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The BRAIN SEGMENTS page shows the parcellation result as an overlay to the MR image.
The BRAIN SEGMENTS image represents a label atlas of the found brain structures. Please check the alignment of the structure information with the patient image with the fusion slider. In the case of a mismatch try changing the GM segment definition on the MR SEGMENTS page and/or the number of included subjects and repeat parcellation. Alternatively, the structure definitions can be adjusted manually after the outlining step.
The next step consists of outlining the brain segments in the Result space which defines, where the MR statistics are calculated:
Atlas |
The MR image is transformed in the Atlas space and statistics are calculated with interpolated MR values. The Modulation option corrects for volume changes during the spatial normalization step. Image intensities are scaled by the amount of contraction that has occurred during spatial normalization, so that the total amount of gray matter remains the same as in the original image. This option should be used when the normalized MR image is used for voxel-based morphometry (VBM). |
Input |
The statistics are calculated with original MR values. |
Sulci Deformation
The Sulci deformation option instructs the program to perform an anatomical optimization of the VOIs. Based on the MR image, the VOI boundaries are adjusted such that the border should essentially follow the sulci bottoms.
Outlining of the brain structures is started with the Outline button.
The VOIS page shows a fusion of the MR image and the brain segments, as well as the outlined brain structures.
VOI Editing and Selection
At this time the contour VOIs can be interactively adjusted using the VOI features of PMOD, which are described in the PMOD Base Functionality Guide and in the Introduction. Note that the List tab should be selected for the adjustment, and that depending on the configuration only a reduced set of VOI tools is available.
Statistics Calculation
Once the VOIs are acceptable, it is recommended to first save them and then proceed with statistics calculation by the Statistics action button. The result (the volume of the selected VOIs only) is shown on the separate Statistics page of the PNEURO tool, from where it can be further evaluated.
