First choose the general phase encoding directions (L>>R and R>>L or A>>P and P>>A) which can be selected with the radiobuttons on top of the tab.
The direction in which the data will be corrected depends on the VDM chosen for correcting the data. The names of the 2 “_vdm.map” files are equal to the names of the 2 FMRs or DMRs used for estimation. For the files used for estimation you typically chose filenames that indicate the phase encoding direction. In that case it will be obvious which “_vdm.map” corrects which phase encoding direction.
Under “Apply correction to:”, enter the FMR or DMR files that should be corrected.
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 will be 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”.
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)."
Latest update of this page: 05 March 2015