[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.

[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")

[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.

[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]

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

[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.

[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.

[shjoshi]

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

[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]

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

[shjoshi]

>> 1) The yellow/pink colours show an increase in cortical thickness and the blue colour a decrease, >> is it right?

That’s right.

>> 2) Is there a way to press on the coloured region and see which structure it is? Some of them are >> easy to identify but some of them not.

We are currently developing this functionality, but I’m afraid it won’t be available at least until a few months.

And yes, stay tuned for the information on the next BrainSuite course.

[shjoshi]

Great. Good luck with the analysis.

[shjoshi]

Hi,

I would not recommend doing either a) or b) above.

1. For within patients analysis only, one could analyze Laterality (left vs right) as the main effect. You could include Sex as a covariate.

2. Again for within patients, you can do separate analyses for all patients with left sided tumors and right sided tumors.

3. If you want an across subject (controls and patients), then you could include laterality as a covariate.

[shjoshi]

Hmm.. This analysis could be done in two different ways, but both of them are not currently supported.

1. For surface based analysis (cbm), you can merge left and right hemispheres and do a combined cortical analysis.

2. For volume based analysis (tbm), you can do the whole brain analysis, and then report the results on the contralateral side.

3. Alternately, one can do an asymmetry analysis by subtracting the thickness of the left from the right hemisphere within subject and then do a group analysis and mask out the location of the tumor (you will find a huge effect there obviously).

Options 1 and 3 are not currently supported in bssr. But you can run option 2.
Is that what you had in mind?

[shjoshi]

Hello,

Can you please clarify? The hemispheric analysis is only available for cortical thickness (left or right hemisphere). I’m guessing if you want to analyze tumors, you want to conduct a volumetric analysis?

Shantanu

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