Select FMRs/DMRs: Choose the EPI files that are phase encoded either in opposite anterior-posterior (A>>P and P>>A) directions or opposite left-right directions (L>>R and R>>L) using the Browse button on the first two lines. Afterwards, in each dataset, select the volume which will be used to estimate the voxel displacement map (VDM). For diffusion-weighted data (spin echo EPI), a b=0 volume is usually best. The voxel displacement map (VDM) will be saved in *.map file format, which can be overlaid on FMR files; this may be useful to see the algorithm's result.
Select volume numbers:
It is recommended to choose volumes acquired shortly after one another in time to minimize motion. Ideally you would aquire one volume in the opposite phase encoding direction directly before starting the run(s) of your experiment. Then you can use that volume and the first volume of your first run for the estimation.
The estimation is based on image intensities and structure on which most of the pre-processing steps have a negligible effect. The only thing to make sure is to not apply any smoothing to the volumes used for estimation.
Type of data: Select whether your data used for estimation is gradient-echo EPI (GE-EPI) or spin-echo EPI (SE-EPI). For spin-echo data the image intensities will be adjusted during optimization depending on the derivative of the Voxel Displacement Map (VDM), while for gradient-echo data it proved to be better to skip this adjustment.
Gradient-echo is typically used for functional scans and for spin-echo for diffusion-weighted imaging (DWI).
When it is unknown whether the data are spin-echo or gradient-echo, it is adviced to run the estimation once with each setting. The setting that provides the highest final NCC value (printed to the BrainVoyager QX log tab) should be the setting that works best for the distortion correction.
Distance measure for optimization: This option offers the possibility to choose between two different distance measures used to estimate the similarity between the images: normalised cross-correlation (NCC) and sum of squared differences (SSD). For more information, please see background.
Apply VDM to input: This option applies the voxel displacement map (VDM) to the data that have been used to estimate the distortion. In case there are no further runs, this eliminates the need to run the second step via the "Apply" tab.
Save derivative of VDM: The second option is to save the derivative of the VDM. To view a map, open a corrected file (e.g., “example_undist.fmr”), go to Analysis > Overlay Volume Maps and load the corresponding map file (e.g. “example_undist_vdmderiv.map”).
The *_vdm map shows the voxel displacement map (see middle column in figure below); in areas marked in yellow/red the voxels have been moved up and in areas marked in green/blue the voxels have been moved down. The *_vdmderiv map contains the first derivative of the voxel displacements in the Y direction. This shows which areas have been compressed (yellow/red) or stretched (green/blue) during distortion correction.
Latest update of this page: 19 July 2015