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

This topic contains 29 replies, has 3 voices, and was last updated by  shjoshi 3 months, 1 week ago.

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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.

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    ankitsahay4321
    Participant

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