This method can answer key questions in the neuroimaging and neurology fields. Such as, whether there are group differences in cortical volume for non-clinical versus clinical populations. The main advantage to this technique is that it enables researchers to use the best tool for their data.
To begin, first open the SPM software by opening a MATLAB command window and typing SPM into the command line. Then, to perform unified segmentation, select PET VBM to open the structural MRI toolbox. Now, open the batch editor to perform segmentation on multiple scans at once.
Select SPM, Spatial, and Segment, then Data, select Files, and choose the T1-Weighted scans as Input. Next, click on Output Files, Grey Matter, and ensure that Native Space is selected, and repeat this for White Matter. If the CSF segmentation is not required, leave this set to None.
If the scans have already been Bias Corrected, change this option to Don't Save Corrected. Then use Clean up any partitions and test all three options prior to running the full analysis. Now, leave the other settings set to defaults and click on the green flag to run the segmentation.
The MATLAB window will say Done when segmentation is finished. Finally, perform Visual Quality Control on the resulting Grey Matter NIfTI file. To perform the New Segment option in SPM 8, first select PET VBM before opening the batch editor.
Then select SPM, Tools, New Segment, and select the NIfTI format T1 image files to be used. Set the Native Tissue Type option to Native Space, and turn off Tissue Classes that are not required. Also turn off Warped Tissue, then click on the green flag to run the segmentation and perform Visual Quality Control when completed.
To perform segmentation in SPM 12 again press PET VBM and open the batch editor. Then select SPM, Spatial Segment, and Data Volumes. Then select Native Space Tissue Type and turn off unneeded Tissue Classes.
Set Warped Tissue to None, and click the green flag. Once the segmentation has completed, again be sure to perform Visual Quality Control as detailed in the next section of this protocol. Visual Quality Control can be performed using FSLeyes.
Begin by opening a terminal window, then open FSLeyes by typing FSLeyes in the terminal. Then select File, Add from File, and select the original T1 and the segmented regions to view them. Once FSLeyes opens, use the opacity toggle to allow visualization of the underlying T1 image.
Also change the color of the segmentation overlay as needed via the color dropdown tab in the top pane. Now, scroll through every slice in the brain and check each one for regions of under or overestimation in the region being inspected. Visual Quality Control is an essential step for this procedure.
By comparing your segmented regions to the original T1 scan, you can ensure that your regions are of a high quality, and that your conclusions are biologically accurate. To perform Visual Quality Control of FreeSurfer data using Freeview, open a terminal window and change the directory to the subject folder that contains the processed FreeSurfer output. Then type the command seen on on the screen here to view the volumetric grey matter region overlaid on the T1.Again, scroll through every slice in the brain and check for regions of under or overestimation for the brain region being inspected.
Here, we see an example of a failed segmentation displayed on a T1 scan. This segmentation should be reprocessed and excluded from analysis if it cannot be improved. This figure shows examples of the performance of different tools on the temporal lobe on a T1 scan.
Examples of a good regional delineation are seen here, while examples of poor regional delineation, showing spillage in the left and right temporal lobes, are shown here. This figure shows examples of the performance of different tools on the occipital lobe on a T1 scan. Here we see the T1 scan with an example of a good regional delineation, while here is an example of a poor regional delineation, showing spillage into the medial dura.
Here we see an example of a grey matter region spilled into the dura, highlighted by the blue region. This figure shows an example of a grey matter region that has excluded regions of the cortex from segmentation, best shown in the axial view. While attempting this procedure, it's important to remember to test different tools in your data, and to perform Visual Quality Control on the process scans.
After it's development, this technique paved the way for neuroimaging researchers to study changes in brain volume over time without requiring invasive tests.
