Usage: apply voxel displacement map (VDM)

Under “Apply correction to:”, enter the FMR or DMR files that should be corrected. These can be the same ones as entered above (but if the first option on the Apply tab has been used, this is not required) or different files (see figure below); in case of several runs, it might be good to run motion correction with intra-session alignment first, with the volume used for estimation as target for the intra-session alignment.
The estimated voxel displacement map (VDM) will be applied to each volume in these files and the files are saved with the suffix “_undist” in the filename. For instance, if the input file is called “example.fmr”, the distortion-corrected data will be saved as “example_undist.fmr”.

The phase encoding direction of the EPI image will be inferred from its filename. To indicate the phase encoding direction, a filename needs to contain "_AP.fmr", "_PA.fmr", "_LR.fmr" or "_RL.fmr" (respectively anterior (A) >> posterior (P) direction, P >> A direction, left (L) >> right (R) direction and R >> L).
The general phase encoding directions (L>>R and R>>L or A>>P and P>>A) can be selected on the Parameters page.

After the file(s) have been selected, click the "Run" button to apply the VDM to the selected files.
To check the existence of the files, use the "Check" button (see figure below)."

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.

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Latest update of this page: 20 July 2018