[glf19780301]

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?

[Anand Joshi]

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.

[glf19780301]

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.

[Anand Joshi]

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

[glf19780301]

Thank you.

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

[Anand Joshi]

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.

[glf19780301]

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.

[shjoshi]

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

[glf19780301]

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’
>

[glf19780301]

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

[shjoshi]

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

[shjoshi]

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

[glf19780301]

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

[shjoshi]

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.

[glf19780301]

> 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(‘”

[glf19780301]

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

[shjoshi]

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.

[glf19780301]

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

[glf19780301]

In my computer， my account is the administrator.

[shjoshi]

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

[glf19780301]

* 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.

[glf19780301]

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=)

[glf19780301]

Load data

bss_data <- load_data(type=,…)

How do I edit the command in this step?

[glf19780301]

Can you recommend me a few articles published using Brainsuite?

[shjoshi]

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).

[shjoshi]

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.

[glf19780301]

> 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?

[shjoshi]

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")

[glf19780301]

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

[shjoshi]

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.

[yemishade]

Hi everyone, I am somewhat new to using Brainsuite and I hope I would find a solution to my problems here. I have a group of MRI scans and I am interested in obtaining the tissue probability ratio (for Grey matter, white matter and CSF) of voxels in every anatomical region in each hemisphere labelled in AAL2. So I wonder if Brainsuite could be used in processing MRI such that I would be able to identify the Tissue probability ration in voxels in every Region.

Also, how can I label the anatomical regions of the brain using Brainsuite?

[Anand Joshi]

Sure, Please have a look at
http://brainsuite.org/processing/surfaceextraction/pvc/

I would go through the brainsuite tutorial which

Also for labeling
http://brainsuite.org/quickstart/svreg/

If you go through getting stated sequence in brainsuite, that will give you good overview of the software as well as answer your questions in more detail. Please feel free to reach out if you still have any questions.
For that click on Getting Started on http://brainsuite.org/ and the first 3 subsections would be very useful.

• This reply was modified 3 years, 8 months ago by Anand Joshi.

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