fMRI Brain Atlas Segmentation Tool

  1. Install Atlas
  2. Getting There
  3. Load Data into the Tool
  4. Select an Output Repository
  5. Customize Analysis Pipeline
  6. Run the Tool

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.

Install Atlas

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

Getting There

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

Load Data into the Tool

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

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 the user to select an output folder and manage the format and number of output files.

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.

Customize Analysis Pipeline

The pipeline section of the fMRI tool allows the user to fully customize their data analysis workflow.

The user 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.

The user can choose to have the tool perform either a slice-by-slice or 3D motion correction. The user 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.

The user can choose to have the tool perform either a slice-by-slice or 3D spatial smoothing. The user 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 (as seen in image above). 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.

The user can choose from the following references:

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 (as seen in image above). 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.

The user can choose from the following masking options:

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 (as seen in image above).

Atlas Registration

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

The user can customize the atlas registration by adjusting the following settings:

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.

Customize the analysis and output materials with the following settings:

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, the user can click on the Continue button to resume processing. To close the tool window, click on the Close button.

The progress bar in the bottom left corner of the GUI window will display the progress for each step of the pipeline including loading the data set. 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.