I ran DIFFPREP command to perform distortion correction using structural data. I used --step 0, assuming that all three corrections would be performed. But in the final image I expected to see an output file with generic name _EPI_field.nii. I got an output(the name that I specified in -o flag) .nii. Does this mean that epi distortion has been done?
--step 0: Big bang. The start of everything...
1: Motion & eddy currents distortion correction. Initial image creation steps are assumed to have been done and that the files are present.
2: EPI distortion correction. Motion and eddy transformation files are assumed to be present.
3: Final resampling and reorientation.
Start step. You can continue a previously interrupted run with this option.
Secondly, Is registration setting required for human data? Can we use example_registration_settings.dmc or TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc.
Or do we have to modify its contents according to fov parameters of T2w image?
Thank you in advance
1) Yes, the output data is EPI distortion corrected. If you do not want it performed, you can override the settings file by providing a specific tag in DIFFPREP command line i.e --epi off
You can check the settings file but default in the last release was to perform EPI correction unless otherwise specified.
2) You do not have to provide a settings file for human data and can override the default by specifying tags in command line:
example: the settings file has output resolution of 1.5 mm isotropic. If you want specific output resolution, you can provide the --res tag with the desired resolution.