6. Visualization of bstr outputs

For visualization tips and guidelines, you can refer to the documentation for the BrainSuite GUI interface.

6.1. Output files

A bstr output folder will typically contain the following files

6.1.1. Statistical Measurements

Measurement	Output files suffix/folders
adjusted log p-value	*log_pvalues_adjusted.[nii.gz/dfs]
adjusted t-statistic	*tvalues_adjusted.[nii.gz/dfs]
adjusted masked correlation	*corr_values_masked_adjusted.[nii.gz/dfs]
unadjusted log p-value	*log_pvalues_adjusted.[nii.gz/dfs]
unadjusted t-statistic	*tvalues_adjusted.[nii.gz/dfs]
unadjusted correlation	*corr_values.[nii.gz/dfs]
cluster table	.tsv

6.1.2. Colormaps/colorbars

Measurement	Output files suffix/folders
rendered colorbar	*cbar.[png/pdf]
colorbar LUT (adjusted)	_adjusted.lut
colorbar LUT	.lut
colorbar JSON format	.cbar

6.1.3. 2D Image slices from 3D Volumes

Type	Output files suffix/folders
Rendered image slices (TBM/DBA only )	png_images folder
Rendered image slices (TBM/DBA only ) with cross-hairs	png_images_crosshairs folder

6.1.4. Statistical Report

Type	Output files
R Markdown report	.Rmd
HTML rendered R Markdown report	.html

6.2. Visualization of Surface-based Analysis (SBA) Results

1. Navigate to the output folder of sba resuls.

2. Open the BrainSuite GUI.

3. Drag and drop the corresponding statistical output dfs file for both left (*.left.*) and right (*.right.*) hemispheres into BrainSuite (see Statistical Measurements table above ).

4. Open the colormap PNG file (see Image slices table above ) to view the color bar with labels.

6.3. Visualization of Tensor-based Morphometry (TBM) / Diffusion-based Analysis (DBA) Results

1. Open the BrainSuite GUI.

2. Load the appropriate brain anatomical atlas in BrainSuite. This will be located inside one of the sub-folders, svreg/BCI-DNI_brain_atlas, svreg/BrainSuiteAtlas1, svreg/USCBrain of the BrainSuite installation folder.

3. Load (overlay) the desired statistical output image file (see Statistical Measurements table above ) on the atlas. As an example, for a correlation analysis, the output file could be bstr_corr*corr_values_masked_adjusted.nii.gz.

4. Press the S button in the Image Display panel. This will make the colormap symmetric.

5. Load (Drag and drop) the appropriate color look up the table file (LUT) corresponding to the statistical output (adjusted or unadjusted). For e.g. an adjusted LUT for correlation values could like like bstr_corr*corr_values_masked_adjusted.lut.

6. Select the LUT by right clicking on the appropriate colorbar and selecting the LUT. It should be equivalent to the LUT file name.

7. The statistical image (volume) will now be displayed in color.

8. Open the colormap PNG file (see Image slices table above ) to view the color bar with labels.

6.4. Visualization of ROI Results

1. Navigate to the output ROI result folder.

2. Open the HTML report file (see Statistical Report above ) in a browser.

3. Optionally, open the R Markdown file (see Statistical Report above ) in RStudio or a suitable R-IDE. One can Preview or Knit this .Rmd file to get the same output as the HTML report.