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);
For the best results you should always first run motion correction with intra-session alignment to the volume used for estimation. This way all volumes that you are applying the VDM to will be indirectly aligned to the VDM.
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 with the radiobuttons on top of the tab.

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)."

Back to "Usage" menu"

index

Latest update of this page: 05 March 2015