Overview

The fMRI Brain Atlas Segmentation Tool uses a species-specific atlas to evaluate functional or structural MRI, fMRI, or phMRI data. Several pre-processing and analysis options are available to enable accurate characterization of signal change for a variety of acquisition paradigms.

fMRI Brain Atlas Segmentation Tool
fMRI Brain Atlas Segmentation Tool

Install Atlas

Before using the fMRI tool, users should download and install the available atlases by going to Advanced Modules -> Install Atlas -> Mouse & Rat. To change the directory where the atlases are automatically stored, go to Advanced Modules -> Install Atlas -> Change Atlas Directory and re-install the atlases to this location.

Install Atlas
Install Atlas

Getting There

The fMRI Tool is accessed by navigating to Advanced Modules -> fMRI Tool.

fMRI Tool
fMRI Tool

Load Data into the Tool

The Load Data section in the upper left corner of the tool window allows users to load in a dataset from a local folder or import a dataset that is already loaded into the software. For Bruker MR data, users can select the 2dseq file from the appropriate folder or use the Bruker Loader to load the data into VivoQuant prior to running the tool.

Load Data
Load Data
Input Data The folder location and file name will be displayed in this window when a data set is loaded in from a local folder.
Click on the ellipsis button to open a window from which the user can locate and load in a locally stored data set.
TR The repetition time in seconds should be entered here. The user should either type the correct value or use the up and down arrows to adjust the TR.
Number of Time Points The number of time points will automatically update upon loading a data set.
Import from DM Click on this button to import data into the fMRI Tool that has already been loaded into VQ.
Reset Settings Click on this button to unload data from the tool and reset the pipeline settings back to the default settings.

Select an Output Repository

The Output section in the upper right corner of the GUI window allows users to select an output folder and manage the format and number of output files.

Output Repository
Output Repository
Output Folder The output folder location will be displayed in this window once a local folder is selected by the user.
Click on the ellipsis button to open a window from which the user can select a local output folder.
prefix Provide a prefix (optional) to be added to all output file names. Adding a prefix is useful when performing multiple analyses that are being saved to the same output folder.
Keep Data Steps Check this box to save intermediate analysis results including the original data set.
Correlation Matrix Check this box to save a region of interest correlation matrix spreadsheet.
Save QC Check this box to save before and after motion correction, smoothing, anatomical registration, brain mask, and/or atlas registration QC movies and images.
Before / After
Before / After

Customize Analysis Pipeline

The Pipeline section of the fMRI tool allows users to fully customize their data analysis workflow.

Users can choose to enable or disable any of the following processing modules:

Depending on which processes are enabled, the analysis workflow will go in order of the display tabs.

Motion Correction

Check the Enable box to perform a motion correction of the input data.

Motion Correction
Motion Correction

Users can choose to have the tool perform either a slice-by-slice or 3D motion correction. Users must also choose to register each time point to a single time point or to the mean of all the time points.

If Keep Data Steps is checked in the Output section of the tool, then the motion corrected data will be stored to the output directory with suffix -mc. Similarly, if the Save QC box is checked, then before and after motion correction QC movies will be stored to the output directory.

Smoothing

Check the Enable box to smooth the input data.

Smooth Input Data
Smooth Input Data

Users can choose to have the tool perform either a slice-by-slice or 3D spatial smoothing. Users can also edit the full width at half maximum (FWHM) setting to adjust the level of smoothing.

If Keep Data Steps is checked in the Output section of the tool, then the smoothed data will be stored to the output directory with suffix -sm. Similarly, if the Save QC box is checked, then before and after smoothing QC images will be stored to the output directory as well as displayed under the smoothing tab. The mean of the functional data set will be used for the QC images.

Anatomical Registration

Check the Enabled box to co-register the input data to an anatomical reference data set.

Anatomical Registration
Anatomical Registration

Users can choose from the following references:

  • Anatomical: Register to a reference anatomical data set. Click on the ellipsis button Ellipsis button to open a window from which the locally stored anatomical file can be located. Users can either provide a manual transformation or have the tool perform an automatic registration. For the automated registration, the user can choose to use the entire field of view (Use Full) or only the brain (Use BBox). The Use BBox setting will use a bounding box around the brain to limit what is used for registration. If the manual box is checked, the user needs to provide a locally stored XML transformation for the registration of the functional to the reference anatomical.
  • Mean Functional: Register to the mean of the functional time series.
  • Time Point: Register to a single time point. Either type a specific time point in the box or use the up and down arrows to edit the time point.

If Keep Data Steps is checked in the Output section of the tool, then the registered data will be stored to the output directory with suffix -anatreg. Similarly, if the Save QC box is checked, then before and after registration QC images will be stored to the output directory as well as displayed under the Anatomical Registration tab . Since the mean of the registered functional will be used for the QC images, no QC images will be stored if the mean functional is used as the reference.

Brain Mask

The Brain Mask tab provides options for skull stripping the input data.

Brain Mask
Brain Mask

Users can choose from the following masking options:

  • None: Does not perform any brain masking.
  • Manual: Pauses the processing and prompts the user to manually segment the brain in the 3D ROI tool using automatic spline tool thresholding.
  • Provided: Users must provide brain segmentation (RMHA file).
  • Automatic: Performs an Otsu thresholding on the brain.

If Keep Data Steps is checked in the Output section of the tool, then the masked data will be stored to the output directory with suffix -masked. Similarly, if the Save QC box is checked, then before and after masking QC images will be stored to the output directory as well as displayed under the Brain Mask tab.

Atlas Registration

Check the Enabled box to co-register the input data to an atlas.

Atlas Registration
Atlas Registration

Users can customize the atlas registration by adjusting the following settings:

  • Data to Atlas/Atlas to Data: Choose to register the atlas to the data or vice versa.
  • Atlas: This should populate with the correct provided atlas based on the header information from the loaded data set.
  • Key: Choose to perform hemisphere (Left/Right) or whole brain analysis using all regions in the provided atlas or using a mapping of all regions to a smaller number of larger regions.
  • H/F Flip: Check this box to flip the data (or atlas) in the head/foot direction before registration.
  • Affine: Check this box to allow the tool to scale and shear the data (or atlas) during registration, if necessary.
  • Allow Inter-Slice Interp: Check this box to allow the tool to interpolate the data (or atlas) between slices.
  • Custom Atlas: Check this box to provide custom atlas RMHA and anatomical files.

If Keep Data Steps is checked in the Output section of the tool, then the registered data will be stored to the output directory with suffix -atlasreg. Similarly, if the Save QC box is checked, then before and after atlas registration QC images will be stored to the output directory as well as displayed under the atlas registration tab.

General Linear Modeling

Check the Enable box to perform modeling analysis. Choose from pre-defined Ramp, Bolus, Boxcar, or Region ideal functions or import a custom design.

General Linear Modeling
General Linear Modeling

Users can customize the analysis and output materials with the following settings:

  • Save Residuals: Check this box to save a map of the residuals to the output folder. The name of the map will be residuals.
  • Voxel Maps: Check this box to save parameter maps for the chosen regressors. These files will be stores with suffix -paramMap.
  • ROI Plots: Check this box to store all ROI plots in a folder within the specified output folder. The name of this folder will be plots.
  • Add Regressor: Click on this button to add a regressor to the design matrix. A window will appear from which the user can select an available regressor from the drop down menu.
    • Each ideal function can be customized for the specific study paradigm. For example, the Bolus option allows users to set the shape and center (both in units of TR).
  • Remove Last: Click on this button to remove the last regressor column of the design matrix.
  • Import Design: Click on this button to load in a custom design matrix that is stored locally in CSV format.

Run the Tool

Click on the Run button at the bottom of the window to run the tool. If the tool pauses due to a missing settings field, click on the Continue button to resume processing. To close the tool window, click Close.

The progress bar on the bottom left corner will display the progress for each step of the pipeline, including loading the dataset. The total processing time will be displayed next to the progress bar once the analysis is complete. A description of what process the tool is working on will also be displayed.