssr and are you able to load the processed data in R?

      Shantanu

    • #2056
      glf19780301
      Participant

      I ran into a problem during the installation, so I followed the instructions to run the command
      “install.packages(c(‘devtools’, ‘htmlwidgets’, ‘iterators’, ‘magrittr’, ‘gtable’, ‘R6’))
      devtools::install_url(‘http://brainsuite.org/wp-content/uploads/2018/05/bssr_0.2.1.tar.gz’)”

      show:

      > install.packages(c(‘devtools’, ‘htmlwidgets’, ‘iterators’, ‘magrittr’, ‘gtable’, ‘R6’))
      Warning in install.packages :
      ‘lib = “C:/Program Files/R/R-3.6.2/library”‘ is not writable
      Warning in install.packages :
      cannot create dir ‘C:\Users\glf19\OneDrive\??’, reason ‘Invalid argument’
      Error in install.packages : unable to create ‘C:/Users/glf19/OneDrive/??/R/win-library/3.6’
      > devtools::install_url(‘http://brainsuite.org/wp-content/uploads/2018/05/bssr_0.2.1.tar.gz’)
      Error in loadNamespace(name) : there is no package called ‘devtools’
      >

    • #2057
      glf19780301
      Participant

      I have installed RStudio and Rtools, I don’t know what the problem is, how to correct it

    • #2058
      shjoshi
      Moderator

      I think this seems to be some permissions issue on your computer for installing packages.
      This is not related to bssr, but concerns your R installation.

      I would suggest getting devtools installed first.
      Since you are using Windows, have you installed Rtools?
      I would just run install.packages(‘devtools’) first and see if you have any error.

      S

    • #2059
      shjoshi
      Moderator

      Can you post the output of
      install.packages(‘devtools’)?

    • #2060
      glf19780301
      Participant

      I want to compare the surface and area of each area of the whole brain.How to compare and count “surface area”?

    • #2061
      shjoshi
      Moderator

      Each individual subject folder contains a file <subjid>.roiwise.stats.txt, where <subjid> should be replaced by your subject Id name.

      This stats.txt file contains the surface areas for the cortical ROIs mapped by SVREG.

      To get the index of the ROI and the label, you should look at
      BrainSuiteXX/svreg/BCI-DNI_brain_atlas/brainsuite_labeldescription.xml
      or
      BrainSuiteXX/svreg/BrainSuiteAtlas1/brainsuite_labeldescription.xml
      depending on the atlas used.

      To perform a statistical ROI analysis in bssr, look at slide 42 onwards.

    • #2062
      glf19780301
      Participant

      > install.packages(‘devtools’)
      Error: unexpected input in “install.packages(‘”

      Hi Shjoshi,
      Thank you very much for your guidance.When I input “> install.packages(‘devtools’) “,it will shows “Error: unexpected input in “install.packages(‘”

    • #2063
      glf19780301
      Participant

      Could you tell me the specific installation steps of “R”? I can uninstall and start again

    • #2064
      shjoshi
      Moderator

      I suspect your R and RStudio installation must be fine. Before you try uninstall/reinstall, can you try running R as an Administrator?

      Look at this link,

      Then post the output of .libPaths().

      If you ran RStudio as an administrator, try installing devtools.
      install.packages("devtools")

      Note devtools is enclosed in double quotes.
      When typing the install.package command above, please type it manually in your R console, since copying pasting from the web may garble some characters.

    • #2065
      glf19780301
      Participant

      How do I run R in administrator mode?Can you take a look at my computer remotely?

    • #2066
      glf19780301
      Participant

      In my computer, my account is the administrator.

    • #2067
      shjoshi
      Moderator

      Ok. Now, when running R, can you find your R installation, right click on it and select “Open as Administrator”?

      Look at this too.
      https://community.rstudio.com/t/error-after-r-update-lib-c-program-files-r-r-3-5-0-library-is-not-writable/7947/4

    • #2068
      glf19780301
      Participant

      * DONE (bssr)
      > library(bssr)
      Finding BrainSuite atlas file paths…Done. Valid BrainSuite installation found at C:/Program Files/BrainSuite19a
      > get_brainsuite_install_path()
      [1] “C:/Program Files/BrainSuite19a”
      > get_brainsuite_install_path()
      [1] “C:/Program Files/BrainSuite19a”
      > ?bssr
      >

      Is that ok? Thank you.

    • #2069
      glf19780301
      Participant

      I have two groups of patients, divided into HP group (39 patients) and HC group (40 volunteers), which have all completed the process of svreg.I want to compare the volume, thickness and surface area of each brain region of the two groups.

      How to type the command?

      1.bss_data <- load_data(type=,…)
      2.bss_model <- bss_anova(main_effect=, covariates=, bss_data)
      bss_model <- bss_corr(corr_var=, bss_data)
      bss_model <- bss_ttest(group_var=, bss_data, paired=)

    • #2070
      glf19780301
      Participant

      Load data

      bss_data <- load_data(type=,…)

      How do I edit the command in this step?

    • #2071
      glf19780301
      Participant

      Can you recommend me a few articles published using Brainsuite?

    • #2072
      shjoshi
      Moderator

      Great that you were able to get this installed.
      To run the cortical thickness analysis, look at slide 27. It shows the 3 steps needed to load the data, execute the model, and save the statistical outputs.

      For the first step, you will need 2 things.
      i. Location of the subject directory (subjdir variable in load_bss_data)
      ii. A demographics csv file (csv variable in load_bss_data, which contains columns such as age, sex, and group. Your group will be HC or HP (for now set it as 1 or 0).

      Step 1. Then call the command given in Step 1 by setting the appropriate variables. For e.g. hemi="left" for left hemisphere. If you haven’t smoothed your data, don’t pass the smooth variable.

      Step 2. Call the command in Step 2 as bss_model <- bss_anova(main_effect = "group", covariates = "age", bss_data = bss_data)

      Step 3. Call save_bss_out(bss_data, bss_model, outdir="/path/to/some/output directory")

      To compare volumes, I’d suggest running the TBM analysis. See slide 34 for the steps. The functions are same as above. The options change.

      To compare surface areas, I’d suggest running the ROI analysis. (Slide 43).

    • #2073
      shjoshi
      Moderator

      BTW, just FYI we are getting ready to release the next version of BrainSuite and the statistical tools. This version of bssr will also have functionality that will create html reports. This will be released in 1-2 weeks.

    • #2074
      glf19780301
      Participant

      > load_bss_data
      function (type = “cbm”, subjdir = “”, csv = “”,
      hemi = “left”, smooth = 0, roiids = 0, roimeas = “gmthickness”,
      measure = “”, atlas = “”, eddy = TRUE)
      {
      valid_types <- c(“cbm”, “tbm”, “roi”, “dbm”,
      “nca”)
      if (!type %in% valid_types)
      stop(sprintf(“Valid data types are %s.”, paste(valid_types,
      collapse = “, “)), call. = FALSE)
      switch(type, cbm = {
      bss_data <- load_cbm_data(subjdir = subjdir, csv = csv,
      hemi = hemi, smooth = smooth)
      }, tbm = {
      bss_data <- load_tbm_data(subjdir = subjdir, csv = csv,
      smooth = smooth, atlas = atlas)
      }, dbm = {
      bss_data <- load_dbm_data(subjdir = subjdir, csv = csv,
      measure = measure, smooth = smooth, atlas = atlas,
      eddy = eddy)
      }, roi = {
      bss_data <- load_roi_data(subjdir, csv, roiids, roimeas)
      })
      return(bss_data)

      I did this step, is it right?

    • #2075
      shjoshi
      Moderator

      You should call the function like this:
      bss_data <- load_bss_data(type="cbm", subjdir = "/path/to/the/top level subject directory", csv = "/path/to/your/demographics.csv", hemi="left")

    • #2076
      glf19780301
      Participant

      I am very glad to get your help. I have a preliminary contact with R language. Please give me your detailed guidance.

    • #2077
      shjoshi
      Moderator

      No problems. It will be a good idea to go step by step. Perhaps only focus on one type of analysis first, get familiar with the command structure, and then move to other analysis.
      Loading data first, then running a basic model, and saving the output.

    • #2132
      ankitsahay4321
      Participant

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